Portable testing device for analyzing biological samples

Abstract

A portable testing device includes a housing with an integrated touchscreen display and a receptacle in which a sample holder containing a biological sample and reagent mixture can be placed. The portable testing device further includes an optical assembly positioned in the housing, an electronic assembly that is configured to receive data from the optical assembly and transmit it for display on the touchscreen display, and a power supply in the housing to power the portable testing device. The optical assembly includes an excitation filter that extends across the entire optical assembly and an emission filter that extends across the entire optical assembly.

Description

<DP=1>²CA 02926253 2016-04-01²WO 2015 / 054245 PCT / US2014 / 059487²PORTABLE TESTING DEVICE FOR ANALYZING BIOLOGICAL SAMPLES²BACKGROUND²

[0001] The present invention relates to devices that are capable of ²analyzing biological ²samples, and in particular, to a portable testing device that is capable of ²being used in the field.²

[0002] Biological samples are typically tested in laboratories after the ²biological samples ²are collected in the field. A number of steps are taken to prepare the sample ²after it has been ²collected, including mixing the sample with reaction buffers, dyes, and any ²other chemical ²solutions needed to prepare the sample for testing. During or after sample ²preparation, testing ²equipment also needs to be prepared. This can include warming up the ²equipment, calibrating ²the equipment for the specific tests to be run, and running through any other ²initial procedures ²required for the specific testing equipment being used. Once the sample and ²the equipment are ²prepared, the prepared sample can be placed in the equipment for testing.²

[0003] The typical process for testing biological samples described above ²has significant ²disadvantages. One disadvantage is that biological samples need to be ²collected in the field, ²brought into the laboratory, and then tested. This can present the following ²issues. One, the ²biological sample can be contaminated between the times whem it was collected ²and time that it ²is to be tested. Two, it can be discovered that not enough biological sample ²was collected in the ²field, preventing the testing from being complete. Three, it can be later ²discovered that the ²biological samples that were taken are otherwise unsuitable for testing. When ²a biological ²sample is unsuitable for testing for any of the above reasons, an additional ²biological sample will ²need to be collected in order to complete the testing. This requires ²additional time, money, and ²other resources to complete.²SUMMARY²

[0004] A portable testing device includes a housing with an integrated ²touchscreen ²display and a receptacle in which a sample holder containing a biological ²sample and reagent ²mixture can be placed. The portable testing device further includes an optical ²assembly ²positioned in the housing, an electronic assembly that is configured to ²receive data from the ²optical assembly and transmit it for display on the touchscreen display, and a ²power supply in the²<DP=2>²housing to power the portable testing device. The optical assembly includes an ²excitation ²filter that extends across the entire optical assembly and an emission filter ²that extends ²across the entire optical assembly.²[0004a] In one aspect the present invention resides in a portable testing ²device ²comprising: a housing with an integrated touchscreen display comprising a ²receptacle ²configured to receive a sample holder containing a biological sample and ²reagent mixture; ²an optical assembly positioned in the housing, wherein the optical assembly is ²configured ²to amplify and detect a signal from the biological sample and reagent mixture ²in the ²sample holder, and wherein the optical assembly comprises: a sample block ²configured to ²receive the sample holder, wherein the sample block comprises: a plurality of ²cavities that ²are shaped to receive the sample holder; a first housing portion positioned on ²a first side ²of the sample block, wherein the first housing portion comprises: a first ²excitation filter; a ²first emission filter; a first plurality of light-emitting diodes positioned ²on a side of the ²first excitation filter opposite the plurality of cavities; and a first ²plurality of ²photodetectors positioned on a side of the first emission filter opposite the ²plurality of ²cavities; and a second housing portion positioned on a second side of the ²sample block, ²opposite the first side, wherein the second housing portion comprises: a ²second excitation ²filter; a second emission filter; a second plurality of light-emitting diodes ²positioned on a ²side of the second excitation filter opposite the plurality of cavities; and a ²second plurality ²of photodetectors positioned on a side of the second emission filter opposite ²the plurality ²of cavities; an electronic assembly configured to receive data from the ²optical assembly ²and transmit the received data to be displayed on the touchscreen display; and ²a power ²supply in the housing to power the portable testing device.²10004b] In one aspect the present invention resides in a method of analyzing a ²²biological sample and reagent mixture in a portable testing device, the method ²²comprising: preparing a biological sample and reagent mixture for testing and ²placing the ²biological sample and reagent mixture in a sample holder; placing the sample ²holder in an ²opening on the portable testing device; beginning an excitation and detection ²test ²sequence to analyze the biological sample and reagent mixture; and collecting ²data in ²real-time from the excitation and detection test sequence, wherein preparing a ²biological ²sample and reaction mixture for testing further includes: collecting a field ²sample; ²preparing the field sample outside of the portable testing device to form a ²prepared ²sample; placing the prepared sample in a first tube that is positioned on a ²first aperture on²2²Date recue / Date received 2021-11-05²<DP=3>²the portable testing device; transferring the prepared sample from the first ²tube into a ²second array of tubes that are positioned in a second plurality of apertures ²on the portable ²testing device, wherein the second array of tubes contain a reaction buffer; ²and ²transferring the prepared sample and the reaction buffer from the second array ²of tubes ²into a third array of tubes that are positioned in a third plurality of ²apertures on the ²portable test device, wherein the third array of tubes contain a master mix.²[0004c] In one aspect the present invention resides in a portable ²testing device for ²analyzing biological samples, the portable testing device comprising: a ²housing with an ²opening on a top side of the housing for an array of tubes; a sample ²preparation area in ²the housing, the sample preparation area comprising: a first aperture that is ²capable of ²holding a tube containing a biological sample; a first plurality of apertures ²positioned in a ²row that are capable of holding an array of tubes; and a second plurality of ²apertures ²positioned in a row that are capable of holding an array of tubes; a cradle on ²a top side of ²the housing in which a tablet computer can be positioned; and an optical ²assembly in the ²housing to excite and detect the biological sample, wherein the optical ²assembly ²comprises: a heating component positioned below the opening in the housing, ²the heating ²component comprising a plurality of apertures in which the array of tubes can ²be ²positioned; an upper optical assembly with a first plurality of light-emitting ²diodes on a ²first side of the heating component and a second plurality of light-emitting ²diodes on a ²second side of the heating component; and a lower optical assembly with a ²first plurality ²of photodiodes positioned in a row and a second plurality of photodiodes ²positioned in a ²row, wherein the first plurality of photodiodes and the second plurality of ²photodiodes are ²positioned underneath the heating component.²BRIEF DESCRIPTION OF THE DRAWINGS²

[0005] FIG. 1 is a perspective view of a portable testing device.²

[0006] FIG. 2A is a perspective view of a top side of the portable ²testing device when ²a cover is placed over a display.²

[0007] FIG. 2B is a bottom plan view of the portable testing device.²

[0008] FIG. 3A is a perspective view of a top side of an alternate ²design of the ²portable testing device when a cover is placed over a display.²2a²Date recue / Date received 2021-11-05²<DP=4>²

[0009] FIG. 3B is a perspective view of a bottom side of the alternate ²design of the ²portable testing device when the cover is stored in a recess on the bottom ²side of the ²portable testing device.²

[0010] FIG. 4A is a perspective view of the portable testing device ²when a sample ²holder in the form of a tube array is being placed in the portable testing ²device.²

[0011] FIG. 4B is a perspective view of the portable testing device ²when a sample ²holder in the form of a card is being placed in the portable testing device.²

[0012] FIG. 4C is a perspective view of the portable testing device ²when the card is ²placed in the portable testing device.²

[0013] FIG. 5 is a block diagram of the portable testing device.²

[0014] FIG. 6A is a perspective view of an optical assembly.²

[0015] FIG. 6B is a cross-sectional view of the optical assembly.²

[0016] FIG. 7 is an exploded view of a heating portion of the optical ²assembly.²

[0017] FIG. 8 is an exploded view of a lens portion of the optical ²assembly.²

[0018] FIG. 9 is an exploded view of a housing portion of the optical ²assembly.²

[0019] FIG. 10A is a partially exploded view of a first optical ²mounting portion of ²the optical assembly.²

[0020] FIG. 10B is a partially exploded view of a second optical ²mounting portion of ²the optical assembly.²2b²Date recue / Date received 2021-11-05²<DP=5>²CA 02926253 2016-04-01²WO 2015 / 054245 PCT / US2014 / 059487²

[0021] FIG. 10C is a partially exploded view of the first optical mounting ²portion and the ²second optical mounting portion of the optical assembly.²

[0022] FIG. 11A is a perspective view of a screen assembly.²

[0023] FIG. 11B is a partially exploded view of the screen assembly.²

[0024] FIG. 11C is a partially exploded view of a machine readable code ²reader attached ²to the screen assembly.²

[0025] FIG. 12 is an exploded view of a second housing portion and a lid of ²the portable ²testing device.²

[0026] FIG. 13A is an exploded view of the screen assembly and a first ²housing portion ²of the portable testing device.²

[0027] FIG. 13B is a partially exploded view of the screen assembly, the ²optical ²assembly, the first housing portion, and the second housing portion in the ²portable testing device.²

[0028] FIG. 13C is a partially exploded view of the portable testing ²device.²

[0029] FIG. 14 is a flowchart showing steps for operating the portable ²testing device.²

[0030] FIG. 15A is a perspective view of a portable testing device with a ²tablet computer ²positioned on the portable testing device.²

[0031] FIG. 15B is a perspective view of the portable testing device seen ²in FIG. 15A ²when an optical lid is opened.²

[0032] FIG. 16A is a perspective view of an upper optical assembly.²

[0033] FIG. 16B is an exploded view of the upper optical assembly seen in ²FIG. 16A.²

[0034] FIG. 17A is a perspective view of an optical assembly, including the ²upper optical ²assembly seen in FIGS. 16A -16B and a lower optical assembly.²

[0035] FIG. 17B is an exploded view of the optical assembly seen in FIG. ²17A.²

[0036] FIG. 18A is a perspective view of a lower portion of the portable ²testing device, ²including the optical assembly seen in FIGS. 16A-16B and a power assembly.²

[0037] FIG. 18B is an exploded view of the lower portion of the portable ²testing device ²seen in FIG. 18A.²

[0038] FIG. 19A is a perspective view of the portable testing device.²

[0039] FIG. 19B is an exploded view of the portable testing device seen in ²FIG. 19A.²

[0040] FIG. 20A is a perspective view of a sample preparation area on the ²portable ²testing device.²3²<DP=6>²CA 02926253 2016-04-01²WO 2015 / 054245 PCT / US2014 / 059487²

[0041] FIG. 20B is a perspective view of a film cover over the sample ²preparation area ²on the portable testing device.²

[0042] FIG. 20C is a perspective view of the sample preparation area seen ²in FIG. 20A, ²when sample arrays are positioned in the sample preparation area.²

[0043] FIG. 20D is a perspective view of the sample preparation area seen ²in FIG. 20A ²when a sample array has been positioned in the portable testing device.²

[0044] FIG. 21 is a flowchart showing steps for operating the portable ²testing device.²

[0045] FIG. 22A is a perspective view of an optical assembly.²

[0046] FIG. 22B is a top view of the optical assembly.²

[0047] FIG. 23 is a cross-sectional side view of the optical assembly taken ²along line 23-²23 of FIG. 22B.²

[0048] FIG. 24A is a perspective view of the optical assembly in a first ²position.²

[0049] FIG. 24B is a perspective view of the optical assembly in a second ²position.²

[0050] FIG. 24C is a perspective view of the optical assembly in a third ²position.²

[0051] FIG. 25 is a cross-sectional side view of an optical assembly.²

[0052] FIG. 26A is a side view of a first side of the optical assembly ²according to a first ²configuration.²

[0053] FIG. 26B is a side view of a second side of the optical assembly ²according to the ²first configuration.²

[0054] FIG. 27A is a side view of a first side of the optical assembly ²according to a ²second configuration.²

[0055] FIG. 27B is a side view of a second side of the optical assembly ²according to the ²second configuration.²[1:056] FIG. 28A is a perspective view of an optical assembly.²

[0057] FIG. 28B is a bottom view of the optical assembly.²

[0058] FIG. 29A is an exploded perspective view of a first side of the ²optical assembly.²

[0059] FIG. 29B is an exploded perspective view of the first side of the ²optical assembly.²

[0060] FIG. 29C is an exploded perspective view of a second side of the ²optical ²assembly.²

[0061] FIG. 29D is an exploded side view of the second side of the optical ²assembly.²

[0062] FIG. 30A is perspective view of a card.²4²<DP=7>²CA 02926253 2016-04-01²WO 2015 / 054245 PCT / US2014 / 059487²

[0063] FIG. 30B is a side elevation view of the card.²

[0064] FIG. 30C is a front elevation view of the card.²

[0065] FIG. 31A is a front elevation view of the card showing well ²variations A-D.²

[0066] FIG. 31B is a front elevation view of the card showing well ²variations E-H.²

[0067] FIG. 32A is a side elevation view of the card showing seals on the ²card.²

[0068] FIG. 32B is a front elevation view of the card showing a first ²permanent seal and ²a removable seal.²

[0069] FIG. 32C is a front elevation view of the card after the removable ²seal is removed.²

[0070] FIG. 32D is a front elevation view of the card after a second ²permanent seal is ²applied.²

[0071] FIG. 33A is a perspective view of a top side of a card.²

[0072] FIG. 33B is a perspective view of a bottom side of the card.²

[0073] FIG. 34A is a perspective view of the card when a second body ²portion is rotated ²down.²

[0074] FIG. 34B is a perspective view of the card with a first permanent ²seal.²

[0075] FIG. 34C is a perspective view of the card with a first removable ²seal.²

[0076] FIG. 34D is a perspective view of the card that can be placed in a ²lyophilizer.²

[0077] FIG. 34E is a perspective view of the card with second removable ²seal placed ²over the first removable seal.²

[0078] FIG. 35A is a perspective view of the card with the first removable ²seal and the ²second removable seal.²

[0079] FIG. 35B is a perspective view of the card with the first removable ²seal and the ²second removable seal removed to provide access to the wells.²

[0080] FIG. 35C is a perspective view of the card when the second body ²portion is folded ²over the wells to seal the wells with the permanent seal.²

[0081] FIG. 35D is a perspective view of the card that is prepared for ²testing.²

[0082] FIG. 36A is a perspective view of a lid assembly.²

[0083] FIG. 36B is a top view of a seal that can be used with the lid ²assembly.²

[0084] FIG. 37A is a perspective view of the lid assembly attached to an ²array of sample ²tubes.²<DP=8>²CA 02926253 2016-04-01²WO 2015 / 054245 PCT / US2014 / 059487²

[0085] FIG. 37B is a perspective view of the lid assembly with the seal ²applied to the lid ²assembly.²

[0086] FIG. 37C is a perspective view of the lid assembly in a closed ²position over the ²seal.²

[0087] FIG. 37D is a perspective view of the lid assembly opened and a ²backing removed ²from the seal.²

[0088] FIG. 37E is a perspective view of the lid assembly in a closed ²position to form a ²seal with the permanent seal.²

[0089] FIG. 38A is a front view of a sample holder including a tube array ²and a lid array.²

[0090] FIG. 38B is a perspective view of the sample holder when the lid ²array is placed ²on the tube array.²

[0091] FIG. 39A is a front view of a sample holder including a tube array ²and a lid array.²

[0092] FIG. 39B is a perspective view of the sample holder when the lid ²array is placed ²on the tube array.²

[0093] FIG. 39C is a side view of the sample holder when the lid array is ²placed on the ²tube array.²

[0094] FIG. 39D is a top view of the sample holder.²

[0095] FIG. 40A is a perspective view of a sample holder when a lid array ²is placed on a ²tube array.²

[0096] FIG. 40B is a front view of the sample holder when the lid array is ²placed on the ²tube array.²

[0097] FIG. 40C is a bottom view of the sample holder.²DETAILED DESCRIPTION²

[0098] In general, the present invention is a portable testing device for ²analyzing ²biological samples. The portable testing device can be taken into the field to ²test biological ²samples as they are collected. This is advantageous over prior art systems, as ²it allows a user to ²test biological samples as the user is collecting them. This can prevent ²problems with ²contamination and degradation of biological samples due to transportation to a ²laboratory for ²testing, later discovery that not enough sample was taken, or later discovery ²that the collected ²biological sample is otherwise unsuitable for use. Allowing a user to test the ²biological sample²6²<DP=9>²CA 02926253 2016-04-01²WO 2015 / 054245 PCT / US2014 / 059487²in the field can save time, money, and resources. Testing in the field also ²provides the ability for ²rapid safety response if test results indicate a pathogen or toxin that may be ²harmful.²

[0099] In the embodiments described below, the portable testing device is ²capable of ²testing biological samples with an isothermal amplification process, such as ²EnviroLogix's ²DNAble0 chemistry or LAMP chemistry. This eliminates the need for ²thermocycling as a ²means to amplify nucleic acid products for endpoint detection. This allows a ²user to obtain data ²from the biological sample while the test is being run. The portable testing ²device displays this ²data on a screen on the portable testing device or on a tablet computer so ²that a user can view the ²results of the test in the field. Allowing a user to view the results of the ²test in the field is ²advantageous, as the user can then make an informed decision of whether ²additional tests are ²needed. Further, if testing indicates that there is a pathogen or toxin in the ²biological sample, a ²user can initiate proper safety protocol right away to protect against the ²pathogen or toxin. In ²alternate embodiments, the portable testing device is also capable of ²incorporating a ²thermocycler to allow for the use of non-isothermal polymerase chain reaction ²(PCR) chemistries ²and result in qPCR and end-point analysis.²PORTABLE TESTING DEVICE 100 WITH OPTICAL ASSEMBLY 156²

[00100] FIG. 1 is a perspective view of portable testing device 100. ²Portable testing ²device 100 includes housing 110 (including first housing portion 112 and ²second housing portion ²114), display 116, handle 118, lid 120, and receptacle 122 (shown in FIG. 4A).²

[00101] Portable testing device 100 is used to analyze biological samples ²that have been ²mixed with a reaction mixture (also referred to as a biological sample and ²reagent mixture). ²Housing 110 forms the body of portable testing device 100. Housing 110 ²includes first housing ²portion 112 and second housing portion 114. First housing portion 112 forms a ²base portion of ²portable testing device 100 and second housing portion 114 forms a top portion ²of portable ²testing device 100. Located on a front top side of housing 110 is display 116. ²Display 116 is a ²touchscreen display in the embodiment shown, but can be any suitable display ²in alternate ²embodiments. A user can use display 116 to select test protocol and set up the ²parameters for ²tests that will be run in portable testing device l 00. A user can also use ²display 116 to provide ²sample and assay traceability information to portable testing device 100. ²Display 116 will also ²display data that is collected during testing.²7²<DP=10>²CA 02926253 2016-04-01²WO 2015 / 054245 PCT / US2014 / 059487²

[00102] Housing 110 further includes handle 118. Handle 118 is located on a ²front side of ²housing 110 in the embodiment shown, but can be located in any suitable ²location in alternate ²embodiments. Handle 118 is shown as an integrated handle with housing 110 in ²the embodiment ²shown, but can be attached to portable testing device 100 in any suitable ²manner in alternate ²embodiments. Handle 118 is included on portable testing device 100 so that ²portable testing ²device 100 can be easily transported in the field.²

[00103] Housing 110 also includes lid 120. Lid 120 is located on a top side ²of housing ²110 in the embodiment shown, but can be located in any suitable location in ²alternate ²embodiments. Lid 120 is included on portable testing device 100 to cover ²receptacle 122 (shown ²in FIG. 4A). Biological samples that are to be tested are loaded into a sample ²holder that can ²then be placed in receptacle 122. Lid 120 covers receptacle 122 to prevent ²contamination from ²entering into receptacle 122 when portable testing device 100 is being used in ²the field. Lid 120 ²further prevents radiation from escaping out of portable testing device 100 ²and prevents ambient ²light from entering into portable testing device 100 when testing is being ²completed. Lid 120 ²can be moved between an open and closed position and can be held in the closed ²position with ²any suitable means. In the embodiment shown, lid 120 is held in a closed ²position with magnets. ²When lid 120 is in a closed position, it puts pressure on the sample holder ²that is placed in a heat ²block in portable testing device 100. This improves engagement and heat ²transfer between the ²sample holder and the heat block in portable testing device 100.²

[00104] Portable testing device 100 is designed for use in the field and ²provides many ²advantages for such use. Biological materials that are collected in the field ²can be tested in the ²field as they are collected. This alleviates concerns about contamination or ²degradation of the ²biological sample. as there is no need to transport the biological sample back ²to a laboratory for ²testing. Further, portable testing device 100 allows a user to quickly react ²to results from tests ²that are run in the field. If a test is inconclusive, additional biological ²material can be collected ²and sampled right away. Further, if testing indicates that there is a pathogen ²or toxin in the ²sample, a user can initiate proper safety protocol right away to protect ²against the pathogen or ²toxin.²

[00105] Portable testing device 100 includes a number of features that make ²it suitable for ²use in the field. Handle 118 is included to easily transport the device. ²Display 116 is integrated ²into portable testing device 100 so that portable testing device 100 can act ²as an all-in-one²8²<DP=11>²CA 02926253 2016-04-01²WO 2015 / 054245 PCT / US2014 / 059487²system, as portable testing device 100 is capable of testing a biological ²sample, processing the ²data that is collected, and displaying the data on display 116. Display 116 ²eliminates the need ²for portable testing device 100 to be connected to another machine or computer ²to process and ²display the results of testing. This can allow a user to avoid having to carry ²an additional device ²in the field or having to wait till they get back to a laboratory to read the ²data. Portable testing ²device 100 includes all of the features that are necessary for testing, ²processing, and displaying ²results of the tests in a compact all-in-one device.²

[00106] FIG. 2A is a perspective view of a top side portable testing device ²100 when ²cover 124 is placed over display 116. FIG. 2B is a bottom plan view of ²portable testing device ²100. Portable testing device 100 includes housing 110, display 116 (not shown ²in FIGS. 2A-2B), ²cover 124, power switch 126, power jack 128, and battery lid 130.²

[00107] Housing 110 forms the body of portable testing device 100. Display ²116 is ²positioned on a top front portion of housing 110. Display 116 is a touchscreen ²display and a user ²can use display 116 to select test protocol and to view data collected during ²testing. Cover 124 is ²provided to cover and protect display 116. Portable testing device 100 is ²designed for use in the ²field, so there is a significant risk that display 116 could be damaged if it ²was exposed when ²portable testing device 100 was being transported in the field. Cover 124 ²forms an interference ²fit with housing 110 over display 116. Cover 124 can be positioned over ²display 116 and ²snapped into place so that it is retained during transportation of portable ²testing device 100. ²Cover 124 protects display 116 from damage during transportation of portable ²testing device ²100. Cover 124 can be removed from display 116 using a notch that is located ²along a perimeter ²portion of cover 124. A user can place a finger in the notch and pull cover ²124 off of display ²116.²

[00108] Portable testing device 100 further includes power switch 126 and ²power jack 128 ²located on a side of housing 110. Power switch 126 can be used by a user to ²turn portable testing ²device 100 on and off. Power jack 128 is used to connect portable testing ²device 100 to a power ²source so that a battery in portable testing device 100 can be charged. ²Battery lid 130 holds the ²battery in portable testing device 100 and can be removed to access the ²battery.²

[00109] Providing cover 124 over display 116 is advantageous, as display ²116 could be ²easily damaged when portable testing device 100 is being used in the field. ²Display 116 is a ²touchscreen display that acts as the main user interface between a user and ²portable testing²9²<DP=12>²CA 02926253 2016-04-01²WO 2015 / 054245 PCT / US2014 / 059487²device 100, thus damage to display 116 could affect overall operation of ²portable testing device ²100. Protecting display 116 with cover 124 prevents display 116 from being ²damaged. Further, ²powering portable testing device 100 with a battery is advantageous, as it ²allows portable testing ²device 100 to be used in the field.²

[00110] FIG. 3A is a perspective view of a top side of an alternate design ²of portable ²testing device 100' when cover 124' is placed over display 116'. FIG. 3B is a ²perspective view ²of a bottom side of the alternate design of portable testing device 100' when ²cover 124' is stored ²in recess 132' on the bottom side of portable testing device 100'. Portable ²testing device 100' ²includes housing 110', display 116' (not shown in FIGS. 3A-3B), cover 124', ²power switch ²126', and recess 132'.²

[00111] Housing 110' forms the body of portable testing device 100'. ²Display 116' is ²positioned on a top front portion of housing 110'. Cover 124' forms an ²interference fit with ²housing 110' over display 116'. Cover 124' can be positioned over display 116' ²and snapped ²into place so that it is retained during transportation of portable testing ²device 100'. Cover 124' ²protects display 116' from damage during transportation of portable testing ²device 100'. Cover ²124' can be removed from display 116' using a notch that is located along a ²perimeter portion of ²cover 124'. A user can place a finger in the notch and pull cover 124' off of ²display 116'.²

[00112] When portable testing device 100' is being used, cover 124' can be ²stored in ²recess 132'. Recess 132' is built into a bottom side of portable testing ²device 100' and is shaped ²to fit cover 124'. Cover 124' forms an interference fit with recess 132' and ²can be snapped into ²place in recess 132'. When portable testing device 100' is no longer being ²used, cover 124' can ²be removed from recess 132' using the notch that is located along the ²perimeter of cover 124' to ²pull cover 124' out of recess 132'. Power switch 126' is also positioned on ²the bottom side of ²portable testing device 100'. Power switch 126' can be used to turn portable ²testing device 100' ²on and off.²

[00113] Providing cover 124' over display 116' is advantageous, as display ²116' could be ²easily damaged when portable testing device 100' is being used in the field. ²Protecting display ²116' with cover 124' prevents display 116' from being damaged. Further, ²providing recess 132' ²to store cover 124' is advantageous, as it allows a user to easily store cover ²124' when portable ²testing device 100' is being used. This prevents a user from forgetting cover ²124' sitting ²somewhere or from purposely removing cover 124' so that the user does not have ²to keep track²<DP=13>²CA 02926253 2016-04-01²WO 2015 / 054245 PCT / US2014 / 059487²of cover 124'. Providing an easy way to store cover 124' in recess 132' will ²ensure proper use of ²cover 124' and protect display 116' from damage.²

[00114] FIG. 4A is a perspective view of portable testing device 100 when a ²sample ²holder in the form of tube array 140 is being placed in portable testing ²device 100. FIG. 4B is a ²perspective view of portable testing device 100 when a sample holder in the ²form of card 142 is ²being placed in portable testing device 100. FIG. 4C is a perspective view of ²portable testing ²device 100 when card 142 is placed in portable testing device 100. Portable ²testing device 100 ²includes housing 110, display 116, handle 118, and lid 120. FIG. 4A also ²includes receptacle ²122 and tube array 140. FIGS. 4B-4C also include receptacle 122' and card 142.²

[00115] As seen in FIG. 4A, receptacle 122 is located on a top side of ²portable testing ²device 100 in the embodiment shown, but can be located in any suitable ²location in alternate ²embodiments. Receptacle 122 is an opening in housing 110 of portable testing ²device 100. A ²sample holder containing a biological sample can be placed in receptacle 122 ²for testing. In FIG. ²4A, receptacle 122 is configured to receive tube array 140. In alternate ²embodiments, receptacle ²122 can be configured in any manner that is capable of receiving a sample ²holder.²

[00116] As seen in FIGS. 4B-4C, receptacle 122' is located on a top side of ²portable ²testing device 100 in the embodiment shown, but can be located in any suitable ²location in ²alternate embodiments. Receptacle 122' is an opening in housing 110 of ²portable testing device ²100. A sample holder containing a biological sample can be placed in ²receptacle 122' for ²testing. In FIGS. 4B-4C. receptacle 122' is configured to receive card 142. In ²alternate ²embodiments, receptacle 122' can be configured in any manner that is capable ²of receiving a ²sample holder.²

[00117] When a sample holder is placed in receptacle 122 (or receptacle ²122') of portable ²testing device 100 it will be positioned in an optical assembly that is held ²in portable testing ²device 100. The optical assembly will be able to amplify, excite, and detect ²the biological ²sample in the sample holder. The optical assembly includes a heating component ²that is used to ²heat the biological sample, causing it to amplify. The optical assembly will ²then use radiation to ²excite the biological sample, so that the biological sample with emit ²radiation. Lid 120 is ²positioned over receptacle 122 to prevent radiation from escaping housing 110 ²through ²receptacle 122. Lid 120 further prevents ambient light from entering housing ²110 through ²receptacle 122, which prevents the ambient light from skewing or negating ²results of the tests²11²<DP=14>²CA 02926253 2016-04-01²WO 2015 / 054245 PCT / US2014 / 059487²that are being run in portable testing device 100. Lid 120 is capable of being ²moved between an ²open and closed position. When lid 120 is in an open position, sample holders ²(including tube ²array 140 or card 142) can be inserted into and removed from receptacle 122. ²When lid 120 is ²closed, sample holders will be held in receptacle 122 and radiation in ²portable testing device 100 ²will not escape from housing 110.²[0011.8] Receptacle 122 can be shaped to receive any sample holder, ²allowing portable ²testing device 100 to be designed to accommodate a wide variety of standard ²and custom ²designed sample holders. Tube array 140 and card 142 are examples of each. ²Tube array 140 is ²a standard sample holder that is widely available on the market. Card 142 is a ²custom designed ²sample holder that is designed to be used with portable testing device 100. ²Receptacle 122 ²allows portable testing device 100 to be designed to accommodate a wide ²variety of sample ²holder shapes and sizes.²

[00119] FIG. 5 is a block diagram of portable testing device 100. Portable ²testing device ²100 includes display 116, power supply 150, electronic assembly 152, machine ²readable code ²reader 154, and optical assembly 156. Optical assembly 156 includes heat block ²160, light-²emitting diodes 162, and photodetectors 164.²

[00120] Portable testing device 100 is used to analyze and obtain data from ²biological ²samples in the field. To accomplish this, portable testing device 100 is ²equipped with display ²116, power supply 150, electronic assembly 152, machine readable code reader ²154, and optical ²assembly 156. In the embodiment shown, display 116 is a touchscreen display ²that acts as a ²primary user interface between a user and portable testing device 100. A user ²can input ²information into display 116 to indicate what testing should be run in ²portable testing device 100 ²for each biological sample. Further, a user can monitor the results of tests ²that are run in portable ²testing device 100 on display 116.²

[00121] Display 116 is connected to electronic assembly 152 with interface ²circuitry. ²Information that is inputted into display 116 will be communicated to ²electronic assembly 152 ²using the interface circuitry. Electronic assembly 152 includes hardware, ²firmware, and software ²to control the operations of portable testing device 100, including a ²microprocessor. Electronic ²assembly 152 will indicate what testing is to be run in portable testing ²device 100 and ²communicates this information throughout the device. Data that is collected in ²portable testing ²device 100 during testing will also be communicated to electronic assembly ²152. Electronic²12²<DP=15>²CA 02926253 2016-04-01²WO 2015 / 054245 PCT / US2014 / 059487²assembly 152 can process this data and transmit it to display 116 to be ²displayed. Electronic ²assembly 152 further stores this data for retrieval or transfer at a later ²time.²

[00122] Electronic assembly 152 is connected to power supply 150 with ²interface ²circuitry. Power supply 150 includes components that are capable of powering ²portable testing ²device 100, including a battery, a power board, a power switch, and a power ²jack that can be ²connected to a power source for recharging. Power from power supply 150 is ²sent to electronic ²assembly 152 through the interface circuitry so that portable testing device ²100 can operate.²

[00123] Portable testing device 100 can further include machine readable ²code reader 154. ²When a sample holder containing a machine readable code is placed in portable ²testing device ²100, machine readable code reader 154 can read the machine readable code on ²the sample ²holder. A machine readable code can also be provided separate from the sample ²holder. The ²machine readable code can contain all of the parameters for the testing ²protocol and the assay ²traceability information for the test that is to be run. Alternatively, the ²machine readable code ²can indicate what test is to be run. This is advantageous, as it allows a user ²to insert a sample ²into portable testing device 100 and portable testing device 100 will ²automatically select a test ²protocol and begin testing.²

[00124] Electronic assembly 152 includes a microprocessor, associated ²memory, and ²interface circuitry for interfacing with display 116 and optical assembly 156. ²Input that is ²received in electronic assembly 152 from display 116 can be processed in ²electronic assembly ²152. This information can be used to control optical assembly 156. Optical ²assembly 156 ²conducts testing of the biological sample that is placed in portable testing ²device 100. As the ²testing is being completed, data that is collected in optical assembly 156 can ²be communicated to ²electronic assembly 152. Electronic assembly 152 processes this data and can ²transmit the data ²to display 116 so that the user can monitor the test results. Electronic ²assembly 152 can also ²transmit the data to an external device with any suitable data transfer means, ²including wireless ²transfer or transfer through a USB port, microUSB port, SD card, or microSD ²card.²

[00125] Optical assembly 156 includes heat block 160, light-emitting diodes ²162, and ²photodetectors 164 to conduct testing of the biological samples that are ²placed in portable testing ²device 100. Optical assembly 156 will amplify the biological sample using heat ²and will then ²excite the biological sample with radiation to detect the presence of a ²specific fluorescent ²marker. Biological samples that are placed in portable testing device 100 will ²be mixed with a²13²<DP=16>²CA 02926253 2016-04-01²WO 2015 / 054245 PCT / US2014 / 059487²reaction mixture that contains one or more fluorescent dyes. When the ²biological sample is ²placed in portable testing device 100, heat block 160 will amplify the ²biological sample with ²heat. Heat block 160 is positioned underneath receptacle 122 in portable ²testing device 100 so ²that when a sample holder containing a biological sample is placed in portable ²testing device ²100, the sample holder will be positioned in heat block 160. As the biological ²sample is ²amplified it can be analyzed using light-emitting diodes 162 and ²photodetectors 164. Light-²emitting diodes 162 transmit radiation to the biological sample to excite the ²biological sample. ²A plurality of light-emitting diodes 162 can be used in portable testing ²device 100 to excite the ²biological sample at a predetermined cycle rate. In the embodiment shown, the ²plurality of light-²emitting diodes 162 cycle on and off at 1.54 kHz. In alternate embodiments, ²light-emitting ²diodes 162 can cycle at any predetermined cycle rate. When the biological ²sample is excited at ²the predetermined cycle rate, it will emit radiation at the same predetermined ²cycle rate and the ²corresponding wavelengths of the fluorescent dyes that were added to the ²biological sample. ²This radiation can be received by photodetectors 164. A plurality of ²photodetectors 164 can be ²used in portable testing device 100 to read the emitted radiation from the ²biological sample at ²different radiation wavelengths. The signals produced by photodetectors 164 ²can then be ²transmitted to electronic assembly 152 for processing and analysis, and ²displayed on display 116 ²as data collected during testing.²

[10126] Portable testing device 100 is advantageous, as it is an all-in-one ²device. Portable ²testing device 100 includes optical assembly 156 to conduct testing of ²biological samples in the ²field. Portable testing device 100 further includes electronic assembly 152 ²and display 116 to ²specify what testing to run and to process and display data that is collected ²during testing. ²Portable testing device 100 further includes power supply 150, including a ²battery, so that ²portable testing device 100 can be used in the field. Portable testing device ²100 includes every ²component that is necessary to conduct testing of a biological sample, and ²does so in a compact ²device that can be easily used in the field. Using portable testing device 100 ²in the field prevents ²concerns about contamination or degradation of biological samples and allows a ²user to quickly ²react to test results in the field.²

[00127] FIG. 6A is a perspective view of optical assembly 156. FIG. 6B is a ²cross-²sectional view of optical assembly 156. Optical assembly 156 includes heating ²portion 170 (not ²shown in FIG. 6A), lens portion 172 (not shown in FIG. 6A), housing portion ²174, first optical²14²<DP=17>²CA 02926253 2016-04-01²WO 2015 / 054245 PCT / US2014 / 059487²mounting portion 176, and second optical mounting portion 178. Also shown in ²FIG. 6B is tube ²array 140.²

[00128] Optical assembly 156 includes heating portion 170 to heat the ²biological sample ²and reagent mixture in tube array 140. Positioned in heating portion 170 is ²lens portion 172 to ²direct radiation through optical assembly 156. Housing portion 174 is ²positioned around heating ²portion 170 and forms the main body portion of optical assembly 156. First ²optical mounting ²portion 176 is positioned on a first side of housing portion 174 and second ²optical mounting ²portion 178 is positioned on a second side of housing portion 174. Both first ²optical mounting ²portion 176 and second optical mounting portion 178 mount light-emitting ²diodes to optical ²assembly 156 to excite the biological sample and reagent mixture in tube array ²140. Further, ²both first optical mounting portion 176 and second optical mounting portion ²178 mount ²photodetectors to optical assembly 156 to detect a signal from the biological ²sample and reagent ²mixture in tube array 140.²

[00129] FIG. 7 is an exploded view of heating portion 170 of optical ²assembly 156. As ²seen in FIGS. 6B and 7, heating portion 170 includes sample block 190, heating ²component 192, ²temperature sensor 194, wells 196, passages 198, passages 200, passages 202, ²and passages 204.²

[00130] Heating portion 170 includes sample block 190 that forms the main ²body portion ²of heating portion 170. Heating component 192 is attached to a second side of ²sample block ²190. Heating component 192 is a flat polyimide heater in the embodiment shown, ²but can be any ²suitable heater in alternate embodiments. Temperature sensor 194 is placed in ²a bottom portion ²of sample block 190 to sense the temperature of sample block 190. Further, in ²alternate ²embodiments, a thermal cut out switch, such as a PEPI switch, can be placed in ²series with a lead ²on heating component 192.²

[00131] Sample block 190 includes wells 196 on a top side of sample block ²190. Each ²well 196 is sized to receive one tube in tube array 140. In the embodiment ²shown in FIG. 7, ²heating component 192 heats each of wells 196 at a constant temperature so ²that portable testing ²device 100 can be used with isothermal amplification chemistries. In alternate ²embodiments, ²heating component 192 can heat each well 196 at a different temperature across ²a gradient, or ²there can be a plurality of heating components so that each well is heated by ²a different heating ²component to a different temperature. This allows a user to conduct a ²preliminary test to ²determine what temperature should be used to analyze a particular biological ²sample. In further²<DP=18>²CA 02926253 2016-04-01²WO 2015 / 054245 PCT / US2014 / 059487²alternate embodiments, heating component 192 can include a thermal cycler that ²is capable of ²cycling heating potion 170 through different temperatures so that portable ²testing device 100 can ²be used with non-isothermal polymerase chain reaction (PCR) chemistries.²

[00132] Sample block 190 further includes passages 198, passages 200, ²passages 202, and ²passages 204. Passages 198 extend from a first side of sample block 190 to ²wells 196. Passages ²200 extending from a bottom side of sample block 190 to wells 196. Passages ²202 extend from ²the second side of sample block 190 to wells 196. Passages 204 extend from a ²bottom side of ²sample block 190 to wells 196. Passages 198, passages 200, passages 202, and ²passages 204 ²extend through sample block 190 to direct radiation into and out of the ²biological sample and ²reagent mixture in tube array 140 in wells 196.²

[00133] FIG. 8 is an exploded view of lens portion 172 of optical assembly ²156. As seen ²in FIGS. 6B and 8, lens portion 172 includes lenses 210 and lens retainer 212.²

[00134] Lens portion 172 includes lenses 210 that are positioned in sample ²block 190 of ²heating portion 170. Passages 198 in sample block 190 are sized to receive ²lenses 210 on the ²first side of sample block 190. One lens 210 is positioned in each passage 198 ²of sample block ²190. Lenses 210 are held in passages 198 with lens retainer 212. Lens retainer ²212 has a ²plurality of apertures so that radiation can pass through lens retainer 212 to ²pass through lenses ²210.²

[00135] FIG. 9 is an exploded view of housing portion 174 of optical ²assembly 156. As ²seen in FIGS. 6A-6B and 9, housing portion 174 includes first housing 220, ²second housing 222, ²heat shield 224, passages 226, passages 228, passages 230, passages 232, and ²apertures 234.²

[00136] Housing portion 174 includes first housing 220 positioned on a ²first side of ²heating portion 170 and second housing 222 positioned on a second side of ²heating portion 170. ²First housing 220 and second housing 222 form a main body portion of housing ²portion 174. ²Heat shield 224 is positioned between first housing 220 and second housing 222 ²on a top side of ²heating portion 170.²

[00137] First housing 220 includes passages 226 and passages 228. Passages ²226 extend ²from a first side of first housing 220 to an interior side of first housing ²220 adjacent sample block ²190. Each passage 226 in first housing 220 is aligned with one passage 198 in ²sample block 190. ²Passages 228 extend from a bottom side of first housing 220 to an interior ²side of first housing ²220 adjacent sample block 190. Each passage 228 in first housing 220 is ²aligned with one²16²<DP=19>²CA 02926253 2016-04-01²WO 2015 / 054245 PCT / US2014 / 059487²passage 200 in sample block 190. Passages 226 and 228 extend through first ²housing 220 to ²direct radiation into and out of the biological sample and reagent mixture in ²tube array 140 in ²wells 196 of sample block 190.²

[00138] Second housing 222 includes passages 230 and passages 232. Passages ²230 ²extend from a second side of second housing 222 to an interior side of second ²housing 222 ²adjacent sample block 190. Each passage 230 in second housing 222 is aligned ²with one passage ²202 in sample block 190. Passages 232 extend from a bottom side of second ²housing 222 to an ²interior side of second housing 222 adjacent sample block 190. Each passage ²232 in second ²housing 222 is aligned with one passage 204 in sample block 190. Passages 230 ²and 232 extend ²through second housing 222 to direct radiation into and out of the biological ²sample and reagent ²mixture in tube array 140 in wells 196 of sample block 190.²

[00139] Heat shield 224 is positioned over sample block 190 and held ²between first ²housing 220 and second housing 222. Apertures 234 extend from a top side to a ²bottom side of ²heat shield 224. Each aperture 234 in heat shield 224 is aligned with one well ²196 in sample ²block 190. This allows tube array 140 to be positioned in wells 196 in sample ²block 190 through ²apertures 234 in heat shield 224. Heat shield 224 is positioned over sample ²block 190 to prevent ²heat from escaping out of the top side of sample block 190. Heat shield 224 ²further provides an ²insulated surface to protect the user from the top side of sample block 190 ²when sample block ²190 is hot.²

[00140] FIG. 10A is a partially exploded view of first optical mounting ²portion 176 of ²optical assembly 156. FIG. 10B is a partially exploded view of second optical ²mounting portion ²178 of optical assembly 156. FIG. 10C is a partially exploded view of first ²optical mounting ²portion 176 and second optical mounting portion 178 of optical assembly 156. ²As seen in FIGS. ²6A-6B, 10A, and 10C, first optical mounting portion 176 includes housing 240, ²housing 242, ²emission filter 244, gasket 246, excitation filter 248, passages 250, passages ²252, photodetectors ²mounting board 254, photodetectors 256, gasket 258, light-emitting diodes ²mounting board 260, ²light-emitting diodes 262, and gasket 264. As seen in FIGS. 6A-6B and 10B-10C, ²second ²optical mounting portion 178 includes housing 270, housing 272, emission ²filter 274, gasket 276, ²excitation filter 278, passages 280, passages 282, photodetectors mounting ²board 284, ²photodetectors 286, gasket 288, light-emitting diodes mounting board 290, ²light-emitting diodes ²292, and gasket 294.²17²<DP=20>²CA 02926253 2016-04-01²WO 2015 / 054245 PCT / US2014 / 059487²

[00141] First optical mounting portion 176 is positioned on a first side of ²housing portion ²174. First optical mounting portion 176 includes housing 240 and housing 242 ²that form a main ²body portion of first optical mounting portion 176. Housing 240 is attached to ²a first side of first ²housing 220 of housing portion 174. Emission filter 244 is positioned between ²housing 240 and ²first housing 220 in a groove on the first side of first housing 220. Gasket ²246 is positioned ²between emission filter 244 and housing 240. Housing 242 is attached to a ²bottom side of first ²housing 220 of housing portion 174. Excitation filter 248 is positioned ²between housing 242 and ²first housing 220 in a groove on the bottom side of first housing 220.²

[00142] Housing 240 includes passages 250. Passages 250 extend from a first ²side of ²housing 240 to an interior side of housing 240 adjacent first housing 220. ²Each passage 250 in ²housing 240 is aligned with one passage 226 in first housing 220. Housing 242 ²includes ²passages 252. Passages 252 extend from a bottom side of housing 252 to an ²interior side of ²housing 242 adjacent first housing 220. Each passage 252 in housing 242 is ²aligned with one ²passage 228 in first housing 220.²

[00143] Photodetectors mounting board 254 is connected to a first side of ²housing 240. ²Photodetectors mounting board 254 is an electronic board that includes ²photodetectors 256. ²Each photodetector 256 on photodetectors mounting board 254 is positioned in ²one passage 250 ²in housing 240. Gasket 258 is positioned between photodetectors mounting board ²254 and ²housing 240. Light-emitting diodes mounting board 260 is attached to a bottom ²side of housing ²242. Light-emitting diodes mounting board 260 is an electronic board that ²includes light-²emitting diodes 262. Each light-emitting diode 262 on light-emitting diodes ²mounting board 260 ²is positioned in one passage 252 in housing 242. Gasket 264 is positioned ²between light-²emitting diodes mounting board 260 and housing 242.²

[00144] Second optical mounting portion 178 is positioned on a second side ²of housing ²portion 174. Second optical mounting portion 178 includes housing 270 and ²housing 272 that ²form a main body portion of second optical mounting portion 178. Housing 270 ²is attached to a ²second side of second housing 222 of housing portion 174. Emission filter 274 ²is positioned ²between housing 270 and second housing 222 in a groove on the second side of ²second housing ²222. Gasket 276 is positioned between emission filter 274 and housing 270. ²Housing 272 is ²attached to a bottom side of second housing 222 of housing portion 174. ²Excitation filter 278 is²18²<DP=21>²CA 02926253 2016-04-01²WO 2015 / 054245 PCT / US2014 / 059487²positioned between housing 272 and second housing 222 in a groove on the ²bottom side of ²second housing 222.²

[00145] Housing 270 includes passages 280. Passages 280 extend from a ²second side of ²housing 270 to an interior side of housing 270 adjacent second housing 222. ²Each passage 280 ²in housing 270 is aligned with one passage 230 in second housing 222. Housing ²272 includes ²passages 282. Passages 282 extend from a bottom side of housing 282 to an ²interior side of ²housing 282 adjacent second housing 222. Each passage 282 in housing 272 is ²aligned with one ²passage 232 in second housing 222.²

[00146] Photodetectors mounting board 284 is connected to a first side of ²housing 270. ²Photodetectors mounting board 284 is an electronic board that includes ²photodetectors 286. ²Each photodetector 286 on photodetectors mounting board 284 is positioned in ²one passage 280 ²in housing 270. Gasket 288 is positioned between photodetectors mounting board ²284 and ²housing 270. Light-emitting diodes mounting board 290 is attached to a bottom ²side of housing ²272. Light-emitting diodes mounting board 290 is an electronic board that ²includes light-²emitting diodes 292. Each light-emitting diode 292 on light-emitting diodes ²mounting board 290 ²is positioned in one passage 282 in housing 272. Gasket 294 is positioned ²between light-²emitting diodes mounting board 290 and housing 272.²

[00147] As seen in FIGS. 6A-10C, optical assembly 156 can excite and detect ²emissions ²from a biological sample and reagent mixture in tube array 140 that is ²positioned in optical ²assembly 156. Light-emitting diodes 262 are bi-color light-emitting diodes ²that can emit ²radiation at two different wavelengths. In the embodiment shown, light-²emitting diodes 262 are ²blue and amber hi-color light-emitting diodes to excite Fluorescein amidite ²(FAM) fluorescence ²dye and 6-Carboxyl-X-Rhodamine (ROX) fluorescence dye, respectively. Further, ²light-emitting ²diodes 262 emit radiation at a predetermine cycle rate of 1.54 kHz. Radiation ²from light-²emitting diodes 262 can pass through passages 252, excitation filter 248, ²passages 228, and ²passages 200 into the biological sample and reagent mixture in tube array 140 ²that is held in ²wells 196. Excitation filter 248 is a dual bandpass excitation filter that is ²capable of passing ²either of the wavelengths emitted by light-emitting diodes 262. Excitation ²filter 248 is a single ²filter that extends across the entire length of tube array 140, thus ²excitation filter 248 extends ²between adjacent passages 228 in first housing 220. Radiation from light-²emitting didoes 262 ²can excite a fluorescent dye in the biological sample and reagent mixture. ²This excitation of the²19²<DP=22>²CA 02926253 2016-04-01²WO 2015 / 054245 PCT / US2014 / 059487²fluorescent dye will emit a signal from the biological sample and reagent ²mixture and the ²emission can pass through passages 198. passages 226, emission filter 244, and ²passages 250 to ²be detected by photodetectors 256. Emission filter 244 is a dual bandpass ²emission filter in the ²embodiment shown. Emission filter 244 is a single filter that extends across ²the entire length of ²tube array 140, thus emission filter 244 extends between adjacent passages 226 ²in first housing ²220.²

[00148] Light-emitting diodes 292 are light-emitting diodes that can emit ²radiation at a ²single wavelength. In the embodiment shown, light-emitting diodes 292 are ²green light-emitting ²diodes to excite 6-carboxy-X-hexachlorofluorescein (HEX) fluorescence dye. ²Further, light-²emitting diodes 292 emit radiation at a predetermine cycle rate of 1.54 kHz. ²Radiation from ²light-emitting diodes 292 can pass through passages 282, excitation filter ²278, passages 232, and ²passages 204 into the biological sample and reagent mixture in tube array 140 ²that is held in ²wells 196. Excitation filter 278 is a single bandpass filter that is capable ²of passing the ²wavelength emitted by light-emitting diodes 292. Excitation filter 278 is a ²single filter that ²extends across the entire length of tube array 140, thus excitation filter 278 ²extends between ²adjacent passages 232 in second housing 222. Radiation from light-emitting ²didoes 292 can ²excite a fluorescent dye in the biological sample and reagent mixture. This ²excitation of the ²fluorescent dye will emit a signal from the biological sample and reagent ²mixture and the ²emission can pass through passages 202, passages 230, emission filter 274, and ²passages 280 to ²be detected by photodetectors 286. Emission filter 274 is a single bandpass ²filter in the ²embodiment shown. Emission filter 274 is a single filter that extends across ²the entire length of ²tube array 140, thus emission filter 274 extends between adjacent passages 230 ²in second ²housing 222.²

[00149] In an alternate embodiment, light-emitting diodes 292 can be bi-²color light-²emitting diodes that can emit radiation at two different wavelengths. Further, ²excitation filter ²278 can be a dual bandpass filter that is capable of passing both of the ²wavelengths emitted by ²light-emitting diodes 292, and emission filter 274 can also be a dual bandpass ²filter. This would ²result in portable testing device 100 being capable of testing four different ²fluorescent dyes that ²can be mixed in with the biological sample and reagent mixture.²

[00150] Light-emitting diodes 262 and light-emitting diodes 292 emit ²radiation in the ²form of light that is cycled at a predetermined rate of 1.54 kHz. This causes ²emissions from the²<DP=23>²CA 02926253 2016-04-01²WO 2015 / 054245 PCT / US2014 / 059487²biological sample and reagent mixture at the same predetermined rate. ²Photodetectors 256 and ²photodetectors 286 thus receive the emissions from the biological sample and ²reagent mixture at ²a rate of 1.54 kHz as well. The electronic circuitry connected to ²photodetectors 256 and ²photodetectors 286 is designed to electronically filter out all other ²frequencies except for 1.54 ²kHz. This will negate any ambient light or other radiation sources in portable ²testing device 100 ²that may interfere with the accuracy of the testing.²

[00151] ²Having a single filter for emission filter 244, excitation filter 248, ²emission filter²274, and excitation filter 278 simplifies the design of portable testing ²device 100. This ²simplified design makes portable testing device 100 more suitable for use in ²the field. If one of ²emission filter 244, excitation filter 248, emission filter 274, or excitation ²filter 278 had to be ²replaced, it would be easy to replace the entire filter instead of a number of ²different individual ²filters. Further, using one filter for each of emission filter 244, excitation ²filter 248, emission ²filter 274, or excitation filter 278 reduces the cost of portable testing ²device 100.²

[00152] FIG. ²11A is a perspective view of screen assembly 300. FIG. 11B is a partially²exploded view of screen assembly 300. FIG. 11C is a partially exploded view of ²machine ²readable code reader 154 attached to screen assembly 300. Screen assembly 300 ²includes screen ²302, screen mount 304, and circuit board 306. Screen 302 includes display 116. ²FIGS. 11A and ²11C further shown machine readable code reader 154.²

[00153] ²Screen assembly 300 includes screen 302 mounted to screen mount 304. Screen²302 includes display 116 on a first side of screen 302. A second side of ²screen 302 is mounted to ²a first side of screen mount 304 with a fastener. In the embodiment shown, ²screen 302 is ²mounted to screen mount 304 with an adhesive fastener, but screen 302 can be ²mounted to ²screen mount 304 with any suitable fastener in alternate embodiments.²

[00154] ²Circuit board 306 is attached to a second side of screen mount 304 with ²fasteners.²In the embodiment shown, circuit board 306 is attached to screen mount 304 ²with screw ²fasteners, but circuit board 306 can be attached to screen mount 304 with any ²suitable fastener in²alternate embodiments. ²Circuit board 306 is a part of electronic assembly 152 that²communicates with screen 302 and that contains a system computer for portable ²testing device ²100. Circuit board 306 can further communicate with other electronic ²components of electronic ²assembly 152 in portable testing device 100.²21²<DP=24>²CA 02926253 2016-04-01²WO 2015 / 054245 PCT / US2014 / 059487²

[00155] Machine readable code reader 154 is also attached to screen mount ²304 with ²fasteners. In the embodiment shown, machine readable code reader 154 is ²attached to screen ²mount 304 with screw fasteners, but machine readable code reader 154 can be ²attached to screen ²mount 304 with any suitable fastener in alternate embodiments. Machine ²readable code reader ²154 is connected to electronic assembly 152 with interface circuitry. When ²machine readable ²code reader 154 is used to scan a code. the code information can be ²communicated to electronic ²assembly 152 to indicate to portable testing device 100 what test protocol is ²to be run.²

[00156] FIG. 12 is an exploded view of second housing portion 114 and lid ²120 of ²portable testing device 100. Second housing portion 114 includes opening 310, ²opening 312, ²gasket 314, hinge inserts 316, magnets 318, and window 320. Lid 120 includes ²first lid portion ²330, second lid portion 332, and magnets 334.²

[00157] Second housing portion 114 includes opening 310 and opening 312. ²Opening 310 ²is an opening on a top side of second housing portion 114 in which screen 302 ²of screen ²assembly 300 can be positioned. Gasket 314 is provided to form a seal between ²opening 310 in ²second housing portion 114 and screen 302. Positioning screen 302 of screen ²assembly 300 in ²opening 310 allows display 116 of screen 302 to be accessed through opening ²310. Opening 312 ²is an opening on a top side of second housing portion 114 in which optical ²assembly 156 can be ²positioned. Positioned optical assembly 156 in opening 312 allows a user to ²place and remove ²tube array 140 from optical assembly 156 for analysis. Lid 116 is positioned ²over opening 312.²

[00158] Hinge inserts 316 are positioned on second housing portion 114 to ²hinge lid 116 ²to second housing portion 114. Magnets 318 are positioned on second housing ²portion 114 to ²hold lid 116 in place over opening 312 when the lid is in a closed position. ²Both hinge inserts ²316 and magnets 318 are positioned adjacent opening 312 on the top side of ²second housing ²portion 114. Window 320 is also provided on a side of second housing portion ²114. Machine ²readable code reader 154 is positioned adjacent to window 320 in portable ²testing device 100 so ²that a code can be read by machine readable code reader 154 through window ²320.²

[00159] Lid 116 is attached to second housing portion 114 with hinge ²inserts 316. Lid 116 ²includes first lid portion 330 and second lid portion 332. First lid portion ²330 includes hinge ²pins that mate with hinge inserts 316 to hold lid 116 on portable testing ²device 100. First lid ²portion 330 further includes a smooth surface on an interior surface to ²interface with tube array ²140 when tube array 140 is placed in portable testing device 100. The smooth ²swface of lid²22²<DP=25>²CA 02926253 2016-04-01²WO 2015 / 054245 PCT / US2014 / 059487²portion 330 that interfaces with tube array 140 can be easily cleaned and ²decontaminated after a ²test is completed in portable testing device 100. Magnets 334 are positioned ²on first lid portion ²330 and are aligned with magnets 318 on second housing portion 114. Magnets ²334 and ²magnets 318 will hold lid 116 on second housing portion 114.²

[00160] Second lid portion 332 is connected to a top of first lid portion ²330 with a space ²provided in between. This space can be left open or it can be filled with an ²insulating material so ²that lid 116 can act as an insulator over receptacle 122 of portable testing ²device 100. This will ²contain the heat from heating component 192 in portable testing device 100. ²Further, in alternate ²embodiments, a heating component can be attached to lid 116 to come into ²contact with the top ²of tube array 140. This can further heat an area surrounding tube array 140 ²and prevent ²condensation on a cap portion of tube array 140.²

[00161] FIG. 13A is an exploded view of screen assembly 300 and first ²housing portion ²112 of portable testing device 100. FIG. 13B is a partially exploded view of ²screen assembly ²300, optical assembly 156, first housing portion 112, and second housing ²portion 114 of portable ²testing device 100. FIG. 13C is a partially exploded view of portable testing ²device 100. ²Portable testing device includes first housing portion 112, second housing ²portion 114, power ²supply 150, electronic assembly 152, optical assembly 156, screen assembly ²300, battery housing ²340, gasket 350, and serial tag 354. Power supply 150 includes power switch ²126, power jack ²128, power board 342, and battery 352. Electronic assembly 152 includes ²electronic board 344, ²communications board 346, and USB ports 348. Electronic board 344 is an input ²output ²controller board.²

[00162] As seen in FIG. 13A, power supply 150, electronic assembly 152, and ²screen ²assembly 300 are positioned in first housing portion 112. Battery housing 340 ²is also positioned ²over battery 352 in first housing portion 112.²

[00163] Power supply 150 includes power switch 126 and power jack 128 ²attached to ²power board 342. Power board 342 is positioned adjacent a back side of first ²housing portion ²112. Power board 342 is further connected to battery 352 that is covered by ²battery housing 340 ²through interface circuitry. Power supply 150 powers portable testing device ²100.²

[00164] Electronic assembly 152 includes electronic board 344, ²communication board ²346, and USB ports 348. Electronic board 344 is positioned in a center of ²first housing portion ²112. Screen assembly 300 is positioned adjacent to a front side of first ²housing portion 112,²23²<DP=26>²CA 02926253 2016-04-01²WO 2015 / 054245 PCT / US2014 / 059487²positioned partially over electronic board 344. Circuit board 306 of screen ²assembly 300 can be ²connected to circuit board 300 with interface circuitry. Communication board ²346 is positioned ²adjacent the back side of first housing portion 112. Positioned on ²communication board 346 are ²two USB ports 348. In alternate embodiments, USB ports 348 can be any ports ²that allow ²portable testing device 100 to be connected to other electronic devices, ²including Bluetooth or ²wireless communication capabilities. Communications board 346 is connected to ²electronic ²board 344 with interface circuitry. A global positioning capability is also ²implemented in ²communications board 346. This allows portable testing device 100 to log the ²location of ²portable testing device 100 when tests are run. This allows a user to track ²the location of ²pathogens that are detected when testing is completed in the field.²

[00165] As seen in FIG. 13B, optical assembly 156 is positioned over power ²board 342 ²and communications board 346 adjacent to the back side of portable testing ²device 100. Second ²housing portion 114 can be placed over the components held in first housing ²portion 112 of ²portable testing device 100. Screen 302 of screen assembly 300 extends through ²opening 310 of ²second housing portion 114 so that display 116 on screen 302 can be accessed ²by a user. Optical ²assembly 156 is positioned adjacent to opening 312 of second housing portion ²314 so that a ²sample holder can be placed in optical assembly 156 through opening 312. ²Gasket 350 is ²positioned between a perimeter of opening 312 and optical assembly 156 to form ²a seal between ²second housing portion 114 and optical assembly 156.²

[00166] As seen in FIG. 13C, battery 352 is inserted into portable testing ²device 100 ²through a bottom side of first housing portion 112. When battery 352 is placed ²in portable ²testing device 100 it will be positioned in battery housing 340 (as seen in ²FIG. 13A). Battery lid ²130 can then be placed over battery 352 and fastened to first housing portion ²112 to hold battery ²352 in portable testing device 100. Cover 124 can also be positioned over ²display 116 of ²portable testing device 100 to protect display 116 from damage. Serial tag 354 ²can be affixed to ²a bottom side of first housing portion 112 using any suitable fastening means.²

[00167] FIG. 14 is a flowchart showing steps for operating portable testing ²device 100. ²The flowchart includes steps 370-386. The process begins with step 370, which ²is preparing a ²biological sample and reagent mixture for testing. The reagent mixture can ²contain the master ²mix necessary for the desired assay, including fluorescent dyes or markers ²such as FAM or ²ROX, necessary for detecting the desired analyte in portable testing device ²100. Once a user²24²<DP=27>²CA 02926253 2016-04-01²WO 2015 / 054245 PCT / US2014 / 059487²acquires a biological sample from the field, the biological sample can then be ²mixed with a ²reagent to form a biological sample and reagent mixture. More specifically, ²the biological ²sample is first mixed with a reaction buffer. Next, a portion of the ²biological sample and ²reaction buffer mixture is transferred to a sample holder containing a dried ²down master mix. ²This forms the biological sample and reagent mixture for testing.²

[00168] In step 372, portable testing device 100 is turned on using power ²switch 126. In ²step 374, a code is scanned with machine readable code reader 154. The code ²will contain ²information about what test protocol is to be run and what parameters should ²be used. This ²information can be communicated through portable testing device 100 so that ²heating assembly ²170 can begin heating to required temperature for the desired test protocol. ²In step 376, the user ²interface on display 116 will visually and audibly notify the user that ²portable testing device 100 ²is ready for testing. The user then opens lid 116 and places the sample holder ²with the biological ²sample and reagent mixture into heating assembly 170 in portable testing ²device 100.²

[00169] In step 378, the user begins the excitation and detection sequence ²for the desired ²assay using the user interface on display 116. Optical assembly 156 begins the ²excitation and ²detection sequence. During the excitation and detection sequence, portable ²testing device 100 ²transmits emission data to electronic assembly 152 and display 116. Step 380 ²includes ²displaying the real time reaction data received from portable testing device ²100 on the user ²interface on display 116. During step 382, electronic assembly 152 and display ²116 logs the data ²received from portable testing device 100 and monitors the data for threshold ²activity. Once the ²assay is complete, during step 384, display 116 signals a positive, negative, ²or indeterminate ²outcome to the user. Finally, during step 386, electronic assembly 152 stores ²the data obtained ²for retrieval or transfer.²

[00170] In general, the present invention relates to a portable testing ²device for analyzing ²biological samples. The portable testing device can be taken into the field to ²test biological ²samples as they are collected. This is advantageous over prior art systems, as ²it allows a user to ²test biological samples as the user is collecting them. This can prevent ²problems with ²contamination and degradation of biological samples due to transportation to a ²laboratory for ²testing, later discovery that not enough sample was taken, or later discovery ²that the collected ²biological sample is otherwise unsuitable for use. Allowing a user to test the ²biological sample²<DP=28>²CA 02926253 2016-04-01²WO 2015 / 054245 PCT / US2014 / 059487²in the field can save time, money, and resources. Testing in the field also ²provides the ability for ²rapid safety response if test results indicate a pathogen or toxin that may be ²harmful.²

[00171] In the embodiment described below, the portable testing device is ²capable of ²testing biological samples with EnviroLogix's DNAble chemistry, which employs ²an ²isothermal amplification process. This eliminates the need for thermocycling ²as a means to ²amplify nucleic acid products for endpoint detection. This allows a user to ²obtain data from the ²sample while the test is being run. In alternate embodiments, the portable ²testing device can be ²used to test biological samples with other isothermal amplification ²chemistries. The portable ²testing device displays this data so that a user can view the results of the ²test in the field. ²Allowing a user to view the results of the test in the field is advantageous, ²as the user can then ²make an informed decision of whether additional tests are needed. In alternate ²embodiments, the ²portable testing device is also capable of incorporating a thermocycler to ²allow for the use of ²non-isothermal polymerase chain reaction (PCR) chemistries and result in qPCR ²and end-point ²analysis.²PORTABLE TESTING DEVICE 400 WITH OPTICAL ASSEMBLY 418²

[00172] FIG. 15A is a perspective view of portable testing device 400 with ²tablet ²computer 404 positioned on portable testing device 400. FIG. 15B is a ²perspective view of ²portable testing device 400, as seen in FIG. 15A, when optical lid 408 is ²opened. Portable ²testing device 400 includes housing 402 and tablet computer 404. Housing 402 ²includes sample ²preparation area 406, optical lid 408, housing opening 410, first housing ²portion 412, second ²housing portion 414, and cradle 416. Also included in portable testing device ²400, but not ²shown in FIGS. 15A-15B, are an optical assembly and a power assembly.²

[00173] Portable testing device 400 is an all-in-one device for sampling ²and testing ²biological samples in the field. Portable testing device 400 includes housing ²402 and tablet ²computer 404. Housing 402 contains an optical assembly and a power assembly, ²not shown in ²FIGS. 15A-15B. The power assembly powers portable testing device 400 and is ²capable of ²being connected to tablet computer 102 to provide power to tablet computer ²102. Tablet ²computer 102 communicates with portable testing device 400 using Bluetooth ²technology or ²other suitable wireless technology. The optical assembly is used to heat ²biological samples for ²isothermal nucleic acid amplification and to analyze biological samples once ²they are placed in ²portable testing device 400. The data collected during testing is transmitted ²to tablet computer²26²<DP=29>²CA 02926253 2016-04-01²WO 2015 / 054245 PCT / US2014 / 059487²404, where it is displayed in real time. In the embodiment shown, the data is ²transferred ²wirelessly from portable testing device 400 to tablet computer 404, but in ²alternate embodiments ²a direct connection can be used.²

[00174] Housing 402 includes sample preparation area 406, where biological ²samples can ²be prepared for testing. Sample preparation area 406 is positioned on a top ²surface of housing ²402 of portable testing device 400. Sample preparation area 406 includes a ²plurality of apertures ²in housing 402 that can be used to prepare a biological sample for testing in ²portable testing ²device 400. Housing 402 also includes optical lid 408 that covers opening 410. ²Optical lid 408 ²can be opened so biological samples can be placed in opening 410 of housing ²402 for testing. ²Once the biological samples are positioned in portable testing device 400, ²optical lid 408 is ²closed. The biological sample can then be tested using the optical assembly. ²Housing 402 also ²includes cradle 416 in which tablet computer 102 can be positioned.²

[00175] Portable testing device 400 is advantageous, as it allows a user to ²test biological ²samples as they are collecting them in the field. This can prevent issues with ²contamination of ²the biological sample, as the biological sample is tested as it is collected. ²This can also prevent ²issues with biological samples that are collected and then later determined to ²be unsuitable for ²testing. Testing in the field allows a user to determine in real-time whether ²a biological sample ²is suitable for testing and prevents users from having to recollect samples, ²saving time and ²money. Data collected in the field can be stored on portable testing device ²400 and downloaded ²or accessed later. Further, the data can be transmitted to a remote site via a ²telephone ²connection, an internet connection, or other suitable means. The data can also ²be transmitted ²using cloud computing for access later or immediately by another person for ²rapid evaluation ²and, if desired, closed-loop response.²

[00176] Additionally, GPS capabilities can be incorporated to allow a user ²to track ²specific sampling locations and to verify that the testing was done at the ²correct location. A ²sampling location can be prescribed and plotted using the GPS mapping ²capabilities. As an ²example, a map of a corn field can be laid-out on the monitor and sample ²points predetermined ²(e.g., a location of a specific corn plant) either graphically or with GPS ²coordinates. The user ²can observe the monitor and utilize the GPS coordinates to arrive at the ²proper sample point.²[I:0177] FIG. 16A is a perspective view of upper optical assembly 420. FIG. ²16B is an ²exploded view of upper optical assembly 420, as seen in FIG. 16A. Upper ²optical assembly 420²27²<DP=30>²CA 02926253 2016-04-01²WO 2015 / 054245 PCT / US2014 / 059487²includes heating component 422, first plurality of light-emitting diodes 424, ²second plurality of ²light-emitting diodes 426, first structural component 428, second structural ²component 430, first ²filter 432, second filter 434, third filter 436, and fourth filter 438.²

[00178] Upper optical assembly 420 is one of two parts that form the ²optical system for ²portable testing device 400. Upper optical assembly 420 includes first ²plurality of light-emitting ²diodes 424 and second plurality of light-emitting diodes 426 that are used to ²excite a biological ²sample when it is placed in portable testing device 400 for testing. First ²plurality of light-²emitting diodes 424 are located on a first side of upper optical assembly 420. ²In the embodiment ²shown, first plurality of light-emitting diodes 424 are blue light-emitting ²diodes to excite ²Fluorescein amidite (FAM) fluorescence dye. Second plurality of light-emitting ²diodes 426 are ²located on a second side of upper optical assembly 420. In the embodiment ²shown, second ²plurality of light-emitting diodes 426 are amber light-emitting diodes to ²excite 6-Carboxyl-X-²Rhodamine (ROX) fluorescence dye. In alternate embodiments, first plurality of ²light-emitting ²diodes 424 and second plurality of light-emitting diodes 426 can be any color ²light-emitting ²diodes corresponding to the dye or marker used in testing a biological sample.²

[00179] Upper optical assembly also includes heating component 422. ²Heating²component 422 is a heat block in the embodiment shown, but can be any suitable ²heating ²component in alternate embodiments. Heating component 422 is capable of ²heating from an ²ambient temperature to a temperature of about 95 degrees Celsius. Heating ²component 422 has a ²plurality of apertures running from a top side of heating component 422 to a ²bottom side of ²heating component 422 in which an array of tubes can be placed. The array of ²tubes will extend ²completely through and beyond the plurality of apertures in heating component ²422. This allows ²first plurality of light-emitting diodes 424 and second plurality of light-²emitting diodes 426 to ²pass light to the array of tubes to excite the biological sample in the array ²of tubes.²

[00180] First structural component 428 and second structural component 430 ²form a ²structural basis for upper optical assembly 420. First structural component ²428 is positioned ²between first plurality of light-emitting diodes 424 and the first side of ²heating component 422. ²First plurality of light-emitting diodes are positioned so that they extend ²into first structural ²component 428. Second structural component 430 is positioned between second ²plurality of ²light-emitting diodes 426 and the second side of heating component 422. Second ²plurality of ²light-emitting diodes are positioned so that they extend into second ²structural component 430.²28²<DP=31>²CA 02926253 2016-04-01²WO 2015 / 054245 PCT / US2014 / 059487²First structural component 428 and second structural component 430 further act ²as heat ²insulators and prevent heat from escaping heating component 422. This improves ²the ²effectiveness and reliability of heating component 422. First structural ²component 428 and ²second structural component 430 provide a path through which light from first ²plurality of light-²emitting diodes 424 and second plurality of light-emitting diodes 426 can ²travel. This prevents ²light from being lost and increases the effectiveness of first plurality of ²light-emitting diodes 424 ²and second plurality of light-emitting diodes 426 exciting the biological ²sample that is placed in ²heating component 422.²

[00181] First structural component 428 and second structural component 430 ²further ²include a cut out portion in which first filter 432 and second filter 434 can ²each be placed, ²respectively. First filter 432 and second filter 434 are both excitation ²filters to filter light from ²light-emitting diodes as it passes through to excite a biological sample. ²Light from first plurality ²of light-emitting diodes 424 passes through first filter 432 that is placed in ²first structural ²component 428 before the light passes into the biological sample in heating ²component 422. ²First filter 432 is a 490 nanometer filter in the embodiment shown to align ²with FAM excitation. ²Light from second plurality of light-emitting diodes 426 passes through second ²filter 434 that is ²placed in second structural component 430 before the light passes into the ²biological sample in ²heating component 422. Second filter 434 is a 580 nanometer filter in the ²embodiment shown to ²align with ROX excitation. In alternate embodiments, first filter 432 and ²second filter 434 can ²be any filters to align with different fluorescent dyes or markers.²

[00182] Upper optical assembly 420 also includes third filter 436 and ²fourth filter 438. ²Third filter 436 and fourth filter 438 are both emission filters that filter ²light to photodiodes 142 ²and 144, respectively (shown in FIG. 3B). Photodiodes 142 and 144 are ²positioned underneath ²heating component 422 in a lower optical assembly, described in relation to ²FIGS. 3A-3B below. ²Third filter 436 is positioned between a first plurality of photodiodes and ²heating component ²422. Third filter 436 is a 610 nanometer filter in the embodiment shown to ²align with ROX ²emission. Fourth filter 438 is positioned between a second plurality of ²photodiodes and heating ²component 422. Fourth filter 438 is a 520 nanometer filter in the embodiment ²shown to align ²with FAM emission. In alternate embodiments, third filter 436 and fourth ²filter 438 can be any ²filters to align with different fluorescent dyes or markers.²29²<DP=32>²CA 02926253 2016-04-01²WO 2015 / 054245 PCT / US2014 / 059487²

[00183] Upper optical assembly 420 is designed to excite biological samples ²that are ²placed in portable testing device 400 for testing. Upper optical assembly 420 ²is advantageous, as ²it contains light from first plurality of light-emitting diodes 424 and second ²plurality of light-²emitting diodes 426. This prevents light from escaping and ensures accurate ²and reliable results ²every time portable testing device 400 is used to analyze biological samples.²

[00184] FIG. 17A is a perspective view of optical assembly 418, including ²upper optical ²assembly 420, as seen in FIGS. 16A -16B, and lower optical assembly 440. FIG. ²17B is an ²exploded view of optical assembly 418, as seen in FIG. 17A. Upper optical ²assembly 420 is ²described above in relation to FIGS. 16A-16B. Lower optical assembly 440 ²includes first ²plurality of photodiodes 442, second plurality of photodiodes 444. spacer 446, ²gasket 448, upper ²board 450, and lower board 452. Also include in lower optical assembly 440 are ²electronic ²components for controlling optical assembly 418, including electronic ²components to control ²heating of heating component 422.²

[00185] Lower optical assembly 440 is positioned below upper optical ²assembly 420 to ²form optical assembly 418. Lower optical assembly 440 includes first plurality ²of photodiodes ²442 and second plurality of photodiodes 444. First plurality of photodiodes ²442 are positioned in ²a first row on upper board 450. Second plurality of photodiodes 444 are ²positioned in a second ²row on upper board 450. Upper board 450 is placed under upper optical assembly ²420 so that ²first plurality of photodiodes 442 and second plurality of photodiodes 444 are ²positioned under ²heating component 422 of upper optical assembly 420. This allows first ²plurality of photodiodes ²442 and second plurality of photodiodes 444 to detect fluorescent emissions ²from biological ²samples that are placed in the array of tubes in heating component 422. In the ²embodiment ²shown, first plurality of photodiodes 442 are selected to align with ROX ²emission and second ²plurality of photodiodes 444 are selected to align with FAM emission. In ²alternate embodiments, ²first plurality of photodiodes 442 and second plurality of photodiodes 444 can ²be selected to ²align with different fluorescent dyes or markers.²

[00186] Lower optical assembly 440 also includes spacer 446 and gasket 448. ²Spacer 446 ²extends between upper board 450 to a bottom side of first structural component ²428 and second ²structural component 430 of upper optical assembly 420. Spacer 446 is placed ²around first ²plurality of photodiodes 442 and second plurality of photodiodes 444. This ²contains light from ²first plurality of photodiodes 442 and second plurality of photodiodes 444 and ²directs the light to²<DP=33>²CA 02926253 2016-04-01²WO 2015 / 054245 PCT / US2014 / 059487²the bottom of the array of tubes that are placed in upper optical assembly ²420. Gasket 448 is ²positioned on top of spacer 446 to form a seal between spacer 446 and upper ²optical assembly ²420.²

[00187] First plurality of photodiodes 442, second plurality of photodiodes ²444, spacer ²446, and gasket 448 are all positioned on upper board 450. Upper board 450 is ²then positioned ²on lower board 452 to form lower optical assembly 156. Electrical components ²are placed on ²upper board 450 and lower board 452 to run optical assembly 418, including ²heating of heating ²component 422.²

[00188] Optical assembly 418, including both upper optical assembly 420 and ²lower ²optical assembly 440, is capable of performing both excitation and detection ²of biological ²samples that are placed in portable testing device 400. Optical assembly 418 ²is designed to be ²compact to allow it to be used in portable testing device 400. Being compact ²is advantageous, as ²it allows excitation and detection of biological samples to occur in the field ²as biological samples ²are collected. Optical assembly 418 can additionally include a light barrier ²around optical ²assembly 418 to prevent light from escaping optical assembly 418. In a first ²embodiment, the ²light barrier can include surrounding optical assembly 418 with light proofing ²tape. In an ²alternate embodiment, the light barrier can include a housing around optical ²assembly 418 to ²prevent light from escaping.²

[00189] In the embodiment seen in FIGS. 17A-17B. optical assembly 418 is ²designed to ²be compatible with EnviroLogix's DNAble chemistry, which employs an ²isothermal ²amplification process. The reaction proceeds at a single, elevated ²temperature, usually 56 ²degrees Celsius. DNAble chemistry allows amplification to be completed in ²less than ten ²minutes. In alternative embodiments, optical assembly 418 may be used for ²other chemistries ²such as assays relating to Salmonella, soy lectin, genetically modified ²organisms, E. coli, and ²influenza.²

[00190] FIG. 18A is a perspective view of a lower portion of portable ²testing device 400, ²including optical assembly 418, as seen in FIGS. 17A-17B, and power assembly ²460. FIG. 18B ²is an exploded view of the lower portion of portable testing device 400, as ²seen in FIG. 18A. ²The lower portion of portable testing device 400 including first housing ²portion 412, optical ²assembly 418, and power assembly 460. Optical assembly 418 includes upper ²optical assembly²31²<DP=34>²CA 02926253 2016-04-01²WO 2015 / 054245 PCT / US2014 / 059487²420 and lower optical assembly 440. Power assembly 460 includes battery 462, ²power jack 464, ²and power board 466.²

[00191] Portable testing device 400 includes first housing portion 412 that ²acts as a base ²for portable testing device 400. Optical assembly 418 and power assembly 460 ²are placed in ²first housing portion 412. Optical assembly 418 includes upper optical ²assembly 420 for ²excitation that is attached to lower optical assembly 440 for detection. ²Optical assembly 418 is ²positioned in first housing portion 412 so heating component 422 of upper ²optical assembly 420 ²aligns with the opening in portable device 100 to receive the biological ²sample. Power assembly ²460 is positioned in first housing portion112 around optical assembly 418 to ²utilize all of the ²space in first housing portion 412. This allows portable testing device 400 to ²be as compact as ²possible for use as a hand-held device.²

[00192] Power assembly 460 includes battery 462. Battery 462 powers ²portable testing ²device 400 so that portable testing device 400 can be used in the field. ²Battery 462 is also ²capable of powering tablet computer 404, shown in FIGS. 15A-15B. Tablet ²computer 404 can ²be connected to power assembly 460 with a pigtail connection and powered ²through battery 462 ²or AC power.²

[00193] Power assembly 460 further includes power board 466. Power board ²466 ²consolidates and distributes power throughout portable testing device 400. ²Power jack 464 is ²also included in power assembly 460 so that power assembly 460 can be ²connected to a power ²source to recharge battery 462 and tablet computer 404. Including power ²assembly 460 on ²portable testing device 400 is advantageous, as it allows portable testing ²device to be used in the ²field. In alternate embodiments, portable testing device 400 can utilize solar ²cells, wind ²generators, manual electrical generators, or other suitable means to provide ²power to the unit. ²These alternate embodiments allow portable testing device 400 to be used in ²remote areas where ²power is not available or where batteries are not available or affordable.²

[00194] FIG. 19A is a perspective view of portable testing device 400. FIG. ²19B is an ²exploded view of portable testing device 400, as seen in FIG. 19A. Portable ²testing device 400 ²includes housing 402, sample preparation area 406, optical lid 408, opening ²410, cradle 416, ²optical assembly 418, power assembly 460, and power switch 468. Housing 402 ²includes first ²housing portion 412 and second housing portion 414.²32²<DP=35>²CA 02926253 2016-04-01²WO 2015 / 054245 PCT / US2014 / 059487²

[00195] First ²housing portion 412 forms a base for portable testing device 400, and²second housing portion 414 is positioned on top of first housing portion 412. ²First housing ²portion 412 and second housing portion 414 are held together with fasteners in ²the embodiment ²shown, but can be held together with any suitable means in alternate ²embodiments.²

[00196] ²Housing 402 contains optical assembly 418 and power assembly 460. Optical²assembly 418 tests biological samples that are placed in portable testing ²device 400. Power ²assembly 460 powers portable testing device and is capable of powering a ²tablet computer that ²can be positioned on portable testing device 400. Power switch 468 extends ²between power ²assembly 460 and an outside of housing 402. Power switch 468 allows a user to ²easily turn ²portable testing device 400 on and off. Cradle 416 is a groove that extends ²from a first side to a ²second side of portable testing device 400 on a top side of housing 402. A ²tablet computer can ²be placed in cradle 416 when to set up the assay protocol, receive data from ²portable testing ²device 400, and display the results of the test in real-time.²

[00197] ²Sample preparation area 406 is on a top side of housing 402. Sample ²preparation²area 406 is used to prepare a biological sample for testing. Opening 410 is on ²a top side of ²housing 402. Opening 410 is positioned over optical assembly 418 so that an ²array of tubes ²containing a biological sample can be placed through opening 410 and into ²optical assembly 418 ²for testing. Optical lid 408 is positioned over opening 410 and is connected ²to housing 402 along ²a hinge. Optical lid 408 can be opened so that biological samples can be ²placed in opening 410 ²and then closed during testing.²

[00198] FIG. ²20A is a perspective view of sample preparation area 406 on portable testing²device 400. FIG. 20B is a perspective view of film cover 476 over sample ²preparation area 406 ²on portable testing device 400. FIG. 20C is a perspective view of sample ²preparation area 406 ²seen in FIG. 20A, when sample anays are positioned in sample preparation area ²406. FIG. 20D ²is a perspective view of sample preparation area 406 seen in FIG. 20A when a ²sample array has ²been positioned in portable testing device 400. Portable testing device 400 ²includes sample ²preparation area 406, optical lid 408, opening 410, and heating component 422. ²Sample ²preparation area 406 includes tube receptacle 470, first plurality of tube ²receptacles 472, and ²second plurality of tube receptacles 474. Also shown in FIG. 20B is film cover ²476.²

[00199] ²Sample preparation area 406 includes tube receptacle 470 located on a first ²side of²sample preparation area 406, first plurality of tube receptacles 472 located ²in a row on a front²33²<DP=36>²CA 02926253 2016-04-01²WO 2015 / 054245 PCT / US2014 / 059487²side of sample preparation area 406, and second plurality of tube receptacles ²474 located in a ²row on a back side of sample preparation area 406. In the embodiment seen in ²FIGS. 20A-20D, ²a single tube containing a biological sample can be placed in tube receptacle ²470, an array of ²tubes containing a reaction buffer can be placed in first plurality of tube ²receptacles 472, and an ²array of tubes containing a master mix can be placed in second plurality of ²tube receptacles 474. ²In alternate embodiments, sample preparation area 406 can include a plurality ²of tube receptacles ²170 to contain a plurality of biological samples. In further alternate ²embodiments, sample ²preparation area 406 can include one or more heating components positioned in ²tube receptacle ²470, first plurality of tube receptacles 472, or second plurality of tube ²receptacles 474. Placing ²heating components in sample preparation area 406 allows the biological ²sample, reaction buffer, ²and / or master mix to be heated during preparation of the biological sample. ²Heating the ²biological sample, reaction buffer, and / or master mix while preparing the ²biological sample will ²help to lyse the biological sample collected in the field to prepare the ²biological sample for ²testing. In alternate embodiments, sample preparation area 406 can be provided ²separate from ²portable testing device 400 and can include additional receptacles and heating ²components.²

[00200] As seen in FIG. 20B, film cover 476 can be positioned over sample ²preparation ²area 406. Film cover 476 is a preformed film structure with a flat portion ²that can be placed ²against the top surface of sample preparation area 406 and a plurality of ²sleeves that can be ²positioned in each of tube receptacle 470, first plurality of tube receptacles ²472, and second ²plurality of tube receptacles 474. Film cover 476 can be placed on sample ²preparation area 406 ²before each test and removed from sample preparation area 406 after each test ²to prevent ²contamination between tests. In an alternate embodiment, film cover 476 can be ²made of a high-²temperature film and extended to cover heating component 422.²

[00201] As seen in FIG. 20C, the biological sample can be prepared for ²testing on sample ²preparation area 406 by distributing the biological sample from the single ²tube in tube receptacle ²470 into the array of tube containing the reaction buffer in first plurality ²of tube receptacles 472. ²The mixture of the reaction buffer and biological sample can then be ²transferred from the array ²of tubes in first plurality of tube receptacles 472 into the array of tubes in ²second plurality of tube ²receptacles 474. This will mix the biological sample and reaction buffer with ²the master mix ²containing the necessary reagents to carry out a desired assay, including ²fluorescent dyes or²34²<DP=37>²CA 02926253 2016-04-01²WO 2015 / 054245 PCT / US2014 / 059487²markers, such as ROX or FAM. In alternate embodiments, the steps for preparing ²the sample ²can vary and different solutions can be used.²

[00202] When the biological sample is prepared for testing, optical lid 408 ²can be opened ²to reveal opening 410 and heating component 422. The array of tubes in second ²plurality of tube ²receptacles 474 can then be placed through opening 410 in the apertures in ²heating component ²422, as seen in FIG. 20D. This will position the array of tubes for testing ²with the optical system ²in portable testing device 400.²

[00203] Preparing biological samples on sample preparation area 406 is ²advantageous, as ²it allows a user to collect a sample, prepare the sample, and test the sample ²all in one hand-held ²device. This allows a user to easily prepare and test the sample in the field, ²without having to ²take the sample back to a laboratory to prepare it. It also allows a user to ²avoid having to carry ²multiple devices along when the user is testing biological samples in the ²field, because a separate ²sample preparation device is not needed.²

[00204] FIG. 21 is a flowchart showing steps for operating portable testing ²device 400. ²The flowchart includes steps 500-522. The process begins with step 500, sample ²preparation. ²Once a user acquires a sample from the field, it can be inserted into tube ²receptacle 470 in ²sample preparation area 406 of portable testing device 400. The field sample ²may be heated in ²sample preparation area 406 to aid in the release of a biological sample from ²the field sample. In ²step 502, portable testing device 400 is turned on using power switch 468. In ²step 504, the user ²then inputs a required assay and sample traceability information in the test ²setup menu on tablet ²computer 404, which sits in cradle 416 of housing 402 of portable testing ²device 400. In step ²506, the user then selects and begins the test protocol for the desired assay. ²When the test ²protocol is initiated, heating component 422 begins to heat to the required ²temperature for the ²desired assay.²

[00205] While heating component 422 is heating up, in step 508, in an array ²of tubes in ²first plurality of tube receptacles 472, the user mixes the biological sample ²from tube receptacle ²470 with reaction buffer necessary for the desired assay. In step 510, the ²user transfers the ²sample and reaction buffer mixture from the array of tubes in first plurality ²of tube receptacles ²472 to a conesponding array of tubes in second plurality of tube receptacles ²474. The array of ²tubes in second plurality of tube receptacles 474 contains a master mix ²required for the desired ²assay, including fluorescent dyes or markers such as FAM or ROX, necessary for ²detecting the²<DP=38>²CA 02926253 2016-04-01²WO 2015 / 054245 PCT / US2014 / 059487²desired analyte in portable testing device 400. The master mix can be liquid ²or lyolphilized. The ²user mixes the sample and buffer mixture with the master mix in the array of ²tubes in the second ²plurality of tube receptacles 474. In step 512, the user interface on tablet ²computer 404 will ²visually and audibly notify the user that portable testing device 400 is ready ²for testing. The user ²then seals the array of tubes in second plurality of tube receptacles 474, ²opens lid 108 and ²transfers the array of tubes through opening 410 into the plurality of ²apertures in heating ²component 422.²

[00206] In step 514, the user begins the excitation and detection sequence ²for the desired ²assay on tablet computer 404. Optical system 118 begins the excitation and ²detection sequence. ²During the excitation and detection sequence, portable testing device 400 ²transmits emission data ²to tablet computer 404. Step 516 includes displaying the real time reaction ²data received from ²portable testing device 400 on the user interface on tablet computer 404. ²During step 518, tablet ²computer 404 logs the data received from portable testing device 400 and ²monitors the data for ²threshold activity. Once the assay is complete, during step 520, tablet ²computer 404 signals a ²positive or negative outcome to the user. Finally, during step 522, tablet ²computer 404 may store ²the data obtained for retrieval or transfer.²

[00207] In general, the present invention relates to a portable testing ²device for analyzing ²biological samples. The portable testing device can be taken into the field to ²test biological ²samples as they are collected. This is advantageous over prior art systems, as ²it allows a user to ²test biological samples as the user is collecting them. This can prevent ²problems with ²contamination and degradation of biological samples due to transportation to a ²laboratory for ²testing, later discovery that not enough sample was taken, or later discovery ²that the collected ²biological sample is otherwise unsuitable for use. Allowing a user to test the ²biological sample ²in the field can save time, money, and resources. Testing in the field also ²provides the ability for ²rapid safety response if test results indicate a pathogen or toxin that may be ²harmful.²

[00208] In the embodiment described below, the portable testing device is ²capable of ²testing biological samples with EnviroLogix's DNAble0 chemistry, which employs ²an ²isothermal amplification process. This eliminates the need for thermocycling ²as a means to ²amplify nucleic acid products for endpoint detection. This allows a user to ²obtain data from the ²sample while the test is being run. In alternate embodiments, the portable ²testing device can be ²used to test biological samples with other isothermal amplification ²chemistries. The portable²36²<DP=39>²CA 02926253 2016-04-01²WO 2015 / 054245 PCT / US2014 / 059487²testing device displays this data on a screen on the device so that a user can ²view the results of ²the test in the field. Allowing a user to view the results of the test in the ²field is advantageous, as ²the user can then make an informed decision of whether additional tests are ²needed. In alternate ²embodiments, the portable testing device is also capable of incorporating a ²thermocycler to allow ²for the use of non-isothermal polymerase chain reaction (PCR) chemistries and ²result in qPCR ²and end-point analysis.²OPTICAL ASSEMBLY 600²

[01209] FIG. 22A is a perspective view of optical assembly 600. FIG. 22B is ²a top view ²of optical assembly 600. Optical assembly 600 includes tube array 602, sample ²block 604, ²movable housing 606, and stationary housing 608. Sample block 604 includes ²wells 620. ²Movable housing 606 includes body portion 610, detection portion 612, and ²excitation portion ²614.²

[00210] Sample block 604, movable housing 606. and stationary housing 608 ²form the ²body of optical assembly 600. Optical assembly 600 is also capable of ²receiving tube array 602 ²in sample block 604. Sample block 604 has a plurality of wells 620 located in ²a top side of ²sample block 604 that are configured to receive tube array 602 in the ²embodiment shown. In ²alternate embodiments, wells 620 can be configured to receive a card or any ²other suitable ²sample holder. Sample block 604 contains a heating component to heat the ²biological material in ²tube array 602.²

[00211] Movable housing 606 includes body portion 610, detection portion ²612, and ²excitation portion 614. Body portion 610 has a rectangular body shape. Sample ²block 604 is ²positioned on a first side of body portion 610. A first side of detection ²portion 612 is attached to ²a second side of body portion 610. Stationary housing 608 is positioned on a ²second side of ²detection portion 612. Detection portion 612 is capable of holding emission ²filters. Stationary ²housing 608 is capable of holding photodetectors to detect emissions from the ²biological sample ²in optical assembly 600. Excitation portion 614 is attached to the first side ²of body portion 206 ²below sample block 604. Excitation portion 614 is capable of holding light-²emitting diodes and ²excitation filters to excite the biological samples in optical assembly 600. ²Body portion 610, ²detection portion 612, stationary housing 608, and excitation portion 614 all ²have a plurality of ²paths running through them so radiation can travel through movable housing 606 ²and into the ²biological samples in sample block 604.²37²<DP=40>²CA 02926253 2016-04-01²WO 2015 / 054245 PCT / US2014 / 059487²

[00212] Movable housing 606 includes a plurality of detection modules that ²can excite and ²detect biological materials at different radiation wavelengths. This allows ²optical assembly 600 ²to be compatible with a number of different fluorescent dyes that are used ²during testing of ²biological samples. Each fluorescent dye is excited and detected at a ²different radiation ²wavelength. In order to ensure that each well 620 in sample block 604 is read ²with each ²detection module, movable housing 606 is capable of moving. Movable housing ²606 will move ²between a first position, a second position, and a third position in the ²embodiment shown, but ²can move between any number of positions in alternate embodiments. Sample ²block 604 and ²stationary housing 608 are stationary parts and movable housing 606 will slide ²between sample ²block 604 and stationary housing 608. As movable housing 606 moves, different ²detection ²modules will be aligned with different wells 620. This will allow each well ²620 to be read with ²different detection modules. Movable housing 606 can be moved with an actuator ²or other ²suitable means.²

[00213] Providing movable housing 606 in optical assembly 600 is ²advantageous, as the ²ability of movable housing 606 to move allows optical assembly 600 to test a ²plurality of ²radiation wavelengths. Optical assembly 600 is designed to be used in a ²portable testing device. ²A portable testing device need to be designed as compact as possible, so that ²it can be easily ²transported and used in the field. Without a moving optical assembly 600, more ²space would be ²required for placement of multiple detection modules that can read at ²different radiation ²wavelengths. Because movable housing 606 moves in optical assembly 600, the ²different ²detection modules can be easily repositioned to read from each of wells 620 in ²sample block 604. ²This saves significant space in the portable testing device, as the number of ²detection modules ²needed to test each of wells 620 is greatly reduced.²

[00214] FIG. 23 is a cross-sectional side view of optical assembly 600 ²taken along line 23-²23 of FIG. 22B. Optical assembly 600 includes tube array 602, sample block ²604, movable ²housing 606, stationary housing 608, and detection modules 616. Sample block ²604 includes ²wells 620, apertures 622, and lenses 624. Movable housing 606 includes body ²portion 610, ²detection portion 612, and excitation portion 614. Each detection module 616 ²includes light-²emitting diode 632, first path 634, second path 636, emission filter 638, and ²excitation filter 640. ²Stationary housing 608 includes photodetector 630.²38²<DP=41>²CA 02926253 2016-04-01²WO 2015 / 054245 PCT / US2014 / 059487²

[00215] Sample block 604 and movable housing 606 form the body of optical ²assembly ²600. Sample block 604 includes a plurality of wells 620 that are configured to ²receive tube array ²602. Tube array 602 includes a plurality of tubes, where each tube contains a ²biological sample ²that is to be tested. Sample block 604 further includes a plurality of ²apertures 622 that extend ²from a first side of sample block 604 to wells 620. Each well 620 will have a ²corresponding ²aperture 622. Lenses 624 can also be positioned in apertures 622 between the ²first side of ²sample block 604 and wells 620. Lenses 624 can direct radiation in optical ²assembly 600 into ²wells 620 and sample tubes 202.²

[00216] Movable housing 606 is capable of moving and can be situated in ²three different ²positions relative to sample block 604. Movable housing 606 includes a ²plurality of detection ²modules 616 that are aligned with wells 620 in sample block 604. Each ²detection module 616 is ²capable of exciting and detecting emissions from a biological sample in one of ²wells 620. Each ²detection module 616 includes one light-emitting diode 632, one first path ²634. one second path ²636, one emission filter 638, and one excitation filter 640.²

[00217] Stationary housing 608 is positioned on a second side of movable ²housing 606. ²Stationary housing 608 includes photodetector 630. As movable housing 606 ²moves between ²three different positions, stationary housing 608 will remain stationary. This ²will align each of ²the different photodetector 630 in stationary housing 608 with a different ²detection module 616.²

[00218] Movable housing 606 includes body portion 610 that forms the base ²of movable ²housing 606. Detection portion 612 is attached to a first side of body portion ²610 of movable ²housing 606. and excitation portion 614 is attached to a second side of body ²portion 610 of ²movable housing 606. First path 634 extends horizontally through body portion ²610 of movable ²housing 606 from detection portion 612 to sample block 604. Second path 636 ²extends at an ²angle through body portion 610 of movable housing 606 from excitation portion ²614 to detection ²portion 612. First path 634 and second path 636 converge at detection portion ²612. First path ²634 and second path 636 are both capable of transmitting radiation through ²movable housing ²606. First path 634 and second path 636 are shown as threaded paths in the ²embodiment shown, ²but can be smooth paths in alternate embodiments. Threading first path 634 and ²second path 636 ²can prevent stray radiation from traveling through movable housing 606, as it ²will be reflected ²when it diverges from the main course.²39²<DP=42>²CA 02926253 2016-04-01²WO 2015 / 054245 PCT / US2014 / 059487²

[00219] Detection portion 612 of movable housing 606 has a plurality of ²apertures that are ²capable of receiving emission filters 638. Emission filters 638 are positioned ²in the apertures in ²detection portion 612 between a first side of detection portion 612 and a ²second side of detection ²portion 612.²

[00220] Stationary housing 608 has a plurality of apertures that are ²capable of receiving ²photodetector 630. Photodetector 630 are positioned on a second side of ²stationary housing 608 ²and extend a distance into stationary housing 608.²

[00221] Excitation portion 614 of movable housing 606 has a plurality of ²apertures that ²are capable of receiving light-emitting diodes 632 and excitation filters 640. ²Light-emitting ²diodes 632 are positioned on a first side of excitation portion 614 and extend ²a distance into ²excitation portion 614. Excitation filters 640 are positioned in excitation ²portion 614 between ²light-emitting diodes 632 and a second side of excitation portion 614.²

[00222] Each detection module 616 works as follows. To excite a biological ²sample ²positioned in well 620, radiation is emitted from light-emitting diode 632. ²The radiation that is ²emitted from light-emitting diode 632 will be filtered by excitation filter ²640. The filtered ²radiation will then travel from a first end to a second end of second path ²636. At the second end ²of second path 636, the radiation will be reflected off of emission filter ²638. The reflected ²radiation will be directed into a first end of first path 634. The radiation ²will then travel from the ²first end to a second end of first path 634. At the second end of first path ²634, the radiation will ²travel through aperture 622 and lens 624 in sample block 604 and into wells ²620. Once in wells ²620, the radiation can excite the biological sample in one of the tubes of ²tube array 602.²

[00223] After the biological sample is excited it will emit radiation ²corresponding with ²fluorescent labels that are mixed with the biological sample. The radiation ²emitted from the ²biological sample can then travel from well 620 through lens 624 and aperture ²622 into second ²end of first path 634. The radiation will then travel from second end to first ²end of first path 634. ²At the first end of first path 634, the radiation will reach and pass through ²emission filter 638. ²Radiation that is filtered through emission filter 638 can then travel through ²the aperture in ²detection portion 612 and into the aperture in stationary housing 608. ²Photodetector 630 ²positioned in stationary housing 608 can then receive the radiation.²

[00224] Different fluorescent dyes can be used to test biological samples ²during nucleic ²acid amplification. To provide an instrument that is capable of reading ²different fluorescent²<DP=43>²CA 02926253 2016-04-01²WO 2015 / 054245 PCT / US2014 / 059487²dyes, movable housing 606 can move in relation to sample block 604 so that a ²different detection ²module 616 is aligned with each well 620, depending on what fluorescent dyes ²have been added ²to the biological sample in each well 620. If multiple fluorescent dyes are ²added to the ²biological sample in each well 620, movable housing 606 can move between ²positions to ensure ²that the different fluorescence of each well 620 are being read.²

[00225] Optical assembly 600 is advantageous for use in a portable testing ²device, as ²optical assembly 600 can read fluorescence at a plurality of different ²radiation wavelengths with ²a compact design. A suitable portable testing device needs to be compact so ²that it can be easily ²transported and used in the field. To design a compact portable testing ²device, optical assembly ²600 also needs to be compact. In previous optical assemblies, being compact ²equated to only ²being able to test at one or two different radiation wavelengths. Optical ²assembly 600 eliminates ²this issue, as optical assembly 600 can move to position different detection ²modules 616 with ²different wells 620 in sample block 604. This allows more than two radiation ²wavelengths to be ²tested without sacrificing compactness of optical assembly 600. Optical ²assembly 600 is ²advantageous for this reason and is suitable for use in portable testing ²devices.²

[00226] FIG. 24A is a perspective view of optical assembly 600 in a first ²position. FIG. ²24B is a perspective view of optical assembly 600 in a second position. FIG. ²24C is a ²perspective view of optical assembly 600 in a third position. Optical assembly ²600 includes tube ²array 602, sample block 604, movable housing 606, stationary housing 608, and ²detection ²modules 616 (including detection module 616A, detection module 616B, detection ²module ²616C, detection module 616D, detection module 616E, detection module 616F, ²detection module ²616G, detection module 616H, detection module 6161, and detection module ²6161). Sample ²block 604 includes wells 620 (including well 620A, well 620B, well 620C, well ²620D, well ²620E, well 620F, well 620G, and well 620H). Stationary housing 608 includes ²photodetector ²630 (including photodetector 630A, photodetector 630B, photodetector 630C, ²photodetector ²630D, photodetector 630E, photodetector 630F, photodetector 630G, and ²photodetector 630H).²

[00227] Sample block 604, movable housing 606, and stationary housing 608 ²form the ²body of optical assembly 600. Sample block 604 is a stationary part with a ²plurality of wells ²620. Tube array 602 can be positioned in wells 620. Tube array 602 includes a ²plurality of ²individual tubes that each contain a biological sample and a reaction mixture ²with fluorescent ²dyes. Each tube in tube array 602 is positioned in one well 620. Stationary ²housing 608 is also a²41²<DP=44>²CA 02926253 2016-04-01²WO 2015 / 054245 PCT / US2014 / 059487²stationary part with a plurality of photodetector 630. One photodetector 630 ²in stationary ²housing 608 is aligned with one well 620 in sample block 604. Photodetector ²630A is aligned ²with well 620A; photodetector 630B is aligned with well 620B; photodetector ²630C is aligned ²with well 620C; photodetector 630D is aligned with well 620D; photodetector ²630E is aligned ²with well 620E; photodetector 630F is aligned with well 620F; photodetector ²630G is aligned ²with well 620G; and photodetector 630H is aligned with well 620H.²

[00228] In the embodiment shown, movable housing 606 is a moving part that ²can move ²between a first position, a second position, and a third position with respect ²to sample block 604 ²and stationary housing 608. In alternate embodiments, movable housing 606 can ²move between ²any number of positions. Movable housing 606 includes a plurality of detection ²modules 616. ²As movable housing 606 moves, each detection module 616 will be aligned with ²one well 620 ²and one photodetector 630. Each detection module 616 includes a light-emitting ²diode to excite ²a biological sample. To detect a plurality of different fluorescent dyes, the ²light-emitting diodes ²that are positioned in each detection module can vary. The embodiment shown in ²FIGS. 24A-²24C includes eight wells 620, eight photodetector 630, and ten detection ²modules 616. This ²allows three different fluorescent dyes to be tested, as movable housing 606 ²can be positioned in ²three different positions. In each different position, each well 620 and ²photodetector 630 will be ²aligned with a different detection module 616 to read different fluorescent ²dyes from each well ²620.²

[00229] In the embodiment shown in FIGS. 24A-24C, optical assembly 600 can ²detect a ²first fluorescent dye, a second fluorescent dye, and a third fluorescent dye. ²Detection module ²616A is configured to detect the first fluorescent dye; detection module 616B ²is configured to ²detect the second fluorescent dye; detection module 616C is configured to ²detect the third ²fluorescent dye; detection module 616D is configured to detect the first ²fluorescent dye; ²detection module 616E is configured to detect the second fluorescent dye; ²detection module ²616F is configured to detect the third fluorescent dye; detection module 616G ²is configured to ²detect the first fluorescent dye; detection module 616H is configured to ²detect the second ²fluorescent dye; detection module 6161 is configured to detect the third ²fluorescent dye; and ²detection module 616J is configured to detect the first fluorescent dye. As ²movable housing 606 ²moves between a first position, a second position, and a third position, each ²well 620 will be²42²<DP=45>²CA 02926253 2016-04-01²WO 2015 / 054245 PCT / US2014 / 059487²excited and detected for each of the first fluorescent dye, the second ²fluorescent dye, and the ²third fluorescent dye.²

[00230] In a first position, well 620A is aligned with detection module ²616A to detect the ²first fluorescent dye; well 620B is aligned with detection module 616B to ²detect the second ²fluorescent dye; well 620C is aligned with detection module 616C to detect the ²third fluorescent ²dye; well 620D is aligned with detection module 616D to detect the first ²fluorescent dye; well ²620E is aligned with detection module 616E to detect the second fluorescent ²dye; well 620F is ²aligned with detection module 616F to detect the third fluorescent dye; well ²620G is aligned with ²detection module 616G to detect the first fluorescent dye; and well 620H is ²aligned with ²detection module 616H to detect the second fluorescent dye.²

[00231] In a second position, well 620A is aligned with detection module ²616B to detect ²the second fluorescent dye; well 620B is aligned with detection module 616C to ²detect the third ²fluorescent dye; well 620C is aligned with detection module 616D to detect the ²first fluorescent ²dye; well 620D is aligned with detection module 616E to detect the second ²fluorescent dye; well²620E is aligned with detection module 616F to detect the third fluorescent ²dye; well 620F is ²aligned with detection module 616G to detect the first fluorescent dye; well ²620G is aligned with ²detection module 616H to detect the second fluorescent dye; and well 620H is ²aligned with ²detection module 6161 to detect the third fluorescent dye.²

[00232] In a third position, well 620A is aligned with detection module ²616C to detect the ²third fluorescent dye; well 620B is aligned with detection module 616D to ²detect the first ²fluorescent dye; well 620C is aligned with detection module 616E to detect the ²second ²fluorescent dye; well 620D is aligned with detection module 616F to detect the ²third fluorescent ²dye; well 620E is aligned with detection module 616G to detect the first ²fluorescent dye; well²620F is aligned with detection module 616H to detect the second fluorescent ²dye; well 620G is ²aligned with detection module 6161 to detect the third fluorescent dye; and ²well 620H is aligned ²with detection module 616J to detect the first fluorescent dye.²

[00233] As seen from this, as movable housing 606 moves between a first ²position, a ²second position, and a third position, each well 620 will be excited and ²detected for each of the ²first fluorescent dye, the second fluorescent dye, and the third fluorescent ²dye. Movable housing ²606 can be repositioned any number of times during a test to repeat excitation ²and detection of ²each of wells 620 until satisfactory test results are obtained. Further, in ²alternate embodiments,²43²<DP=46>²CA 02926253 2016-04-01²WO 2015 / 054245 PCT / US2014 / 059487²movable housing 606 can include more detection modules to read additional ²fluorescent dyes. ²This will increase the number of positions that movable housing 606 will move ²to so that each ²well 620 is excited and detected at each different fluorescence wavelength.²

[00234] Optical assembly 600 is advantageous, as it can excite and detect ²at a plurality of ²different radiation wavelengths with a compact and streamlined design. This ²makes optical ²assembly 600 suitable for use in a portable testing device, as the compactness ²of optical ²assembly 600 will reduce the overall size of a portable testing device. ²Further, optical assembly ²600 allows a portable testing device to test at a number of radiation ²wavelengths that was not ²feasible with previous designs.²OPTICAL ASSEMBLY 700²

[00235] FIG. 25 is a cross-sectional side view of optical assembly 700. ²Optical assembly ²700 includes tube array 702, sample block 704, first housing 706, second ²housing 708, well 710, ²first aperture 712, second aperture 714, first light-emitting diode 720, ²second light-emitting ²diode 722. third light-emitting diode 724, first excitation path 726, second ²excitation path 728, ²third excitation path 730, excitation filter 732, first photodetector 740, ²second photodetector 742, ²first detection path 744, second detection path 746, first emission filter ²748, second emission ²filter 750, first lens 752, and second lens 754.²

[00236] Sample block 704, first housing 706, and second housing 708 form ²the body of ²optical assembly 700. Sample block 704 includes a plurality of wells 710. ²Wells 710 are ²capable of receiving tube array 702. Sample block 704 also includes a heating ²component to ²heat a biological sample in tube array 702. Sample block 704 includes first ²apertures 712 that ²extend from a first side of sample block 704 into wells 710. Sample block 704 ²also includes ²second apertures 714 that extend from a second side of sample block 704 into ²wells 710. First ²housing 706 is located on a first side of sample block 704 and second housing ²708 is located on a ²second side of sample block 704.²

[00237] First housing 706 and second housing 708 are both capable of ²holding light-²emitting diodes and photodetectors to excite and detect emissions from the ²biological samples in ²tube array 702. In the embodiment shown in FIG. 8, light-emitting diodes are ²located in first ²housing 706 and photodetectors are located in second housing 708. In alternate ²embodiments, ²photodetectors can be located in first housing 706 and light-emitting diodes ²can be located in ²second housing 708, or a mix of light-emitting diodes and photodetectors can ²be alternated in²44²<DP=47>²CA 02926253 2016-04-01²WO 2015 / 054245 PCT / US2014 / 059487²both first housing 706 and second housing 708. In each arrangement, one light-²emitting diode is ²positioned on one side of well 710 and one photodetector is positioned on the ²opposite side of ²well 710.²

[00238] As seen in FIG. 25, first light-emitting diode 720, second light-²emitting diodes ²722, and third light-emitting diode 724 are positioned in first housing 706. ²First light-emitting ²diode 720, second light-emitting diodes 722, and third light-emitting diode ²724 are located in a ²triangular configuration. Each light-emitting diode is capable of exciting a ²different fluorescent ²dye in the biological sample by emitting radiation at a different wavelength. ²First light-emitting ²diode 720 excites a first fluorescent dye, second light-emitting diodes 722 ²excites a second ²fluorescent dye, and third light-emitting diode 724 excites a third ²fluorescent dye in the ²embodiment shown. First light-emitting diode 720 is positioned in first path ²726 that runs from ²first light-emitting diode 720 to sample block 704. Second light-emitting ²diodes 722 is ²positioned in second path 728 that runs from second light-emitting diodes 722 ²to sample block ²704. Third light-emitting diode 724 is positioned in third path 730 that runs ²from third-light ²emitting diode 724 to sample block 704. Excitation filter 732 is positioned in ²sample block 704 ²to filter light from first light-emitting diode 720, second light-emitting ²diodes 722, and third ²light-emitting diode 724. Excitation filter 732 is a triple bandpass filter ²that is capable of ²filtering radiation at wavelengths for the first fluorescent dye, the second ²fluorescent dye, and the ²third fluorescent dye. In alternate embodiments, separate excitation filters ²can be used for each ²light-emitting diode.²

[00239] First photodetector 740 and second photodetector 742 are positioned ²in second ²housing 708. First photodetector 740 is capable of detecting both the first ²fluorescent dye and ²the third fluorescent dye. Second photodetector 742 is capable of detection ²the second ²fluorescent dye. First photodetector 740 is positioned in first path 744 that ²extends from first ²photodetector 740 to sample block 704. Second photodetector 742 is positioned ²in second path ²346 that extends from second photodetector 742 to sample block 704. First ²emission filter 748 is ²positioned in first path 744 between first photodetector 740 and sample block ²704. First ²emission filter 748 is a dual bandpass filter that is capable of filtering ²radiation at wavelengths ²for the first fluorescent dye and the third fluorescent dye. Second emission ²filter 750 is ²positioned in second path 746 between second photodetector 742 and sample ²block 704. Second ²emission filter 750 is a single bandpass filter that is capable of filtering ²radiation at wavelengths²<DP=48>²CA 02926253 2016-04-01²WO 2015 / 054245 PCT / US2014 / 059487²for the second fluorescent dye. Also positioned in first path 744 is first ²lens 752. Also ²positioned in second path 746 is second lens 754. First lens 752 and second ²lens 754 will direct ²emitted radiation from the biological sample in tube 702 into first ²photodetector 740 and second ²photodetector 742, respectively.²

[01240] ²Optical assembly 700 is designed so that biological samples can be excited and²detected at three different radiation wavelengths. Detecting and exciting at ²three different ²radiation wavelengths is advantageous, as each biological sample can be tested ²for each of the ²first fluorescent dye, the second fluorescent dye, and the third fluorescent ²dye. Using first ²photodetectors 740 and second photodetectors 742 is also advantageous, as it ²will limit crosstalk ²between detection channels to improve detection performance. The design of ²optical assembly ²700 with clustering of light-emitting diodes and photodetectors is also ²advantageous, as it allows ²optical assembly 700 to be designed with a compact configuration. Being ²compact allows ²optical assembly 700 to be used in a portable testing device. Portable testing ²devices need to be ²compact so that they can be easily transported and used in the field.²

[00241] FIG. ²26A is a side view of a first side of optical assembly 700 according to a ²first²configuration. FIG. 26B is a side view of a second side of optical assembly ²700 according to the ²first configuration. Optical assembly 700 includes first housing 706, second ²housing 708, first ²light-emitting diodes 720 (including first light-emitting diode 720A, first ²light-emitting diode ²720B, first light-emitting diode 720C, first light-emitting diode 720D, first ²light-emitting diode ²720E, first light-emitting diode 720F, first light-emitting diode 720G, and ²first light-emitting ²diode 720H), second light-emitting diodes 722 (including second light-emitting ²diodes 722A, ²second light-emitting diodes 722B, second light-emitting diodes 722C, second ²light-emitting ²diodes 722D, second light-emitting diodes 722E, second light-emitting diodes ²722F, second ²light-emitting diodes 722G, and second light-emitting diodes 722H), third ²light-emitting diodes ²724 (including third light-emitting diode 724A, third light-emitting diode ²724B, third light-²emitting diode 724C, third light-emitting diode 724D, third light-emitting ²diode 724E, third ²light-emitting diode 724F, third light-emitting diode 724G, and third light-²emitting diode 724H), ²first photodetectors 740 (including first photodetector 740A, first ²photodetector 740B, first ²photodetector 740C, first photodetector 740D, first photodetector 740E, first ²photodetector 740F, ²first photodetector 740G, and first photodetector 740H), and second ²photodetectors 742 ²(including second photodetector 742A, second photodetector 742B, second ²photodetector 742C,²46²<DP=49>²CA 02926253 2016-04-01²WO 2015 / 054245 PCT / US2014 / 059487²second photodetector 742D, second photodetector 742E, second photodetector ²742F, second ²photodetector 742G, and second photodetector 742H).²

[00242] First light-emitting diodes 720, second light-emitting diodes 722, ²and third light-²emitting diodes 724 are positioned in first housing 706. First light-emitting ²diodes 720 are ²capable of exciting a first fluorescent dye. Second light-emitting diodes 722 ²are capable of ²exciting a second fluorescent dye. Third light-emitting diodes 724 are capable ²of exciting a third ²fluorescent dye. First light-emitting diodes 720, second light-emitting diodes ²722, and third ²light-emitting diodes 724 are arranged in a triangular configuration in first ²housing 706. As an ²exemplary explanation, this configuration can be seen with first light-²emitting diode 720A, ²second light-emitting diodes 722A, and third light-emitting diode 724A which ²are arranged in a ²triangular configuration. This triangular configuration is repeated in an ²alternating fashion ²throughout first housing 706 to provide a compact configuration.²

[00243] First photodetectors 740 and second photodetectors 742 are ²positioned in second ²housing 708. First photodetectors 740 are capable of detecting emissions from ²the first ²fluorescent dye and the third fluorescent dye. Second photodetectors 742 are ²capable of ²detecting emissions from the second fluorescent dye. First photodetectors 740 ²and second ²photodetectors 742 are stacked one on top of the other in second housing 708. ²As an exemplary ²explanation, this configuration can be seen with first photodetector 740A and ²second ²photodetector 742A which are stacked one on top of the other. This stacked ²configuration is ²repeated throughout second housing 708.²

[00244] In the configuration seen in FIGS. 26A-26B, light-emitting diodes ²are positioned ²in first housing 706 on a first side of a sample block and photodetectors are ²positioned in second ²housing 708 on a second side of a sample block. First light-emitting diodes ²720 and third light-²emitting diodes 724 are located opposite of first photodetectors 740. Second ²light-emitting ²diodes 722 are located opposite of second photodetectors 742. When first light-²emitting diodes ²720 or third light-emitting diodes 724 are activated, first photodetectors 740 ²will read emissions ²from the biological sample. When second light-emitting diodes 722 are ²activated, second ²photodetectors 742 will read emissions from the biological sample.²

[00245] The first configuration of light-emitting diodes and photodetectors ²seen in FIGS. ²26A-26B is advantageous, as it provides a compact arrangement that is capable ²of exciting and²47²<DP=50>²CA 02926253 2016-04-01²WO 2015 / 054245 PCT / US2014 / 059487²detecting at three different radiation wavelengths. This makes optical ²assembly 700 suitable for ²use in a portable testing device.²

[00246] FIG. 27A is a side view of a first side of optical assembly 700 ²according to a ²second configuration. FIG. 27B is a side view of a second side of optical ²assembly 700 ²according to a second configuration. Optical assembly 700 includes first ²housing 706, second ²housing 708, first light-emitting diodes 720 (including first light-emitting ²diode 720A, first light-²emitting diode 720B, first light-emitting diode 720C, first light-emitting ²diode 720D, first light-²emitting diode 720E, first light-emitting diode 720F, first light-emitting ²diode 720G, and first ²light-emitting diode 720H), second light-emitting diodes 722 (including second ²light-emitting ²diodes 722A, second light-emitting diodes 722B, second light-emitting diodes ²722C, second ²light-emitting diodes 722D, second light-emitting diodes 722E, second light-²emitting diodes ²722F, second light-emitting diodes 722G, and second light-emitting diodes ²722H), third light-²emitting diodes 724 (including third light-emitting diode 724A, third light-²emitting diode 724B, ²third light-emitting diode 724C, third light-emitting diode 724D, third light-²emitting diode 724E, ²third light-emitting diode 724F, third light-emitting diode 724G, and third ²light-emitting diode ²724H), first photodetectors 740 (including first photodetector 740A, first ²photodetector 740B, ²first photodetector 740C, first photodetector 740D, first photodetector 740E, ²first photodetector ²740F, first photodetector 740G, and first photodetector 740H), and second ²photodetectors 742 ²(including second photodetector 742A, second photodetector 742B, second ²photodetector 742C, ²second photodetector 742D, second photodetector 742E, second photodetector ²742F, second ²photodetector 742G, and second photodetector 742H).²

[00247] First light-emitting diodes 720, second light-emitting diodes 722, ²third light-²emitting diodes 724, first photodetectors 740, and second photodetectors 742 ²are positioned in ²alternating patterns in first housing 706 and second housing 708. First light-²emitting diodes 720 ²are capable of exciting a first fluorescent dye. Second light-emitting diodes ²722 are capable of ²exciting a second fluorescent dye. Third light-emitting diodes 724 are capable ²of exciting a third ²fluorescent dye. First photodetectors 740 are capable of detecting emissions ²from the first ²fluorescent dye and the third fluorescent dye. Second photodetectors 742 are ²capable of ²detecting emissions from the second fluorescent dye.²

[00248] First light-emitting diodes 720, second light-emitting diodes 722, ²and third light-²emitting diodes 724 are arranged in a triangular configuration in both first ²housing 706 and²48²<DP=51>²CA 02926253 2016-04-01²WO 2015 / 054245 PCT / US2014 / 059487²second housing 708. As an exemplary explanation, this configuration can be ²seen with first ²light-emitting diode 720A, second light-emitting diodes 722A, and third light-²emitting diode ²724A which are arranged in a triangular configuration. First photodetectors ²740 and second ²photodetectors 742 are arranged in a diagonal configuration in both first ²housing 706 and second ²housing 708. As an exemplary explanation, this configuration can be seen with ²first ²photodetector 740B and second photodetector 742B which are arranged in a ²diagonal ²configuration. The triangular configuration of the light-emitting diodes is ²alternated with the ²diagonal configuration of the photodetectors throughout both first housing 706 ²and second ²housing 708.²

[00249] In the configuration seen in FIGS. 27A-27B, first light-emitting ²diodes 720 and ²third light-emitting diodes 724 are located opposite of first photodetectors ²740. Second light-²emitting diodes 722 are located opposite of second photodetectors 742. When ²first light-emitting ²diodes 720 or third light-emitting diodes 724 are activated, first ²photodetectors 740 will read ²emissions from the biological sample. When second light-emitting diodes 722 ²are activated, ²second photodetectors 742 will read emission from the biological sample.²

[00250] The second configuration of light-emitting diodes and ²photodetectors seen in ²FIGS. 27A-27B is advantageous, as it provides a compact arrangement that is ²capable of exciting ²and detecting at three different radiation wavelengths. This makes optical ²assembly 700 suitable ²for use in a portable testing device.²OPTICAL ASSEMBLY 800²

[00251] FIG. 28A is a perspective view of optical assembly 800. FIG. 28B is ²a bottom ²view of optical assembly 800.²

[00252] Optical assembly 800 includes first housing portion 802, second ²housing portion ²804, first optical housing 806, second optical housing 808, heat block 810, ²and plate 820. Heat ²block 810 includes wells 812. Plate 820 includes apertures 822.²

[00253] Optical assembly 800 is capable of receiving an array of tubes for ²testing. Heat ²block 810 receives the array of tubes in wells 812. Wells 812 are positioned ²on a top side of heat ²block 810 and each well 812 is configured to receive one tube in the array of ²tubes. Heat block ²810 forms a base of optical assembly 800 and heats a biological sample that is ²placed in each of ²the tubes in the array of tubes. In alternate embodiments, heat block 810 can ²be a sample block ²that is capable of receiving an array of tubes and the tubes can be heated ²using a different means.²49²<DP=52>²CA 02926253 2016-04-01²WO 2015 / 054245 PCT / US2014 / 059487²

[00254] Plate 820 is also included in optical assembly 800 and is placed ²over the top side ²of heat block 810. Plate 820 includes a plurality of apertures 822 that run ²from a top side of ²plate 820 to a bottom side of plate 820. Each aperture 822 in plate 820 can be ²aligned with one ²well 812 in heat block 810. When an array of tubes is placed in heat block ²810, one tube can ²pass through each aperture 822 of plate 820 before being positioned in well ²812. Plate 820 is ²made out of an opaque material in the embodiment shown. This prevents ²radiation from ²escaping out of optical assembly 800 and prevents ambient light from entering ²into optical ²assembly 800. Plate 820 also acts as an insulator to keep heat from heat block ²810 in optical ²assembly 800.²

[00255] A housing portion is also positioned on each side of heat block ²810. First housing ²portion 802 is positioned on a first side of heat block 810 and second housing ²portion 804 is ²positioned on a second side of heat block 810. First housing portion 802 and ²second housing ²portion 804 join one another around heat block 810. First housing portion 802 ²and second ²housing portion 804 can be connected to one another with any suitable means.²

[00256] Optical assembly 800 also includes first optical housing 806 and ²second optical ²housing 808. First optical housing 806 is connected to first housing portion ²802 on the first side ²of heat block 810. First optical housing 806 can be connected to first housing ²portion 802 with ²any suitable means. First optical housing 806 is capable of holding a first ²set of light-emitting ²diodes and a first set of photodetectors. Second optical housing 808 is ²connected to second ²housing portion 804 on the second side of heat block 810. Second optical ²housing 808 can be ²connected to second housing portion 804 with any suitable means. Second ²optical housing 808 ²is capable of holding a second set of light-emitting diodes and a second set ²of photodetectors.²

[00257] First housing portion 802, second housing portion 804, first ²optical housing 806, ²and second optical housing 808 are formed out of opaque materials. This allows ²radiation that is ²passed through optical assembly 800 to be retained in passages that runs ²through first housing ²portion 802, second housing portion 804, first optical housing 806, and second ²optical housing ²808. Further, in alternate embodiments optical assembly 800 can include one ²housing portion on ²each side of heat block 810, can include one single housing piece, or any ²other suitable ²configuration.²

[00258] Optical assembly 800 is advantageous, as it has a compact design ²that allows a set ²of light-emitting diodes and a set of photodetectors to be positioned on both ²sides of heat block²<DP=53>²CA 02926253 2016-04-01²WO 2015 / 054245 PCT / US2014 / 059487²810. This allows more light-emitting diodes to be placed in each set of light-²emitting diodes, ²increasing the overall capabilities of optical assembly 800. Light-emitting ²diodes can excite a ²biological sample at different radiation wavelengths. Thus, allowing more ²light-emitting diodes ²to be positioned in optical assembly 800 is advantageous, as optical assembly ²will be able to ²excite and detect emissions that correspond with different fluorescent dyes.²

[00259] FIG. 29A is an exploded perspective view of a first side of optical ²assembly 800. ²FIG. 29B is an exploded perspective view of the first side of optical assembly ²800. FIG. 29C is ²an exploded perspective view of a second side of optical assembly 800. FIG. ²29D is an exploded ²side view of the second side of optical assembly 800.²

[00260] Optical assembly 800 includes first housing portion 802, second ²housing portion ²804, first optical housing 806, second optical housing 808, heat block 810, ²plate 820, first light-²emitting diode set 830, second light-emitting diode set 832, first ²photodetector set 834, second ²photodetector set 836, excitation filters 852, excitation filters 862, ²emission filter 872, and ²emission filter 882. Heat block 810 includes wells 812, passages 856, passages ²866, passages ²876, and passages 886. Plate 820 includes apertures 822. First housing portion ²802 includes ²passages 854 and passages 874. Second housing portion 804 includes passages ²864 and passages ²884. First optical housing 806 includes passages 850 and passages 870. Second ²optical housing ²808 includes passages 860 and passages 880. First light-emitting diode set 830 ²includes light-²emitting diodes 840, light-emitting diodes 842, and light-emitting diodes 844. ²Second light-²emitting diode set 832 includes light-emitting diodes 840, light-emitting ²diodes 842, and light-²emitting diodes 844. First photodetector set 834 includes photodetectors 846. ²Second ²photodetector set 836 includes photodetectors 846.²

[00261] Optical assembly 800 is capable of receiving an array of tubes for ²testing. Heat ²block 810 receives the array of tubes in wells 812. Wells 812 are positioned ²on a top side of heat ²block 810 and each well 812 is configured to receive one tube in the array of ²tubes. Heat block ²810 forms a base of optical assembly 800 and heats a biological sample that is ²placed in each of ²the tubes in the array of tubes. Heat block 810 further includes passages 856, ²passages 866, ²passages 876, and passages 886. Passages 856 and passages 876 extend from a ²first side of heat ²block 810 to wells 812. Passages 866 and passages 886 extend from a second ²side of heat block ²810 to wells 812. Passages 856, passages 866, passages 876, and passages 886 ²provide pathways ²through which radiation can travel through optical assembly 800.²51²<DP=54>²CA 02926253 2016-04-01²WO 2015 / 054245 PCT / US2014 / 059487²

[00262] Plate 820 is also included in optical assembly 800 and is placed ²over the top side ²of heat block 810. Plate 820 includes a plurality of apertures 822 that run ²from a top side of ²plate 820 to a bottom side of plate 820. Each aperture 822 in plate 820 can be ²aligned with one ²well 812 in heat block 810. When an array of tubes is placed in heat block ²810, one tube can ²pass through each aperture 822 of plate 820 before being positioned in well ²812.²

[00263] A housing portion is also positioned on each side of heat block ²810. First housing ²portion 802 is positioned on a first side of heat block 810 and second housing ²portion 804 is ²positioned on a second side of heat block 810. First housing portion 802 ²includes passages 854 ²and passages 874 that extend from a first side of first housing portion 802 to ²a second side of ²first housing portion 802. Second housing portion 804 includes passages 864 ²and passages 884 ²that extend from a first side of second housing portion 804 to a second side ²of second housing ²portion 804. Passages 854, passages 864, passages 874, and passages 884 ²provide pathways ²through which radiation can travel through optical assembly 800.²

[00264] Optical assembly 800 further includes first optical housing 806 and ²second optical ²housing 808. First optical housing 806 is connected to first housing portion ²802 on the first side ²of heat block 810. First optical housing 806 can be connected to first housing ²portion 802 with ²any suitable means. First optical housing 806 includes passages 850 and ²passages 870 that ²extend from a first side of first optical housing 806 to a second side of ²first optical housing 806. ²Second optical housing 808 is connected to second housing portion 804 on the ²second side of ²heat block 810. Second optical housing 808 can be connected to second housing ²portion 804 ²with any suitable means. Second optical housing 808 includes passages 860 and ²passages 880 ²that extend from a first side of second optical housing 808 to a second side ²of second optical ²housing 808. Passages 850, passages 860, passages 870, and passages 880 ²provide pathways ²through which radiation can travel through optical assembly 800.²

[00265] Excitation filters 852 are positioned between first optical housing ²806 and first ²housing portion 802. Excitation filters 852 are aligned with passages 850 in ²first optical housing ²806 and passages 854 in first housing portion 802. Excitation filters 862 are ²positioned between ²second optical housing 808 and second housing portion 804. Excitation filters ²862 are aligned ²with passages 860 in second optical housing 808 and passages 864 in second ²housing portion ²804. In the embodiment shown, excitation filters 852 and excitation filters ²862 are shown as a ²plurality of filters but it could be one filter in alternate embodiments.²52²<DP=55>²CA 02926253 2016-04-01²WO 2015 / 054245 PCT / US2014 / 059487²

[00266] Emission filter 872 is positioned between first optical housing 806 ²and first ²housing portion 802. Emission filter 872 is aligned with passages 870 in first ²optical housing ²806 and passages 874 in first housing portion 802. Emission filter 882 is ²positioned between ²second optical housing 808 and second housing portion 804. Emission filter 882 ²is aligned with ²passages 880 in second optical housing 808 and passage 884 in second housing ²portion 804. In ²the embodiment shown, emission filter 872 and emission filter 882 are each ²shown as one filter, ²but they could be a plurality of filters in alternate embodiments.²

[00267] First light-emitting diode set 830 and first photodetector set 834 ²are positioned in ²first optical housing 806. Each light-emitting diode in first set 830 is ²positioned in one passage ²850 in first optical housing 806. Each photodetector in first set 834 is ²positioned in one passage ²870 in first optical housing 806. First light-emitting diode set 830 includes ²four clusters of three ²different light-emitting diodes, including light-emitting diode 840, light-²emitting diode 842, and ²light-emitting diode 844. Each of light-emitting diode 840, light-emitting ²diode 842, and light-²emitting diode 844 excites a biological sample at a different fluorescent ²wavelength. In the ²embodiment shown, light-emitting diode 840 can excite a first fluorescent dye, ²light-emitting ²diode 842 can excite a second fluorescent dye, and light-emitting diode 844 ²can excite a third ²fluorescent dye. First photodetector set 834 includes eight photodetectors ²846. In the ²embodiment shown, each photodetector 846 detects radiation of two different ²wavelength band, ²here detecting the first fluorescent dye and the third fluorescent dye.²

[00268] Second light-emitting diode set 832 and second photodetector set ²836 are ²positioned in second optical housing 808. Each light-emitting diode in second ²set 832 is ²positioned in one passage 860 in second optical housing 808. Each ²photodetector in second set ²836 is positioned in one passage 880 in second optical housing 808. Second ²light-emitting diode ²set 832 includes four clusters of three different light-emitting diodes, ²including light-emitting ²diode 840, light-emitting diode 842, and light-emitting diode 844. Each of ²light-emitting diode ²840, light-emitting diode 842, and light-emitting diode 844 excites a ²biological sample at a ²different fluorescent wavelength. In the embodiment shown, light-emitting ²diode 840 can excite ²the first fluorescent dye, light-emitting diode 842 can excite the second ²fluorescent dye, and ²light-emitting diode 844 can excite the third fluorescent dye. Second ²photodetector set 836 ²includes eight photodetectors 846. In the embodiment shown, each photodetector ²846 detects ²radiation of one wavelength band, here detecting the second fluorescent dye.²53²<DP=56>²CA 02926253 2016-04-01²WO 2015 / 054245 PCT / US2014 / 059487²

[00269] Multiple excitation passages extend through optical assembly 800 on ²both sides ²so that radiation can travel from first plurality of light-emitting diodes 830 ²and second plurality ²of light-emitting diodes 832 to heat block 810. A first plurality of ²excitation passages are formed ²on the first side of heat block 810. Each of the first plurality of excitation ²passages extend ²through one passage 850, one passage 854, and one passage 856. There are a ²plurality of ²passages 850 to accommodate each of the light-emitting diodes in first set ²830. Thus, three ²passages 850 are positioned to pass into one passage 854. Further, excitation ²filters 852 are also ²positioned in the first plurality of excitation passages between passages 850 ²and passages 854. A ²second plurality of excitation passages are formed on the second side of heat ²block 810. Each of ²the second plurality of excitation passages extend through one passage 860, ²one passage 864, and ²one passage 866. There are a plurality of passages 860 to accommodate each of ²the light-²emitting diodes in second set 832. Thus, three passages 860 are positioned to ²pass into one ²passage 864. Further, excitation filters 862 are also positioned in the second ²plurality of ²excitation passages between passages 860 and passages 864.²

[00270] Multiple emission passages also extend through optical assembly 800 ²on both ²sides so that radiation can travel from heat block 810 to first set of ²photodetectors 834 and ²second set of photodetectors 836. A first plurality of emission passages are ²formed on the first ²side of heat block 810. Each of the first plurality of emission passages ²extend through one ²passage 876, one passage 874, and one passage 870. Further, emission filter ²872 is positioned in ²each of the first plurality of emission passages between passages 874 and ²passages 870. A ²second plurality of emission passages are formed on the second side of heat ²block 810. Each of ²the second plurality of emission passages extend through one passage 886, one ²passage 884, and ²one passage 880. Further, emission filter 882 is positioned in each of the ²second plurality of ²emission passages between passages 884 and passages 880.²

[00271] To excite a biological sample that is positioned in heat block 810, ²a light-emitting ²diode in either first light-emitting diode set 830 or second light-emitting ²diode set 832 is ²activated. If a light-emitting diode from first set 830 is activated, ²radiation will travel through ²passage 850, excitation filter 852, passage 854, and passage 856 into well 812 ²of heat block 810. ²If a light-emitting diode from second set 832 is activated, radiation will ²travel through passage ²860, excitation filter 862, passage 864, and passage 866 into well 812 of heat ²block 810.²54²<DP=57>²CA 02926253 2016-04-01²WO 2015 / 054245 PCT / US2014 / 059487²

[00272] Radiation emitted from the biological sample that is positioned in ²heat block 810 ²will be detected by a photodetector in either first set 834 or second set 836. ²Each photodetector ²from first set 834 will read emission that has traveled from well 812 of heat ²block 810 through ²passage 876, passage 874, emission filter 872, and passage 870. Each ²photodetector from second ²set 836 will read emission that has traveled from well 812 of heat block 810 ²through passage ²886, passage 884, emission filter 882, and passage 880.²

[00273] Optical assembly 800 is advantageous, as it allows for multiple ²light-emitting ²diodes to be positioned around each well 812 in heat block 810. This allows a ²biological sample ²in wells 812 to be excited at a plurality of different radiation wavelengths. ²In the embodiment ²shown in FIGS. 29A-29D, a biological sample can include a first fluorescent ²dye, a second ²fluorescent dye, and a third fluorescent dye that can all be excited by a ²light-emitting diode. ²Optical assembly 800 is further advantageous, as it is a compact design with ²no moving parts. ²The compact design allows optical assembly 800 to be used in portable testing ²devices to test ²biological materials in the field.²CARD 900²

[00274] FIG. 30A is perspective view of card 900. FIG. 30B is a side ²elevation view of ²card 900. FIG. 30C is a front elevation view of card 900. Card 900 includes ²body 902, wells ²904, handle or tab 906, and code 908. Each well 904 includes first cavity 910, ²second cavity ²912, and channel 914.²

[00275] Card 900 is capable of receiving a biological material that will ²undergo nucleic ²acid amplification and then be tested. Card 900 is formed by body 902. Body ²902 is made out ²of a transparent plastic in the embodiment shown, but can be made out of any ²suitable material in ²alternate embodiments. Card 900 includes a plurality of wells 904 on body 902. ²Wells 904 are ²embossed into body 902 during manufacturing of card 900. Body 902 also ²includes handle 906 ²at a top side of body 902. Handle 906 is a rectangular protrusion from body ²902 in the ²embodiment shown and allows a user to easily grasp card 900. Code 908 is also ²printed on body ²902 of card 900. Code 908 is a machine readable code that can be read by a ²machine code reader ²when card 900 is placed in a device for testing.²

[00276] Each well 904 on card 900 includes first cavity 910, second cavity ²912, and ²channel 914. First cavity 910 and second cavity 912 are positioned apart from ²one another. ²Channel 914 runs between first cavity 910 and second cavity 912 and connects ²them. First²<DP=58>²CA 02926253 2016-04-01²WO 2015 / 054245 PCT / US2014 / 059487²cavity 910 is capable of receiving a biological sample. After the biological ²sample is placed in ²first cavity 910 it will travel through channel 914 into second cavity 912. ²Second cavity 912 can ²contain a reaction mixture that the biological sample can mix with. Nucleic ²acid amplification ²can then be conducted when the biological sample is in second cavity 912. The ²biological ²sample in second cavity 912 can be excited and detected from a first side and ²a second side of ²card 900.²

[00277] Card 900 is a sample holder in which a biological material can ²undergo nucleic ²acid amplification. Card 900 is advantageous over previous sample holder ²products for ²conducting nucleic acid amplification, as card 900 has a streamlined design ²and is easy to ²manage. With previous sample holders, there were multiple parts and components ²that were ²difficult to grasp and hold steady when dispensing a biological material into ²the sample holder. ²Card 900 is formed with one main body 902, making it easy to manage. Card 900 ²can be held ²with handle 906 or laid flat on a table when a biological material is being ²dispensed. This makes ²card 900 capable of being used in a field with a portable testing device, as ²no separate holding ²station or support structure is required to support card 900.²

[00278] Card 900 is further advantageous, as card 900 can come preloaded ²with a reaction ²mixture in second cavities 912. This streamlines the process of preparing card ²900 for testing. ²Further, card 900 includes code 908. Code 908 is a machine readable code that ²can be read by ²the device in which card 900 is placed. Code 908 can include information about ²what test ²protocol to run with a specific card 900, including embedded end point call ²algorithms and ²reaction mixture traceability information. Code 908 can further include ²additional information ²that can be read by the portable testing device.²

[00279] FIG. 31A is a front elevation view of card 900 showing well ²variations A-D. FIG. ²31B is a front elevation view of card 900 showing well variations E-H. Card ²900 includes body ²902 and wells 904, including wells 904A, wells 904B. wells 904C, wells 904D, ²wells 904E, ²wells 904F, wells 904G, and wells 904H. Wells 904 can include first cavities ²910, second ²cavities 912, channels 914, air ducts 916, and third cavities 918.²

[00280] Card 900 includes body 902. Wells 904 are positioned on body 902. ²Wells 904 ²can take any number of shapes, some variations of which are seen in FIGS. 31A-²31B. Wells 904 ²are all capable of receiving a biological sample and mixing the biological ²sample with a reaction²56²<DP=59>²CA 02926253 2016-04-01²WO 2015 / 054245 PCT / US2014 / 059487²mixture that is preloaded in wells 904. The biological sample in each well 904 ²can then undergo ²nucleic acid amplification and testing.²

[00281] Wells 904A each include first cavity 910A, second cavity 912A, and ²channel ²914A. First cavity 910A and second cavity 912A are positioned apart from one ²another. First ²cavity 910A has a circular shape and a first depth. Second cavity 912A has an ²oval shape and a ²second depth. Channel 914A runs between first cavity 910A and second cavity ²912A and ²connects them. Channel 914A has a changing depth, starting with the first ²depth at first cavity²910A and ending with the second depth at second cavity 912A. First cavity 910A ²is capable of ²receiving a biological sample. After the biological sample is placed in first ²cavity 910A it will ²travel through channel 914A into second cavity 912A. Second cavity 912A can ²contain a ²reaction mixture that the biological sample can mix with. Nucleic acid ²amplification can then be ²conducted when the biological sample is in second cavity 912A.²

[00282] Wells 904B each include first cavity 910B, second cavity 912B, ²channel 914B, ²and air duct 916B. First cavity 910B and second cavity 912B are positioned ²apart from one ²another. First cavity 910B has a circular shape. Second cavity 912B has an ²oval shape. Channel ²914B runs between first cavity 910B and second cavity 912B and connects them. ²First cavity²910B is capable of receiving a biological sample. After the biological sample ²is placed in first ²cavity 910B it will travel through channel 914B into second cavity 912B. Air ²duct 916B is ²connected to channel 914B and allows air in channel 914B to be expelled when ²the biological ²sample travels through channel 914B. Second cavity 912B can contain a reaction ²mixture that ²the biological sample can mix with. Nucleic acid amplification can then be ²conducted when the ²biological sample is in second cavity 912B.²

[00283] Wells 904C each include first cavity 910C, second cavity 912C, and ²channel ²914C. First cavity 910C and second cavity 912C are positioned apart from one ²another. First ²cavity 910C has a circular shape and has a first depth. Second cavity 912C has ²an oval shape ²and has the same depth as first cavity 910C. Channel 914C runs between first ²cavity 910C and ²second cavity 912C and connects them. Channel 914C has the same depth as both ²first cavity²910C and second cavity 912C. First cavity 910C is capable of receiving a ²biological sample. ²After the biological sample is placed in first cavity 910C it will travel ²through channel 914C into ²second cavity 912C. Second cavity 912C can contain a reaction mixture that the ²biological²57²<DP=60>²CA 02926253 2016-04-01²WO 2015 / 054245 PCT / US2014 / 059487²sample can mix with. Nucleic acid amplification can then be conducted when the ²biological ²sample is in second cavity 912C.²

[00284] Wells 904D each include first cavity 910D, second cavity 912D, and ²channel ²914D. First cavity 910D and second cavity 912D are positioned apart from one ²another. First ²cavity 910D has a circular shape. Second cavity 912D has a shape that mimics ²three overlapping ²circles. Channel 914D runs between first cavity 910D and second cavity 912D ²and connects ²them. First cavity 910D is capable of receiving a biological sample. After the ²biological sample ²is placed in first cavity 910D it will travel through channel 914D into second ²cavity 912D. ²Second cavity 912D can contain a reaction mixture that the biological sample ²can mix with. ²Nucleic acid amplification can then be conducted when the biological sample is ²in second cavity ²912D. The shape of second cavity 912D allows for a light-emitting diode and a ²photodetector to ²be positioned over each of one of the three overlapping circles. This allows ²three different light-²emitting diodes and three different photodetectors to be aligned with second ²cavity 912D.²

[00285] Wells 904E each include first cavity 910E, second cavity 912E, and ²third cavity²918E. First cavity 910E has a thin rectangular shape. Second cavity 912E has a ²circular shape. ²Third cavity 918E has a thin horseshoe shape. First cavity 910E is connected ²directly to second ²cavity 912E and second cavity 912E is connected directly to third cavity 918E. ²First cavity 910E ²is capable of receiving a biological sample. After the biological sample is ²placed in first cavity²910E it will travel into second cavity 912E. Second cavity 912E can contain a ²reaction mixture ²that the biological sample can mix with. Nucleic acid amplification can then ²be conducted when ²the biological sample is in second cavity 912E. Any excess air or fluid in ²well 904E can travel ²into third cavity 918E. In an alternate embodiment, the biological sample ²could be received in ²third cavity 918E and excess air or fluid could accrue in first cavity 910E.²

[00286] Wells 904F each include first cavity 910F, second cavity 912F, and ²third cavity²918F. First cavity 910F has a thin rectangular shape. Second cavity 912F has a ²circular shape. ²Third cavity 918F has a teardrop shape. First cavity 910F is connected ²directly to second cavity ²912F and second cavity 912F is connected directly to third cavity 918F. First ²cavity 910F is ²capable of receiving a biological sample. After the biological sample is ²placed in first cavity²910F it will travel into second cavity 912F. Second cavity 912F can contain a ²reaction mixture ²that the biological sample can mix with. Nucleic acid amplification can then ²be conducted when²58²<DP=61>²CA 02926253 2016-04-01²WO 2015 / 054245 PCT / US2014 / 059487²the biological sample is in second cavity 912F. Any excess air or fluid in ²well 904F can travel ²into third cavity 918F.²

[00287] Wells 904G each include first cavity 910G, second cavity 912G, and ²channel ²914G. First cavity 910G and second cavity 912G are positioned apart from one ²another. First ²cavity 910G has a circular shape. Second cavity 912G has a circular shape. ²Channel 914G runs ²between first cavity 910G and second cavity 912G and connects them. First ²cavity 910G is ²capable of receiving a biological sample. After the biological sample is ²placed in first cavity ²910G it will travel through channel 914G into second cavity 912G. Second ²cavity 912G can ²contain a reaction mixture that the biological sample can mix with. Nucleic ²acid amplification ²can then be conducted when the biological sample is in second cavity 912G.²

[00288] Wells 904H each include first cavity 910H, second cavity 912H, and ²third cavity ²918H. First cavity 910H has a thin rectangular shape. Second cavity 912H has a ²rectangular ²shape with rounded corners. Third cavity 918H has a thin horseshoe shape. ²First cavity 910H is ²connected directly to second cavity 912H. Second cavity 912H is connected to ²third cavity 918H ²with a restriction feature. First cavity 910H is capable of receiving a ²biological sample. After ²the biological sample is placed in first cavity 910H it will travel into ²second cavity 912H. ²Second cavity 912H can contain a reaction mixture that the biological sample ²can mix with. The ²restriction feature between second cavity 912H and third cavity 918H allows ²air to pass from ²second cavity 912H to third cavity 918H, but retains fluids in second cavity ²912H. Nucleic acid ²amplification can then be conducted when the biological sample is in second ²cavity 912H.²

[00289] Card 900 is advantageous because a plurality of differently shaped ²wells 904 can ²be used. Wells 904A-904H shown in FIGS. 31A-31B are a small sampling of the ²variety of ²differently shaped wells 904 that could be produced. Card 900 allows a ²biological material to be ²placed in wells 904 and travel through each well 904 to mix with a reaction ²mixture. The ²biological sample and reagent mixture can then undergo nucleic acid ²amplification and can be ²tested. Each well 904 requires a small amount of reaction mixture and ²biological material to ²conduct the nucleic acid amplification and testing. This will save money in ²materials. Further, ²less biological sample needs to be collected in order to complete a test.²

[00290] FIG. 32A is a side elevation view of card 900 showing seals on card ²900. FIG. ²32B is a front elevation view of card 900 showing first permanent seal 920 and ²removable seal ²922. FIG. 32C is a front elevation view of card 900 after removable seal 922 ²is removed. FIG.²59²<DP=62>²CA 02926253 2016-04-01²WO 2015 / 054245 PCT / US2014 / 059487²32D is a front elevation view of card 900 after second permanent seal 924 is ²applied. Card 900 ²includes body 902, wells 904, first permanent seal 920, removable seal 922, ²second permanent ²seal 924, and backing 926. Each well 904 includes first cavity 910, second ²cavity 912, and ²channel 914.²

[00291] Card 900 includes wells 904 that are positioned on body 902 of card ²900. Each ²well 904 on card 900 includes first cavity 910, second cavity 912, and channel ²914. First cavity ²910 and second cavity 912 are positioned apart from one another. Channel 914 ²runs between ²first cavity 910 and second cavity 912 and connects them. First cavity 910 is ²capable of ²receiving a biological sample. After the biological sample is placed in first ²cavity 910 it will ²travel through channel 914 into second cavity 912. Second cavity 912 can ²contain a reaction ²mixture with which the biological sample can mix. Nucleic acid amplification ²can then be ²conducted when the biological sample is in second cavity 912.²

[00292] Card 900 further includes first permanent seal 920, removable seal ²922, second ²permanent seal 924, and backing 926. First permanent seal 920 is positioned on ²body 902 of ²card 900 and covers channels 914 and second cavities 912 of wells 904. ²Removable seal 922 is ²positioned on body 902 of card 900 and covers first cavities 910 of wells 904. ²Second ²permanent seal 924 is attached to a top portion of body 902 of card 900, but ²second permanent ²seal 924 is not initially sealed onto body 902 of card 900. Backing 926 is ²attached to second ²permanent seal 924.²

[00293] First permanent seal 920 and removable seal 922 can be sealed to ²card 900 prior ²to the sale of card 900. During manufacturing of the card, a reaction mixture ²can be added to ²second cavities 912 of wells 904. The reaction mixture can come in liquid form ²or it can be ²lyophilized. After the reaction mixture is added, first permanent seal 920 can ²be applied to card ²900 to seal channels 914 and second cavities 912 of wells 904. Removable seal ²922 can also be ²applied to card 900 to seal first cavities 910 of wells 904. Second permanent ²seal 924 and ²backing 926 can also be attached to a top portion of body 902 of card 900. ²This can be seen in ²FIGS. 32A-32B.²

[00294] When a user wants to place a biological material in wells 904, ²removable seal 922 ²can be removed from body 902 of card 900, as seen in FIG. 32C. This will ²expose first cavities ²910 of wells 904. A biological sample can then be placed in first cavities ²910, usually by ²pipetting the biological sample in liquid form into first cavities 910. As the ²biological sample is²<DP=63>²CA 02926253 2016-04-01²WO 2015 / 054245 PCT / US2014 / 059487²placed in first cavities 910, it can travel through channels 914 into second ²cavities 912. When ²the biological sample reaches second cavities 912 it can mix with the reaction ²mixture that was ²previously placed in second cavities 912. After the biological sample has been ²fully loaded into ²card 900, backing 926 can be removed from second permanent seal 924. Second ²permanent seal ²924 can then be placed on body 902 of card 900 to fully seal wells 904, as ²seen in FIG. 32D. ²Second permanent seal 924 covers first cavities 910 and first permanent seal ²920 in the ²embodiment shown. In alternate embodiments, second permanent seal 924 can ²cover only first ²cavities 910 or it can cover first cavities 910 and a portion of first ²permanent seal 920.²

[00295] Card 900 is advantageous, as it allows a user to easily load a ²biological sample ²into a sample holder. Card 900 is further advantageous, as it can come ²preloaded with a reaction ²mixture. After the biological sample is loaded into card 900, it will mix with ²the reaction ²mixture to prepare it for nucleic acid amplification. This is a simple way to ²prepare the ²biological sample for testing. Further, the seals that are provided on card ²900 make it easy for a ²user to load a biological sample into card 900 while preventing contamination ²of wells 904. ²CARD 1000²

[00296] FIG. 33A is a perspective view of a top side of card 1000. FIG. 33B ²is a ²perspective view of a bottom side of card 1000. Card 1000 includes body 1002 ²and wells 1004. ²Body 1002 includes first body portion 1010, second body portion 1012, and ²hinge 1014.²

[00297] Card 1000 is capable of receiving a biological material that will ²undergo nucleic ²acid amplification and be tested. Card 1000 is formed with body 1002. Body ²1002 is made out ²of a transparent plastic in the embodiment shown, but can be any suitable ²material in alternate ²embodiments. Body 1002 includes first body portion 1010, second body portion ²1012, and hinge ²1014. First body portion 1010 is a rectangular shape. Second body portion 1012 ²is a T-shape. A ²first long side of first body portion 1010 is attached to the top long portion ²of the T-shape of ²second body portion 1012 along hinge 1014. First body portion 1010 and second ²body portion ²1012 can be folded towards or away from one another along hinge 1014. First ²body portion ²1010 is wider than second body portion 1012, which allows first body portion ²1010 to be secured ²when a biological sample is placed in first body portion 1010 or when second ²body portion 1012 ²is sealed with first body portion 1010.²

[00298] A plurality of wells 1004 are positioned on first body portion ²1010. Each well ²1004 is a circular shape and wells 1004 are positioned in a line on first body ²portion 1010. Wells²61²<DP=64>²CA 02926253 2016-04-01²WO 2015 / 054245 PCT / US2014 / 059487²1004 are capable of receiving biological samples and reactions mixtures to ²undergo nucleic acid ²amplification.²

[00299] The T-shape of second body portion 1012 allows the vertical portion ²of the T-²shape to act as a handle for card 1000. Second body portion 1012 can be easily ²grasped by a ²user to hold and move card 1000. Further, a machine readable code can be ²printed on the handle ²of second body portion 1012. When card 1000 is placed in a device, a code ²reader can read the ²machine readable code on second body portion 1012. The machine readable code ²can indicate ²what test protocol to run, among other information.²

[00300] Card 1000 is advantageous, as it allows a user to prepare a ²biological sample for ²testing on a compact and easy-to-use sample holder. Biological materials can ²be easily placed in ²wells 1004 and mixed with reaction mixtures. Further, the design of card 1000 ²with a handle on ²second body portion 1012 makes card 1000 easy to grasp and maneuver. Card 1000 ²allows a ²user to conduct nucleic acid amplification of small sample amounts in wells ²1004.²

[00301] FIG. 34A is a perspective view of card 1000 when second body ²portion 1012 is ²rotated down. FIG. 34B is a perspective view of card 1000 with permanent seal ²1020. FIG. 4C ²is a perspective view of card 1000 with first removable seal 1022. FIG. 34D is ²a perspective ²view of card 1000 that can be placed in a lyophilizer. FIG. 34E is a ²perspective view of card ²1000 with second removable seal 1026 placed over first removable seal 1022. ²Card 1000 ²includes body 1002, wells 1004, permanent seal 1020, first removable seal ²1022, openings 1024, ²and second removable seal 1026. Body 1002 includes first body portion 1010, ²second body ²portion 1012, and hinge 1014.²

[00302] Card 1000 is capable of receiving a biological material to undergo ²nucleic acid ²amplification. Card 1000 is formed with body 1002. Body 1002 includes first ²body portion ²1010, second body portion 1012, and hinge 1014. First body portion 1010 and ²second body ²portion 1012 are attached along hinge 1014 and can be folded towards or away ²from one another ²along hinge 1014. A plurality of wells 1004 are positioned on first body ²portion 1010. Each ²well 1004 is a circular shape and wells 1004 are positioned in a line on first ²body portion 1010. ²In alternate embodiments, wells 1004 can be any shape, including oval, ²rectangular, or tear drop ²shaped. Wells 1004 are capable of receiving biological samples and reactions ²mixtures to ²undergo nucleic acid amplification.²62²<DP=65>²CA 02926253 2016-04-01²WO 2015 / 054245 PCT / US2014 / 059487²

[00303] To prepare card 1000 for testing, second body portion 1012 can ²first be folded ²downwards along hinge 1014. This allows a user to either grasp second body ²portion 1012 to ²hold card 1000 steady or to place second body portion 1012 in a holder to ²support card 1000. ²When card 1000 is held steady or supported, a reaction mixture can be ²dispensed into wells ²1004, as seen in FIG. 34A. The reaction mixture is typically dispensed in ²liquid form.²

[00304] Either before or right after the reaction mixture is dispensed into ²wells 1004, ²permanent seal 1020 can be applied to first body portion 1010, as seen in FIG. ²34B. Permanent ²seal 1020 is a permanent adhesive that is applied to a top side of first body ²portion 1010 ²surrounding wells 1004 in the embodiment shown. In alternate embodiments, ²permanent seal ²1020 can be any suitable seal.²

[00305] After permanent seal 1020 is applied and the reaction mixture has ²been dispensed ²into wells 1004, first removable seal 1022 is placed over permanent seal 1020, ²as seen in FIG. ²34C. First removable seal 1022 can be any material that is suitable for use as ²a seal and that can ²be easily removed from permanent seal 1020. First removable seal 1022 has a ²plurality of ²openings 1024 in it. One opening 1024 is positioned over each well 1004. ²Openings 1024 are ²provided to allow moisture laden air to flow into and out of wells 1004 during ²the remaining ²preparation steps.²

[00306] After first removable seal 1022 has been placed over wells 1004, ²card 1000 can ²be placed in a lyophilizer, as seen in FIG. 34D. Card 1000 can be inserted ²into the lyophilizer in ²any orientation. A lyophilizer will dry-down the liquid reaction mixture that ²is in wells 1004. ²Openings 1024 in first removable seal 1022 allow air to pass into and out of ²wells 1004 during ²lyophilization.²

[00307] After the reaction mixture in wells 1004 is lyophilized, second ²removable seal ²1026 can be placed over openings 1024 in first removable seal 1022, as seen in ²FIG. 34E. ²Second removable seal 1026 can be any material that is suitable for use as a ²seal. Placing second ²removable seal 1026 over first removable seal 1022 will cover openings 1024 in ²first removable ²seal 1022. This will seal the lyophilized reaction mixture into wells 1004 and ²it will prevent ²wells 1004 from being contaminated.²

[00308] As seen from the above steps, card 1000 can be easily prepared for ²nucleic acid ²amplification and testing. First removable seal 1022 and second removable seal ²1026 are applied ²to card 1000 during preparation of card 1000 to protect card 1000 from ²contamination. First²63²<DP=66>²CA 02926253 2016-04-01²WO 2015 / 054245 PCT / US2014 / 059487²removable seal 1022 and second removable seal 1026 can be easily removed from ²card 1000 ²when a biological material is to be placed in wells 1004. Card 1000 is further ²advantageous, as it ²comes with a lyophilized reaction mixture preloaded into wells 1004. This ²makes it easy to ²prepare a biological sample in card 1000 for nucleic acid amplification. The ²ease of preparation ²makes card 1000 suitable for use in the field.²

[00309] FIG. 35A is a perspective view of card 1000 with first removable ²seal 1022 and ²second removable seal 1026. FIG. 35B is a perspective view of card 1000 with ²first removable ²seal 1022 and second removable seal 1026 removed to provide access to wells ²1004. FIG. 35C ²is a perspective view of card 1000 when second body portion 1012 is folded ²over wells 1004 to ²seal wells 1004 with permanent seal 1020. FIG. 35D is a perspective view of ²card 1000 that is ²prepared for testing. Card 1000 includes body 1002, wells 1004, permanent seal ²1020, first ²removable seal 1022, openings 1024, and second removable seal 1026. Body 1002 ²includes first ²body portion 1010, second body portion 1012, and hinge 1014.²

[00310] Card 1000 is capable of receiving a biological material to undergo ²nucleic acid ²amplification. Card 1000 is formed with body 1002. Body 1002 includes first ²body portion ²1010, second body portion 1012, and hinge 1014. First body portion 1010 and ²second body ²portion 1012 are attached along hinge 1014 and can be folded towards or away ²from one another ²along hinge 1014. A plurality of wells 1004 are positioned on first body ²portion 1010. Each ²well 1004 is a circular shape and wells 1004 are positioned in a line on first ²body portion 1010. ²Wells 1004 are capable of receiving biological samples and reactions mixtures ²that can undergo ²nucleic acid amplification.²

[00311] After a user has obtained card 1000, the user can place a ²biological sample into ²wells 1004 of card 1000 to test the biological sample. Card 1000 is shown in ²FIG. 35A as it ²would be received by a user. To prepare the biological sample and card 1000 ²for testing, first ²removable seal 1022 and second removable seal 1026 are removed from card 1000 ²by peeling ²them off of card 1000, as seen in FIG. 35B. This will expose permanent seal ²1020. After first ²removable seal 1022 and second removable seal 1026 are removed, a biological ²sample can be ²placed in wells 1004. The biological sample that is placed in wells 1004 is ²typically in liquid ²form. The liquid can then mix with the lyophilized reaction mixture that was ²placed in wells ²1004 during preparation of card 1000.²64²<DP=67>²CA 02926253 2016-04-01²WO 2015 / 054245 PCT / US2014 / 059487²

[00312] After a biological sample is placed in wells 1004, second body ²portion 1012 of ²card 1000 can be folded along hinge 1014 towards first body portion 1010. As ²seen in FIG. 35C, ²second body portion 1012 will come into contact with permanent seal 1020 on ²first body portion ²1010. This will permanently seal wells 1004 of card 1000, as seen in FIG. 35D. ²After card 1000 ²is permanently sealed, a user can grasp the handle of second body portion 1012 ²to place card ²1000 in a testing, device.²

[00313] Card 1000 is advantageous, as a biological sample can be easily ²loaded into card ²1000 by removing first removable seal 1022 and second removable seal 1026. ²After the ²biological sample is loaded, card 1000 can be folded along hinge 1014 to form ²a permanent seal ²between first body portion 1010 and second body portion 1012. Card 1000 can ²then be placed in ²a device for testing. The ease of loaded a biological material into card 1000 ²and sealing card ²1000 for testing making card 1000 suitable for use in the field.²LID ASSEMBLY 1100²

[00314] FIG. 36A is a perspective view of lid assembly 1100. FIG. 36B is a ²top view of ²seal portion 1110 that can be used with lid assembly 1100. Lid assembly 1100 ²includes base ²portion 1102, lid portion 1104, apertures 1106, and flanges 1108. Seal portion ²1110 includes ²permanent seal 1112, backing 1114, and tab 1116.²

[00315] Lid assembly 1100 includes base portion 1102 and lid portion 1104. ²Lid portion ²1104 is attached to base portion 1102 with a plurality of hinge members so ²that lid portion 1104 ²can be folded along the hinge members towards base portion 1102. Base portion ²1102 includes a ²plurality of apertures 1106. Each aperture 1106 is sized to fit on a standard ²tube so that base ²portion 1102 can be attached to a tube array. Lid portion 1104 includes a ²plurality of flanges ²1108. Each flange 1108 is sized to be positioned in a standard tube so that ²lid portion 1104 can ²be folded over base portion 1102 and each flange 1108 can be placed in one ²tube in the tube ²array to seal the tubes.²

[00316] Also included with lid assembly 1100 is seal portion 1110. Seal ²portion 1110 ²includes permanent seal 1112, backing 1114, and tab 1116. Permanent seal 1112 ²forms a first ²layer of seal portion 1110 and backing 1114 is positioned over permanent seal ²1112 to form a ²second layer. Seal portion 1110 can be placed on base portion 1102 of lid ²assembly 1100 so that ²permanent seal 1112 is positioned on base portion 1102 and backing 1114 is ²positioned on a top ²side of permanent seal 1112. Backing 1114 is capable of being removed from ²permanent seal²<DP=68>²CA 02926253 2016-04-01²WO 2015 / 054245 PCT / US2014 / 059487²1112 by peeling backing 1114 off of permanent seal 1112. Tab 1116 extends ²outward from a ²first side of backing 1114. Tab 1116 is a rectangular shape that can be ²grasped by a user to ²position seal portion 1110 on base portion 1102 of lid assembly 1100. A ²machine readable code ²can also be printed on tab 1116. When the tube array carrying lid assembly ²1100 and seal ²portion 1110 is placed in a device for testing, the device can scan the ²machine readable code on ²tab 1116. The machine readable code can indicate what test is to be run, ²including information ²about end point call algorithms and reaction mixture traceability information, ²among other ²information.²

[00317] When seal portion 1110 is positioned on base portion 1102 of lid ²assembly 1100, ²lid portion 1104 can be folded onto base portion 1102 when backing 1114 is on ²seal portion ²1110. This will form a mechanical seal between base portion 1102 and lid ²portion 1104. When ²backing 1114 is removed, permanent seal 1112 will be exposed. Lid portion 1104 ²can then be ²folded onto base portion 1102 to form a permanent seal between base portion ²1102 and lid ²portion 1104.²

[00318] Using a standard tube array is advantageous, as the tube array can ²be used with ²devices that are already available on the market. One issue that arises when ²using a standard ²tube array is that the lid portion of the tube array can be removed either ²intentionally or ²accidentally. This poses concerns with contamination of the biological sample ²in the tube array. ²Lid assembly 1100 is thus advantageous, as it allows a user to create a ²permanent seal with a ²standard tube array. Lid assembly 1100 can be closed over backing 1114 of seal ²portion 1110 to ²form a mechanical seal that can be opened and closed when the tube array is ²being prepared for ²testing. When a biological sample in placed in the tube array. backing 1114 ²can be removed to ²expose permanent seal 1112. When lid assembly 1100 is closed over permanent ²seal 1112, the ²tube array will be permanently sealed. This eliminates concerns about ²contamination of the ²biological sample in the tube array, as it would be difficult to remove lid ²assembly 1100 from the ²tube array.²

[00319] FIG. 37A is a perspective view of lid assembly 1100 attached to ²tube array 1120. ²FIG. 37B is a perspective view of lid assembly 1100 with seal portion 1110 ²applied to lid ²assembly 1100. FIG. 37C is a perspective view of lid assembly 1100 in a closed ²position over ²seal portion 1110. FIG. 37D is a perspective view of lid assembly 1100 opened ²and backing ²1114 removed from seal portion 1110. FIG. 37E is a perspective view of lid ²assembly 1100 in a²66²<DP=69>²CA 02926253 2016-04-01²WO 2015 / 054245 PCT / US2014 / 059487²closed position to form a seal with permanent seal 1112. Lid assembly 1100 ²includes base ²portion 1102, lid portion 1104. apertures 1106, and flanges 1108. Seal portion ²1110 includes ²permanent seal 1112, backing 1114, and tab 1116. Also shown is tube array ²1120.²

[00320] Lid assembly 1100 is capable of being positioned on tube array ²1120. Tube array ²1120 is a standard tube array that is readily available on the market. Lid ²assembly 1100 includes ²base portion 1102 and lid portion 1104. Lid portion 1104 is attached to base ²portion 1102 with a ²plurality of hinge members so that lid portion 1104 can be folded along the ²hinge members ²towards base portion 1102. Base portion 1102 includes a plurality of apertures ²1106. Each ²aperture 1106 is sized to fit on a standard tube so that base portion 1102 can ²be attached to tube ²array 1120. Lid portion 1104 includes a plurality of flanges 1108. Each flange ²1108 is sized to ²be positioned in a standard tube so that lid portion 1104 can be folded over ²base portion 1102 ²and flanges 1108 can be placed in tubes in tube array 1120 to seal the tubes.²

[00321] Also included with lid assembly 1100 is seal portion 1110. Seal ²portion 1110 ²includes permanent seal 1112, backing 1114, and tab 1116. Permanent seal 1112 ²forms a first ²layer of seal portion 1110 and backing 1114 is positioned over permanent seal ²1112 to form a ²second layer. Seal portion 1110 can be placed on base portion 1102 of lid ²assembly 1100 so that ²permanent seal 1112 is positioned on base portion 1102 and backing 1114 is ²positioned on a top ²side of permanent seal 1112. Backing 1114 is capable of being removed from ²permanent seal ²1112 by peeling backing 1114 off of permanent seal 1112. Tab 1116 extends ²outward from a ²first side of backing 1114. Tab 1116 is a rectangular shape that can be ²grasped by a user to ²position seal portion 1110 on base portion 1102 of lid assembly 1100.²

[00322] To prepare tube array 1120 for testing. a biological material needs ²to be placed in ²each of the tubes in tube array 1120 and tube array 1120 needs to be sealed. ²To do this, a user ²first obtains tube array 1120 and lid assembly 1100. Lid assembly 1100 can be ²connected to tube ²array 1120 by placing apertures 1106 of lid assembly 1100 around each of the ²tubes in tube array ²1120, as seen in FIG. 37A. Apertures 1106 form an interference fit with the ²tubes in tube array ²1120 to hold lid assembly 1100 on tube array 1120. Further, in alternate ²embodiments, apertures ²1106 and the tubes in tube array 1120 can have protrusions so that lid ²assembly 1100 will snap ²onto tube array 1120. Tube array 1120 is placed in apertures 1106 of lid ²assembly 1100 so that ²when lid assembly 1100 is closed, the members connecting the tubes in tube ²array 1120 are ²positioned between base portion 1102 and lid portion 1104. This prevents lid ²assembly 1100²67²<DP=70>²CA 02926253 2016-04-01²WO 2015 / 054245 PCT / US2014 / 059487²from being removed from tube array 1120 after lid assembly 1100 is permanent ²sealed. In ²alternate embodiments, lid assembly 1100 can be welded or bonded onto tube ²array 1120 prior to ²the sale of tube array 1120.²

[00323] After lid assembly 1100 has been placed on tube array 1120, seal ²portion 1110 ²can be placed on base portion 1102 of lid assembly 1100. Seal portion 1110 ²includes permanent ²seal 1112 as a first layer and backing 1114 as a second layer. Permanent seal ²1112 will be ²placed on base portion 1102 of lid assembly 1100 and backing 1114 will face ²upwards from base ²portion 1102, as seen in FIG. 37B.²

[00324] After seal portion 1110 has been placed on base portion 1102 of lid ²assembly ²1100, a reaction mixture can be placed in each of the tubes in tube array ²1120. The reaction ²mixture will typically be pipetted into each of the tubes in tube array 1120. ²After the reaction ²mixture is dispensed, it can be lyophilized. Lyophilization will dry down the ²reaction mixture. ²After the reaction mixture is lyophilized, lid portion 1104 of lid assembly ²1100 can be folded ²over base portion 1102 and seal portion 1110. Flanges 1108 of lid portion 1104 ²can be inserted ²into one of each of the tubes in tube array 1120. Lid portion 1104 will come ²into contact with ²backing 1114 of seal portion 1110. This will form a mechanical seal between ²lid portion 1104 ²and base portion 1102 of lid assembly 1100, as seen in FIG. 37C. Tube array ²1120 can then be ²stored until it is needed to test a biological material. Further, lid assembly ²1100 can be opened ²and closed over backing 1114 to provide access to tube array 1120.²

[00325] When a biological material is to be placed in tube array 1120 for ²testing, lid ²assembly 1100 can be opened by separating lid portion 1104 from base portion ²1102. This will ²expose each of the tubes in tube array 1120. A biological material can then be ²dispensed into ²each of the tubes in tube array 1120, which is usually done with pipetting. ²The biological ²material is typically added to tube array 1120 in liquid form and can be mixed ²with the reaction ²mixture that was previously placed in tube array 1120. After the biological ²material has been ²added to tube array 1120, backing 1114 and tab 1116 can be removed from tube ²array 1120, as ²seen in FIG. 37D. This will expose permanent seal 1112. Tab 1116 can have a ²machine ²readable code printed on it. A user may retain tab 1116 to be scanned by a ²testing device before ²disposing of tab 1116.²

[00326] After permanent seal 1112 has been exposed, lid portion 1104 of lid ²assembly ²1100 can be folded over base portion 1102 of lid assembly 1100. Flanges 1108 ²on lid portion²68²<DP=71>²CA 02926253 2016-04-01²WO 2015 / 054245 PCT / US2014 / 059487²1104 can be placed in each of the tubes in tube array 1120. Lid portion 1104 ²of lid assembly ²1100 will come into contact with permanent seal 1112, which will form a ²permanent seal ²between lid portion 1104 and base portion 1102, as seen in FIG. 37E. Tube ²array 1100 and lid ²assembly 1100 can then be placed in a device to undergo nucleic acid ²amplification and testing.²

[00327] Lid assembly 1100 is advantageous, as it allows a user to ²permanently seal a ²standard array of tubes. Using a standard array of tubes allows a user to test ²a biological sample ²using devices that are already available on the market. Placing lid assembly ²1100 on a standard ²array of tubes allows a user to place a reaction mixture in the tubes and then ²close the tubes over ²seal portion 1110, including backing 1114, until the tubes are to be used for ²testing. At this ²point, the tubes can be opened and a biological sample can be placed in them. ²Backing 1114 can ²then be removed and lid assembly 1100 can be closed over permanent seal 1112. ²This ²permanently seals the array of tubes and prevents contamination of the ²biological sample in the ²tubes.²SAMPLE HOLDER 1200²

[00328] FIG. 38A is a front view of sample holder 1200 including tube array ²1202 and lid ²array 1204. FIG. 38B is a perspective view of sample holder 1200 when lid ²array 1204 is placed ²on tube array 1202. Sample holder 1200 includes tube array 1202 and lid array ²1204. Tube ²array 1202 includes wells 1206, well lips 1210, and tube lip 1214. Lid array ²1204 includes ²flanges 1208, flange lips 1212, and lid lip 1216.²

[00329] Sample holder 1200 includes tube array 1202 and lid array 1204. ²Tube array ²1202 includes a plurality of wells 1206. Wells 1206 extend downward from a ²base portion of ²tube array 1202. Each well 1206 is capable of receiving a reaction mixture and ²biological ²material that are to be tested. In the embodiment seen in FIGS. 38A-38B, wells ²1206 have a ²standard shape and configuration. In alternate embodiments, wells 1206 can be ²any shape that is ²capable of being tested. Lid array 1204 includes a plurality of flanges 1208. ²Flanges 1208 ²extend downward from a base portion of lid array 1204. Lid array 1204 can be ²placed on tube ²array 1202 to form sample holder 1200. Each flange 1208 on lid array 1204 can ²be placed in one ²well 1206 on tube array 1202 to form a first mechanical seal between tube ²array 1202 and lid ²array 1204.²

[00330] To strengthen the first mechanical seal between tube array 1202 and ²lid array ²1204, flanges 1208 and wells 1206 may include a plurality of protrusions to ²strengthen the seal²69²<DP=72>²CA 02926253 2016-04-01²WO 2015 / 054245 PCT / US2014 / 059487²between tube array 1202 and lid array 1204. Wells 1206 include well lips 1210 ²on an upper ²inside perimeter of each well 1206. Well lips 1210 can include a plurality of ²protrusions that run ²along the perimeter of wells 1206. Flanges 1208 include flange lips 1212 on a ²lower outer ²perimeter of each flange 1208. Flange lips 1212 can include a plurality of ²protrusions that run ²along the perimeter of flanges 1208. When flanges 1208 are placed in wells ²1206, flange lips ²1212 will come into contact with well lips 1210. The protrusions in both ²flange lips 12] 2 and ²well lips 1210 will fonu a first mechanical seal. The first mechanical seal is ²strengthened by the ²protrusions, as the protrusions make it harder for lid array 1204 to be ²removed from tube array ²1202.²

[00331] A second mechanical seal can be formed between the base portion of ²tube array ²1202 and the base portion of lid array 1204. The base portion of tube array ²1202 includes a ²recessed area surrounding wells 1206. In the embodiment shown in FIGS. 38A-²38B, the ²recessed area is shaped as a plurality of circles connected to one another ²down the middle. Lid ²array 1204 is designed to mimic this shape, so that when lid array 1204 is ²placed on tube array ²1202 it will fit in the recessed area on tube array 1202. This forms the ²second mechanical seal ²between tube array 1202 and lid array 1204. This also allows lid array 1204 to ²fit flush with tube ²array 1202, which makes it difficult for lid array 1204 to be removed from ²tube array 1202. In ²alternate embodiments, the recessed area in tube array 1202 and the shape of ²lid array 1204 can ²be any suitable shape.²

[00332] To strengthen the second mechanical seal between tube array 1202 ²and lid array ²1204, tube array 1202 and lid array 1204 may include a plurality of ²protrusions to strengthen the ²seal between the base portion of tube array 1202 and the base portion of lid ²array 1204. Tube ²array 1202 includes tube lip 1214 on an upper inside perimeter of the recessed ²area of tube array ²1202. Tube lip 1214 can include a plurality of protrusions that run along the ²perimeter of the ²recessed portion of tube array 1202. Lid array 1204 includes lid lip 1216 on ²an outer perimeter ²of the base portion of lid array 1204. Lid lip 1216 can include a plurality of ²protrusions that run ²along the perimeter of the base portion of lid array 1204. When lid array 1204 ²is placed on tube ²array 1202, lid lip 1216 will come into contact with tube lip 1214. The ²protrusions in both lid lip ²1216 and tube lip 1214 will form a second mechanical seal. The second ²mechanical seal is ²strengthened by the protrusions, as the protrusions make it harder for lid ²array 1204 to be ²removed from tube array 1202.²<DP=73>²CA 02926253 2016-04-01²WO 2015 / 054245 PCT / US2014 / 059487²

[00333] Sample holder 1200 is advantageous, as lid array 1204 can be placed ²securely on ²tube array 1202. A problem that exists with previous tube arrays is that the ²lid can easily come ²off of the tube array, either intentionally or accidently. This presents ²concerns with ²contamination of the materials in the tube array. To prevent this from ²happening, sample holder ²1200 provides a double-seal mechanism. The first seal is formed between ²flanges 1208 of lid ²array 1204 and wells 1206 of tube array 1202. A second seal is formed between ²a base portion ²of lid array 1204 and a base portion of tube array 1202. This double-seal ²mechanism is ²advantageous, as it is harder for lid array 1204 to be removed from tube array ²1202. Further, ²both the first mechanical seal and the second mechanical seal are strengthened ²by protrusions ²that engage lid array 1204 with tube array 1202, making it harder for lid ²array 1204 to be ²removed from tube array 1202. In alternate embodiments, the second seal could ²be an adhesive ²seal or any other suitable seal.²

[00334] Further, lid array 1204 is placed into a recessed area in the base ²portion of tube ²array 1202. This allows lid array 1204 to sit flush with tube array 1202 and ²make it difficult for ²lid array 1204 to be removed from tube array 1202, both intentionally and ²accidently. Making it ²this difficult for lid array 1204 to be removed from tube array 1202 is ²advantageous, as it ²alleviates concerns about contamination of the material in tube array 1202.²

[00335] FIG. 39A is a front view of sample holder 1200 including tube array ²1202 and lid ²array 1204. FIG. 39B is a perspective view of sample holder 1200 when lid ²array 1204 is placed ²on tube array 1202. FIG. 39C is a side view of sample holder 1200 when lid ²array 1204 is placed ²on tube array 1202. FIG. 39D is a top view of sample holder 1200. Sample ²holder 1200 ²includes tube array 1202 and lid array 1204. Tube array 1202 includes wells ²1206, well lips ²1210, and tube lip 1214. Lid array 1204 includes flanges 1208, flange lips ²1212, and lid lip ²1216.²

[00336] Sample holder 1200 includes tube array 1202 and lid array 1204. ²Tube array ²1202 includes a plurality of wells 1206. Wells 1206 extend downward from a ²base portion of ²tube array 1202. Each well 1206 is capable of receiving a reaction mixture and ²biological ²material that are to be tested. In the embodiment seen in FIGS. 39A-39D, wells ²1206 have an ²oblong oval shape with a first flat side and a second flat side. This shape ²allows the biological ²sample in wells 1206 to be read through both the first flat side and the ²second flat side.²71²<DP=74>²CA 02926253 2016-04-01²WO 2015 / 054245 PCT / US2014 / 059487²

[00337] Lid array 1204 includes a plurality of flanges 1208. Flanges 1208 ²extend ²downward from a base portion of lid array 1204. Lid array 1204 can be placed ²on tube array ²1202 to form sample holder 1200. Each flange 1208 on lid array 1204 can be ²placed in one well ²1206 on tube array 1202 to form a first mechanical seal between tube array ²1202 and lid array ²1204.²

[00338] To strengthen the first mechanical seal between tube array 1202 and ²lid array ²1204, flanges 1208 and wells 1206 may include a plurality of protrusions to ²strengthen the seal ²between tube array 1202 and lid array 1204. Wells 1206 include well lips 1210 ²on an upper ²inside perimeter of each well 1206. Well lips 1210 can include a plurality of ²protrusions that run ²along the perimeter of wells 1206. Flanges 1208 include flange lips 1212 on a ²lower outer ²perimeter of each flange 1208. Flange lips 1212 can include a plurality of ²protrusions that run ²along the perimeter of flanges 1208. When flanges 1208 are placed in wells ²1206, flange lips ²1212 will come into contact with wells lips 1210. The protrusions in both ²flange lips 1212 and ²well lips 1210 will form a first mechanical seal. The first mechanical seal is ²strengthened by the ²protrusions, as the protrusions make it harder for lid array 1204 to be ²removed from tube array ²1202.²

[00339] A second mechanical seal can be formed between the base portion of ²tube array ²1202 and the base portion of lid array 1204. The base portion of tube array ²1202 includes a ²recessed area surrounding wells 1206. In the embodiment shown in FIGS. 39A-²39D, the ²recessed area has a rectangular shape with rounded corners. Lid array 1204 is ²designed to mimic ²this shape, so that when lid array 1204 is placed on tube array 1202 it will ²fit in the recessed area ²on tube array 1202. This forms the second mechanical seal between tube array ²1202 and lid ²array 1204. This also allows lid array 1204 to fit flush with tube array 1202, ²which makes it ²difficult for lid array 1204 to be removed from tube array 1202.²

[00340] To strengthen the second mechanical seal between tube array 1202 ²and lid array ²1204, tube array 1202 and lid array 1204 may include a plurality of ²protrusions to strengthen the ²seal between the base portion of tube array 1202 and the base portion of lid ²array 1204. Tube ²array 1202 includes tube lip 1214 on an upper inside perimeter of the recessed ²area of tube array ²1202. Tube lip 1214 can include a plurality of protrusions that run along the ²perimeter of the ²recessed area of tube array 1202. Lid array 1204 includes lid lip 1216 on an ²outer perimeter of ²the base portion of lid array 1204. Lid lip 1216 can include a plurality of ²protrusions that run²72²<DP=75>²CA 02926253 2016-04-01²WO 2015 / 054245 PCT / US2014 / 059487²along the perimeter of the base portion of lid array 1204. When lid array 1204 ²is placed on tube ²array 1202, lid lip 1216 will come into contact with tube lip 1214. The ²protrusions in both lid lip ²1216 and tube lip 1214 will form a second mechanical seal. The second ²mechanical seal is ²strengthened by the protrusions, and the protrusions make it harder for lid ²array 1204 to be ²removed from tube array 1202.²

[00341] Sample holder 1200 is advantageous, as it is very difficult to ²remove lid array ²1204 from tube array 1202 either intentionally or accidently. First, there is ²a double-seal ²mechanism between lid array 1204 and tube array 1202. Second, there are ²protrusions on both ²lid array 1204 and tube array 1202 that make it difficult for them to be ²separated. Third, lid ²array 1204 sits flush with tube array 1202 so that it is very difficult for ²lid array 1204 to be ²removed from tube array 1202. Making it hard for lid array 1204 to be removed ²from tube array ²1202 is advantageous, as it alleviates concerns about contamination of the ²biological sample in ²tube array 1202.²

[00342] Sample holder 1200 is further advantageous because of the shape of ²wells 1206. ²Wells 1206 have a first flat side and a second flat side. This allows ²radiation to travel into and ²out of wells 1206 from either side. The flat sides of wells 1206 provide a ²wide basis for such ²radiation to travel into and out of the biological sample in wells 1206.²

[00343] FIG. 40A is a perspective view of sample holder 1200 when lid array ²1204 is ²placed on tube array 1202. FIG. 40B is a front view of sample holder 1200 when ²lid array 1204 ²is placed on tube array 1202. FIG. 40C is a bottom view of sample holder 1200. ²Sample holder ²1200 includes tube array 1202 and lid array 1204. Tube array 1202 includes ²wells 1206, well ²lips 1210, and tube lip 1214. Lid array 1204 includes flanges 1208, flange ²lips 1212, and lid lip ²1216. Also shown is adhesive 1220.²

[00344] Sample holder 1200 includes tube array 1202 and lid array 1204. ²Tube array ²1202 includes a plurality of wells 1206. Wells 1206 extend downward from a ²base portion of ²tube array 1202. Each well 1206 is capable of receiving a reaction mixture and ²biological ²material that are to be tested. In the embodiment seen in FIGS. 40A-40C, wells ²1206 have a ²hexagonal shape with a flat bottom. The hexagonal shape of the wells provides ²six different ²sides for each well 1206. This shape allows the biological material in each ²well 1206 to be read ²through any of the six sides.²73²<DP=76>²CA 02926253 2016-04-01²WO 2015 / 054245 PCT / US2014 / 059487²

[00345] Lid array 1204 includes a plurality of flanges 1208. Flanges 1208 ²extend ²downward from a base portion of lid array 1204. Lid array 1204 can be placed ²on tube array ²1202 to form sample holder 1200. Each flange 1208 on lid array 1204 can be ²placed in one well ²1206 on tube array 1202 to form a first mechanical seal between tube array ²1202 and lid array ²1204.²

[00346] To strengthen the first mechanical seal between tube array 1202 and ²lid array ²1204, flanges 1208 and wells 1206 may include a plurality of protrusions to ²strengthen the seal ²between tube array 1202 and lid array 1204. Wells 1206 include well lips 1210 ²on an upper ²inside perimeter of each well 1206. Well lips 1210 can include a plurality of ²protrusions that run ²along the perimeter of wells 1206. Flanges 1208 include flange lips 1212 on a ²lower outer ²perimeter of each flange 1208. Flange lips 1212 can include a plurality of ²protrusions that run ²along the perimeter of flanges 1208. When flanges 1208 are placed in wells ²1206, flange lips ²1212 will come into contact with well lips 1210. The protrusions in both ²flange lips 1212 and ²well lips 1210 will form a first mechanical seal. The first mechanical seal is ²strengthened by the ²protrusions, as the protrusions make it harder for lid array 1204 to be ²removed from tube array ²1202.²

[00347] A second seal can be formed between the base portion of tube array ²1202 and the ²base portion of lid array 1204. When lid array 1204 is placed on tube array ²1202, a bottom side ²of the base portion of lid array 1204 will come into contact with a top side ²of the base portion of ²tube array 1202. Adhesive 1220 can be placed between the bottom side of the ²base portion of lid ²array 1204 and the top side of the base portion of tube array 1202 to seal lid ²array 1204 onto tube ²array 1202. Adhesive 1220 can be any suitable adhesive and can be applied ²using any suitable ²process.²

[00348] Sample holder 1200 is advantageous, as it is very difficult to ²remove lid array ²1204 from tube array 1202 either intentionally or accidently. There is a ²double-seal mechanism ²between lid array 1204 and tube array 1202. The first seal is a mechanical ²seal and the second ²seal is an adhesive seal. There are also protrusions on both lid array 1204 ²and tube array 1202 ²that make it difficult for them to be separated. Making it hard for lid array ²1204 to be removed ²from tube array 1202 is advantageous, as it alleviates concerns about ²contamination of the ²biological sample in tube array 1202.²74²<DP=77>²CA 02926253 2016-04-01²WO 2015 / 054245 PCT / US2014 / 059487²

[00349] Sample holder 1200 is further advantageous because of the shape of ²wells 1206. ²Wells 1206 have a hexagonal shape with six distinct sides. This allows ²radiation to travel into ²and out of wells 1206 from any of the six sides. This allows three different ²light-emitting diodes ²to be positioned on three sides of wells 1206 and three photodetectors to be ²positioned on the ²remaining three sides of wells 1206. Each light-emitting diode can excite the ²biological sample ²in wells 1206 at a different radiation wavelength and each photodetector can ²detect different ²radiation wavelengths that are emitted from the biological sample. This allows ²three different ²fluorescent dyes to be tested out of wells 1206.²

[00350] While the invention has been described with reference to an ²exemplary ²embodiment(s), it will be understood by those skilled in the art that various ²changes may be ²made and equivalents may be substituted for elements thereof without departing ²from the scope ²of the invention. In addition, many modifications may be made to adapt a ²particular situation or ²material to the teachings of the invention without departing from the ²essential scope thereof. ²Therefore, it is intended that the invention not be limited to the particular ²embodiment(s) ²disclosed, but that the invention will include all embodiments falling within ²the scope of the ²appended claims.²

Claims

<DP=1>²We claim:²1. A portable testing device comprising:²a housing with an integrated touchscreen display comprising a receptacle²configured to receive a sample holder containing a biological sample and ²reagent²mixture;²an optical assembly positioned in the housing, wherein the optical assembly is²configured to amplify and detect a signal from the biological sample and ²reagent mixture²in the sample holder, and wherein the optical assembly comprises:²a sample block configured to receive the sample holder, wherein the sample ²block²comprises:²a plurality of cavities that are shaped to receive the sample holder;²a first housing portion positioned on a first side of the sample block, ²wherein the²first housing portion comprises:²a first excitation filter;²a first emission filter;²a first plurality of light-emitting diodes positioned on a side of the first²excitation filter opposite the plurality of cavities; and²a first plurality of photodetectors positioned on a side of the first emission²filter opposite the plurality of cavities; and²a second housing portion positioned on a second side of the sample block,²opposite the first side, wherein the second housing portion comprises:²a second excitation filter;²a second emission filter;²a second plurality of light-emitting diodes positioned on a side of the second²excitation :filter opposite the plurality of cavities; and²a second plurality of photodetectors positioned on a side of the second²emission filter opposite the plurality of cavities;²an electronic assembly configured to receive data from the optical assembly ²and²transmit the received data to be displayed on the touchscreen display; and²a power supply in the housing to power the portable testing device.²76²Date Recue / Date Received 2023-02-14²<DP=2>²2. The portable testing device of claim 1, wherein the housing of the ²portable testing ²device further comprises:²an integrated handle to allow for transport of the device; and a lid over the ²receptacle that is movable between an open and closed position.²3. The portable testing device of claim 1, and further comprising:²a machine readable code reader in the housing for reading a machine readable²code.²4. The portable testing device of claim 1, wherein the receptacle includes ²a plurality ²of cavities that are configured to receive a tube array.²5. The portable testing device of claim 1, wherein the receptacle includes ²one cavity ²that is configured to receive a card.²6. The portable testing device of claim 5, wherein the card comprises: a ²body portion defining a shape of the card;²a plurality of wells that are integrally formed with the body portion, wherein ²each ²well has a first cavity, a second cavity, and a channel connecting the first ²cavity to the second cavity;²a first permanent seal covering the channel and the second cavity of each of ²the ²plurality of wells;²a removable seal covering the first cavity of each of the plurality of wells ²that can ²be removed to provide access to each of the plurality of wells; and²a second permanent seal with a removable backing attached to the body portion ²of ²the card sample holder, wherein the removable backing can be removed and the ²second ²permanent seal can be placed on the body portion of the card to seal the first ²cavity of ²each of the plurality of wells.²77²Date Recue / Date Received 2023-02-14²<DP=3>²7. The portable testing device of claim 1, wherein the optical assembly ²further ²comprises:²a heating component to heat the biological sample and reagent mixture in ²the sample holder.²8. A method of analyzing a biological sample and reagent mixture in a ²portable ²testing device that includes a housing and a touchscreen display, a receptacle ²in which a ²sample holder containing a biological sample and reagent mixture can be ²placed, an ²optical assembly positioned in the housing and having one or more excitation ²filters and ²one or more emission filters, an electronic assembly configured to receive ²data from the ²optical assernbly and transrnit data for display on the touchscreen display, ²and a power ²supply in the housing to power the portable testing device, the method ²comprising:²preparing a biological sample and reagent mixture for testing and placing the²biological sample and reagent mixture in a sample holder;²placing the sample holder in an opening on the portable testing device; ²beginning an excitation and detection test sequence to analyze the biological ²sample and reagent mixture; and²collecting data in real-time from the excitation and detection test sequence, ²wherein preparing a biological sample and reaction mixture for testing further ²²includes:²collecting a field sample;²preparing the field sample outside of the portable testing device to form a ²prepared sample;²placing the prepared sarnple in a first tube that is positioned on a first ²aperture on ²the portable testing device;²transferring the prepared sample from the first tube into a second array of ²tubes ²that are positioned in a second plurality of apertures on the portable testing ²²device,²wherein the second array of tubes contain a reaction buffer; and ²transferring the prepared sample and the reaction buffer from the second array ²of²78²Date Recue / Date Received 2023-02-14²<DP=4>²tubes into a third array of tubes that are positioned in a third plurality of ²apertures on the portable test device, wherein the third array of tubes ²contain a master mix.²9. The method of claim 8, and further comprising:²turning on the portable testing device;²inputting required assay and sample traceability information into a test setup²menu in the portable testing device;²selecting the test protocol in the portable testing device; and²pre-heating the portable testing device in accordance with the selected test²protocol.²10. The method of claim 8, and further comprising:²turning on the portable testing device to pre-heat the portable testing ²device; and ²scanning a machine readable code with a machine readable code reader, wherein ²the machine readable code contains testing parameters and sarnple²traceability information.²11. The method of claim 8, and further comprising:²displaying the collected data real-time on a tablet computer;²logging and storing the collected data for retrieval or transfer;²monitoring the collected data for threshold activity; and²signaling a positive, a negative, or an indeterminate outcome at the ²completion of²the test.²12. A portable testing device for analyzing biological samples, the ²portable testing²device comprising:²a housing with an opening on a top side of the housing for an array of tubes;²a sample preparation area in the housing, the sample preparation area ²comprising:²79²Date Recue / Date Received 2023-02-14²<DP=5>²a first aperture that is capable of holding a tube containing a ²biological sample;²a first plurality of apertures positioned in a row that are capable of ²holding an array of tubes; and²a second plurality of apertures positioned in a row that are capable of ²holding an array of tubes;²a cradle on a top side of the housing in which a tablet computer can be ²positioned; and²an optical assembly in the housing to excite and detect the biological ²sample, wherein the optical assembly comprises:²a heating component positioned below the opening in the housing, the heating ²component comprising a plurality of apertures in which the array of tubes ²can be positioned;²an upper optical assembly with a first plurality of light-emitting diodes on a ²first ²side of the heating component and a second plurality of light-emitting²diodes on a second side of the heating component; and²a lower optical assembly with a first plurality of photodiodes positioned in a ²row ²and a second plurality of photodiodes positioned in a row, wherein the ²first plurality of photodiodes and the second plurality of photodiodes are ²positioned underneath the heating component.²13. The portable testing device of claim 12, and further comprising: ²a lid positioned over the opening in the housing.²14. The portable testing device of claim 12, wherein the heating component ²is a heat ²block.²15. The portable testing device of claim 14, wherein the heat block is ²capable of ²heating from an ambient temperature to about 95 degrees Celsius.² Date Recue / Date Received 2023-02-14²<DP=6>²16. The portable testing device of claim 12, wherein the first plurality of ²light-²emitting diodes are positioned in a row.²17. The portable testing device of claim 12, wherein the first plurality of ²light-²ernitting diodes are blue light-emitting diodes.²18. The portable testing device of claim 12, wherein the second plurality ²of light-²emitting diodes are positioned in a row.²19. The portable testing device of claim 12, wherein the second plurality ²of light-²emitting diodes are amber light-emitting diodes.²20. The portable testing device of claim 12, and further comprising:²a first filter positioned between the first plurality of light-emitting diodes ²and the²heating component;²a second fdter positioned between the second plurality of light-emitting ²diodes²and the heating component;²a third filter positioned between the first plurality of photodiodes and the ²heating²cornponent; and²a fourth filter positioned between the second plurality of photodiodes and the²heating component.²21. The portable testing device of claim 20, wherein:²the first filter is a 490 nanometer filter.²the second filter is a 580 nanometer filter.²the third filter is a 610 nanometer filter.²the fourth filter is a 520 nanometer filter.²22. The portable testing device of claim 12, and further comprising: ²a first support structure on a first side of the heating component in which ²the first²81²Date Recue / Date Received 2023-02-14²<DP=7>²plurality of light-emitting diodes can be positioned; and²a second support structure on a second side of the heating component in²which the second plurality of light-emitting diodes can be positioned.²23. The portable testing device of claim 22, wherein the first support ²structure ²extends from the heating component to the first plurality of light-emitting ²diodes to ²contain light from the first plurality of light-emitting diodes in the upper ²optical ²assembly.²24. The portable testing device of claim 22, wherein the second support ²structure ²extends from the heating component to the second plurality of light-emitting ²diodes to ²contain light from the second plurality of light-emitting diodes in the upper ²optical ²assembly.²25. The portable testing device of claim 12, and further comprising:²a spacer positioned between the fffst and second plurality of photodiodes and ²the ²heating component; and²a gasket positioned between the spacer and the heating component to form a ²seal ²between the spacer and the heating component.²26. The portable testing device of claim 12, and further comprising:²a power assembly in the housing comprising:²a battery;²an AC power adapter connected to the battery;²a power board to consolidate and distribute power in the portable testing²device; and²a power jack connected to the power board.²27. The portable testing device of claim 26, wherein a tablet computer can ²be ²connected to the power jack.²82²Date Recue / Date Received 2023-02-14²<DP=8>²28. A portable testing device for analyzing biological samples, the ²portable testing ²device comprising:²a housing with an opening on a top side of the housing for an array of²tubes; an optical assembly in the housing, the optical assernbly comprising:²a heating component positioned below the opening in the housing, ²the heating component comprising a plurality of apertures in which the ²array of tubes can be positioned;²an upper optical assembly with a first plurality of light-emitting diodes on ²a first side of the heating component and a second plurality of ²light-emitting diodes on a second side of the heating component; ²and²a lower optical assembly with a first plurality of photodiodes positioned in ²a row and a second plurality of photodiodes positioned in a row, ²wherein the first plurality of photodiodes and the second plurality ²of photodiodes are positioned underneath the heating component; ²and²a sample preparation area in the housing comprising: ²a first aperture;²a first plurality of apertures positioned in a row; and a²second plurality of apertures positioned in a row.²29. A card for use in a portable testing device that includes a housing and ²a ²touchscreen display, a receptacle in which a sample holder containing a ²biological sample ²and reagent mixture can be placed, an optical assembly positioned in the ²housing and ²having a heating component, light-emitting diodes, photodetectors, one or more ²²excitation filters and one or more emission filters, an electronic assembly ²configured to ²receive data from the optical assembly and transmit data for display on the ²touchscreen ²display, and a power supply in the housing to power the portable testing ²device, the card ²comprising:²83²Date Recue / Date Received 2023-02-14²<DP=9>²a body portion defining a shape of the card;²a plurality of wells that are integrally formed with the body portion, wherein ²each ²well has a first cavity, a second cavity, and a channel connecting the first ²cavity to the second cavity;²a first permanent seal covering the channel and the second cavity of each of ²the ²plurality of wells;²a removable seal covering the first cavity of each of the plurality of wells ²that can ²be removed to provide access to each of the plurality of wells; and²a second permanent seal with a removable backing attached to the body portion ²of ²the card sample holder, wherein the removable backing can be removed ²and the second permanent seal can be placed on the body portion of the ²card to seal the first cavity of each of the plurality of wells.²30. The card of claim 29, wherein the second cavity of each of the ²plurality of wells ²contains a reaction mixture.²31. The card of claim 30, wherein a biological sample can be placed in the ²first cavity ²of each of the plurality of wells.²32. The card of claim 31, wherein after the biological sample is placed in ²the first ²cavity of each of the plurality of wells it can travel through the channel ²into the second ²cavity to mix with the reaction mixture.²84²Date Recue / Date Received 2023-02-14²