Systems and methods for independent thermal protocols on a thermocycler system

Abstract

A system for performing biological reactions is provided. The system includes a set of sample blocks configured to have at least a first and a second sample block, where each sample block is configured to receive a biological sample. The system further includes a thermal insulation material disposed around each sample block and a plurality of heating / cooling devices including at least a first set and a second set of heating / cooling devices. The first set of heating / cooling devices is disposed to correspond to the first sample block, and the second set of heating / cooling devices is disposed to correspond to the second sample block. The system includes a control system configured to initiate biological reactions in a first biological sample of the first sample block and the second biological sample of the second sample block. The system includes a detection system configured to detect biological reactions of the biological samples.

Description

Matter No. TP389518WO1SYSTEMS AND METHODS FOR INDEPENDENT THERMAL PROTOCOLS ON A THERMOCYCLER SYSTEMCROSS REFERENCE TO RELATED APPLICATION

[0001] This application claims priority to U.S. Provisional Patent Application No.63 / 761 ,482 filed February 21, 2025, U.S. Provisional Application No. 63 / 895,659 filed October 8, 2025, and U.S. Provisional Application No. 63 / 963,197 filed January 19, 2026. The entire contents of each of which are incorporated herein by reference.BACKGROUND

[0002] Testing of biological or chemical samples often requires a device for repeatedly subjecting multiple samples though a series of temperature cycles. Such devices are described as thermocyclers or thermocycling devices and are used to generate specific temperature cycles, i.e. to set predetermined temperatures in partitions and to maintain predetermined intervals of time, called protocols. Thermocyclers include sample blocks with several recesses arranged in a regular pattern to receive microtubes holding biological samples. Thermocyclers include heating and cooling devices for heating and cooling the partitions based on the type of test protocol desired.

[0003] For example, a type of protocol is a PCR reaction. For PCR, a biological sample is put into individual partitions and the temperature cycles necessary to perform the PCR reaction are executed. A cycle of this kind is repeated several times, leading to amplification of a predetermined DNA sequence. The annealing temperature, at which the primer is added, has a powerful influence on the result. However, the elongation temperature too can have beneficial or adverse effects on the result. At a higher elongation temperature, the addition of the bases is accelerated, with the probability of errors increasing with higher temperature. One way to a PCR result may be improved is by determining the optimal denaturing, annealing temperature, and elongation temperatures of a PCR reaction.

[0004] Such a temperature cycle comprises the heating of the reaction mixture to the denaturing temperature, which usually lies in the range 90°-95° C., cooling to the annealingMatter No. TP389518WO1temperature, which is usually in the range 40°-60° C. and heating to the elongation temperature, which is usually in the range70°-75° C. To determine the optimal temperature with conventional devices, these parameters cannot be varied in one test series. Several test series are required would need to be performed either consecutively in one thermocycling device or simultaneously in several thermocycling devices.

[0005] Further, in some cases, a user may want to combine several different experiments into one run in a thermocycler to save time and effort. For example, a user may want to perform a standard PCR protocol with 40 cycles, while simultaneously performing a fast PCR protocol, genotyping protocol, and also running a thermal melt protocol.

[0006] As such, a thermocycler for performing more than one protocol simultaneously is desired.SUMMARY

[0007] In one exemplary embodiment, a system for performing biological reactions is provided. The system includes a set of sample blocks configured to have at least a first and a second sample block, where each sample block is configured to receive a biological sample. The system further includes a thermal insulation material disposed around each sample block and a plurality of heating / cooling devices including at least a first set and a second set of heating / cooling devices. The first set of heating / cooling devices is disposed to correspond to the first sample block, and the second set of heating / cooling devices is disposed to correspond to the second sample block. The system includes a control system configured to initiate biological reactions in a first biological sample of the first sample block and the second biological sample of the second sample block. The system includes a detection system configured to detect biological reactions of the biological samples. The detection system is configured to detect, take images for, and / or collect data from, samples on at least both of the sample blocks simultaneously.

[0008] In another exemplary embodiment, a system for performing biological reactions is provided. The system includes a set of sample blocks configured to have at least a first and a second sample block, where each sample block is configured to receive biological samples. The first sample block is configured to receive a first biological sample and the second sample blockMatter No. TP389518WO1is configured to receive a second biological sample. The system further includes a thermal insulation material disposed around each sample block, and a plurality of heating / cooling devices. The plurality of heating / cooling devices includes at least a first set and a second set of heating / cooling devices, where the first set of heating / cooling devices is disposed to correspond to the first sample block, and the second set of heating / cooling devices is disposed to correspond to the second sample block. Further, the first set of heating / cooling devices is configured to run a first thermal protocol and the second set of heating / cooling devices is configured to run a second thermal protocol, where the first and second thermal protocols are different.

[0009] In yet another exemplary embodiment, a method of running at least two thermal protocols on a biological sample in a set of sample blocks with at least two sample blocks is provided. The method includes loading a first biological sample on a first sample block and a second biological sample on a second sample block, where the first and second sample blocks are thermally isolated by a thermal insulation material. The method further includes initiating a biological reaction in the first biological sample of the first sample block using a first set of heating / cooling devices controlled by a first thermal protocol, and initiating a biological reaction in the second sample block using a second set of heating / cooling devices controlled by a second thermal protocol, where the first and second thermal protocols are different.DESCRIPTION OF THE FIGURES

[0010] FIG. 1 illustrates a thermocycler system with independent thermal zone according to various embodiments described herein.

[0011] FIG. 2 is a block diagram that illustrates a thermocycler instrument, upon which embodiments of the present teachings may be implemented.

[0012] FIG. 3 illustrates an exemplary optics system that can be used to image the sample support device according to embodiments of the present teachings.

[0013] FIG. 4 illustrates an exemplary computing system that various embodiments described herein may be implemented.Matter No. TP389518WO1

[0014] FIG. 5A illustrates a graph of temperature of different zones of a previous thermocycler.

[0015] FIG. 5B illustrates zones of a sample block corresponding to the temperature graph of FIG. 5A.

[0016] FIGS. 6A-6M illustrate a plurality of sample blocks of a set of sample blocks running independent thermal protocols according to various embodiments described herein.

[0017] FIGS. 7A and 7B illustrate configurations of sample blocks of a set of sample blocks according to various embodiments of the present teachings.

[0018] FIG. 8 illustrates an exemplary flowchart of a method of biological analysis according to various embodiments of the present teachings.

[0019] FIGS. 9 A and 9B illustrate a set of sample blocks according to various embodiments described herein.

[0020] FIGS. 10A and 10B illustrate various configurations of a sample block configured for gradient temperatures according to various embodiments described herein.

[0021] FIG. 11 illustrates an exemplary schematic of a thermocycler system configured for gradient temperatures according to various embodiments described herein.

[0022] FIG. 12A illustrates six zones of a sample block according to various embodiments described herein. FIG. 12B is a chart of the varying temperatures to create a temperature gradient in each of the zones according to various embodiments described herein.

[0023] FIG. 13 illustrates thermal block water drainage path according to various embodiments described herein.

[0024] FIGS. 14A and 14B illustrate sample block well geometry according to various embodiments described herein.

[0025] FIGS. 15A and 15B illustrate thermal block assembly with multiple sample blocks and each with its own heatsink base, according to various embodiments described herein.Matter No. TP389518WO1

[0026] FIG. 16 illustrates a block clamp disposed across the middle section of a sample block, according to various embodiments.DETAILED DESCRIPTION

[0027] To provide a more thorough understanding of the present invention, the following description sets forth numerous specific details, such as specific configurations, parameters, examples, and the like. It should be recognized, however, that such description is not intended as a limitation on the scope of the present invention but is intended to provide a better description of the exemplary embodiments.

[0028] Furthermore, as used herein, thermal cycling may include using a thermocycler, isothermal amplification, thermal convention, infrared mediated thermal cycling, or helicase dependent amplification, for example.

[0029] According to various embodiments, detection of a target may be, but is not limited to, fluorescence detection, detection of positive or negative ions, pH detection, voltage detection, or current detection, alone or in combination, for example.

[0030] Also, as mentioned above, various samples may have different optimal amplification temperatures. More specifically, some samples may have different optimal denaturing temperatures, optimal annealing temperatures, and optimal elongation temperatures for the PCR reaction. Thus, providing a system to accurately determine optimal annealing temperatures is needed. Further, providing a system to carry out different types of experiment protocols with a plurality of different samples at different temperatures and time intervals simultaneously is needed.

[0031] A biological analysis system according to various embodiments described herein can have a plurality of different temperature zones that can be controlled independently. In this way, a user may be able to run more efficient experiments, saving time, and get more accurate results.

[0032] According to various embodiments, the biological analysis system can include a thermal block assembly comprising sample block, heat / cool elements, and heatsink. The thermal blockMatter No. TP389518WO1assembly may not include seal material other than air-gap between different temperature zones. The thermal block assembly may be configured to provide enhanced water management features to dissipate condensation accumulated around the heatsink. Additionally, the well geometries of the sample block is configured with controlled material thickness, shape, and gradient base structures to improve thermal uniformity, thereby enhancing the overall thermal performance the thermal block.

[0033] In various embodiments, the devices, instruments, systems, and methods described herein may be used to detect one or more types of target molecules, or biological components of interest. These target molecules may include, but are not limited to, DNA sequences, RNA sequences, genes, oligonucleotides, proteins, or cells (e.g., circulating tumor cells), the latter two of which have been converted to molecules amenable to PCR amplification, and example of which is using the proximity ligation assay. In various embodiments, such target molecules may be used in conjunction with various PCR, qPCR, and / or dPCR methods and systems in applications such as fetal diagnostics, multiplex dPCR, viral detection and quantification standards, genotyping, sequencing validation, mutation detection, detection of genetically modified organisms, rare allele detection, copy number variation, quantification of genetic material, quantification of proteins, assessment of viral particles containing intact copies of genetic material of interest, and proximity ligation assays.

[0034] According to various embodiments of the present disclosure, partitions may be, but are not limited to, recesses, wells, droplets, cavities, indentations, spots, reaction chambers, sample retainment regions, or through-holes, for example, located in a substrate. Partitions may be any structure that allows a sample to be independent of other samples located on the substrate.Thermocyclers include sample blocks with several recesses arranged in a regular pattern to receive biological samples.

[0035] FIG. 1 illustrates an exemplary thermocycler system 100 with independent thermal zones according to various embodiments described herein.

[0036] Thermocycler system 100 includes set of sample blocks 104. In this embodiment, set of sample blocks 104 includes 12 sample blocks. It should be recognized that various embodimentsMatter No. TP389518WO1of the present teachings may include a plurality of individual sample blocks. Set of sample blocks 104 may include at least two sample blocks in various embodiments described herein.

[0037] Thermal insulation material 102 is configured to surround each of the sample blocks in set of sample blocks 104. Thermal insulation material 102 is configured to seal each sample block so each sample block is thermally isolated. In this way, the sample blocks may be independently heated and cooled based on the protocol assigned for that particular sample block. Other sample blocks may run other protocols with no or minimal thermal interference from adjacent sample blocks. In some embodiments, thermocycler system 100 may not include and sample blocks 104 are separated by air gaps. The air gaps are configured to substantially prevent or reduce heat transfer between the sample blocks such that each sample block can be operated independently.

[0038] According to some embodiments, the distance between the adjacent sample blocks is less than 5 mm including ranges of 0 to 1mm, 1 to 2 mm, 2 to 3 mm, 3 to 4 mm, 4 to 5 mm and all ranges and values therebetween. In some embodiments, the distance between the adjacent sample blocks is about 1 mm.

[0039] For example, a sample block in set of sample blocks 104 may run a standard curve PCR protocol, while an adjacent block runs a thermal melt protocol. Other sample blocks in set of sample blocks 104 may run other protocols, such as a fast PCR protocol, comparative Ct protocol, or a genotyping protocol. Thermal insulation material 102 thermally isolates each sample block in set of sample blocks 104 so that the various temperatures at various time intervals can independently run. In some embodiments, the set of sample blocks 104 can be configured to receive a single sample holder (or sample plate) therein. Within the single sample holder or sample plate, samples corresponding to each of sample blocks can be heated or cooled according to independent protocols from the set of sample blocks 104.

[0040] Thermal insulation material 102 may be in a frame apparatus that is configured to go over set of sample blocks 104 according to various embodiments described herein. Thermal insulation material goes around each of the sample blocks so that thermal insulation material 102 is positioned between each of the walls of each of the sample blocks of the set of the sampleMatter No. TP389518WO1blocks 104. Thermal insulation material 102 is configured to minimize interference with thermal uniformity between adjacent sample blocks.

[0041] Thermal insulation material 102 is configured to have a high thermal resistance and a low thermal conductivity allowing for independent thermal control of each sample block. In various embodiments, thermal insulation material 102 has a thermal resistance of less than 0.02 W / mK. In various embodiments, thermal insulation material 102 may be an aerogel or a polyurethane. In other embodiments, thermal insulation material 102 is a silicone gasket.

[0042] Thermocycler system 100 may also include block sensors 106. Each sample block of set of sample blocks 104 may include a block sensor 106 so that temperature of each block may be measured to provide feedback on the real-time temperature of the sample block. In various embodiments, block sensors 106 may be used in conjunction with heat sink sensors 118 to get a more accurate measurement of temperature of the sample block 104. Block sensors 106 and heat sink sensors 118 allow for measurement of the sample block temperature set point, the actual temperature of sample blocks after heating and cooling, and can provide measurements to determine the current needed to the heating / cooling devices to run a thermal protocol. Using both heat sink sensors 118 and block sensors can help determine the temperatures below and above the heating / cooling modules.

[0043] Thermocycler system may also include a set of heating / cooling modules 110. In various embodiments, set of heating / cooling modules 110 are thermoelectric coolers. The number of heating / cooling modules in the set of heating / cooling modules 110 correspond to the number of sample blocks in the set of sample blocks 104. Each heating cooling module 110 is configured to heat / cool the corresponding sample block.

[0044] In various embodiments described herein, oversized heating / cooling modules 110 may be used to improve thermal uniformity. In other words, the footprint area of each heating / cooling module may be larger than the footprint area of its corresponding sample block. In this way, heat loss on the edges of the sample block may be reduced to improve thermal uniformity.

[0045] In various embodiments described herein, heating / cooling modules may be oversized compared to the sample block area in one, two, or three dimensions. This can still provideMatter No. TP389518WO1improved thermal uniformity on the fringes. The bigger size of the heating / cooling modules provide continued heating beyond the sample block, which prevents heat loss on the edges. In various configurations of the thermocycler, air movement may also contribute to improving thermal uniformity. In various embodiments of the present teachings, the heating / cooling module area may be 5-10% larger than the area of a sample block.

[0046] To improve thermal uniformity, a first interface material 108 may be disposed between set of sample blocks 104 and set of heating / cooling modules 110. First interface material 108 may provide better contact between various components, such as the sample block and heating / cooling modules and / or heat sink, in the thermocycler system to improve thermal uniformity.

[0047] According to various embodiments described herein, heat spreader 112 may be optionally included to further increase thermal uniformity. Heat spreader 112 may be a good conductor of heat to improve heat transfer to components in the thermocycler system. Heat spreader 112 may be disposed between set of heating / cooling modules 110 and heat sink 116. Heat spreader 112 may be a copper plate according to various embodiments.

[0048] Second interface material 114 may also be disposed between the heat spreader 112 and heatsink 116. Second interface material 114 is configured to also improve thermal uniformity of each sample block. Similar to first interface material 108, second interface material 114 may provide improve contact between various components in the thermocycler system to improve thermal uniformity.

[0049] FIG. 2 illustrates a typical PCR instrument 200. Various embodiments described herein may utilize some or all of the functions of the exemplary PCR instrument 200.

[0050] In various embodiments, the devices, instruments, systems, and methods described herein may be used to detect one or more types of biological components of interest. These biological components of interest may be any suitable biological target including, but are not limited to, DNA sequences (including cell-free DNA), RNA sequences, genes, oligonucleotides, molecules, proteins, biomarkers, cells (e.g., circulating tumor cells), or any other suitable targetbiomolecule.Matter No. TP389518WO1

[0051] In various embodiments, such biological components may be used in conjunction with various PCR, qPCR, and / or dPCR methods and systems in applications such as fetal diagnostics, multiplex dPCR, viral detection and quantification standards, genotyping, sequencing validation, mutation detection, detection of genetically modified organisms, rare allele detection, and copy number variation. Embodiments of the present disclosure are generally directed to devices, instruments, systems, and methods for monitoring or measuring a biological reaction for a large number of small volume samples. As used herein, samples may be referred to as sample volumes, or reactions volumes, for example.

[0052] While generally applicable to quantitative polymerase chain reactions (qPCR) where a large number of samples are being processed, it should be recognized that any suitable PCR method may be used in accordance with various embodiments described herein. Suitable PCR methods include, but are not limited to, digital PCR, allele-specific PCR, asymmetric PCR, ligation-mediated PCR, multiplex PCR, nested PCR, qPCR, genome walking, and bridge PCR, for example.

[0053] Thermocycler instrument 200 may include control system 220 to control the functions of the detection system, heated cover, and thermal block assembly. Control system 220 may be accessible to an end user through user interface 222 of thermocycler instrument 200 in FIG. 2. Also, a computing system 400, as depicted in FIG. 4, may serve as to provide the control the function of thermocycler instrument 200 in FIG. 2, as well as the user interface function.Additionally, computing system 400 of FIG. 4 may provide data processing, display and report preparation functions. All such instrument control functions may be dedicated locally to the thermocycler instrument, or computer system 400 of FIG. 4 may provide remote control of part or all of the control, analysis, and reporting functions, as will be discussed in more detail subsequently. Instrument control functions may be provided on the instrument, accessible through a graphical user interface (GUI). Further, in various embodiments, data analysis controls may be provided on the instrument, accessible through a GUI. In various embodiments, data analysis of the results of the system may be performed at a local computer system, connected to the instrument. In other embodiments, data analysis functions may be accessed over a network by a user. Data from performing biological reactions by the system, according to various embodiments, may be stored on a server system to be accessible by users over a network.Matter No. TP389518WO1

[0054] As mentioned above, an instrument that may be utilized according to various embodiments, but is not limited to, is a thermocycler instrument. FIG. 2 is a block diagram that illustrates a thermocycler instrument 200, upon which embodiments of the present teachings may be implemented. Thermocycler instrument 200 may include a heated cover 210 that is placed over a plurality of samples 212 contained in a sample support device (not shown). In biological analysis systems according to various embodiments, a heated cover may not be included.

[0055] In various embodiments, a sample support device may be a sample support device, or glass or plastic slide with a plurality of partitions, which partitions have a cover between the partitions and heated cover 210. Some examples of a sample support device may include, but are not limited to, a sample support device according to embodiments of the present teachings, a multi-well plate, such as a standard microtiter 96-well, a 384-well plate, or a microcard, or a substantially planar support, such as a glass or plastic slide. The partitions in various embodiments of a sample support device may include depressions, indentations, ridges, and combinations thereof, patterned in regular or irregular arrays formed on the surface of the substrate.

[0056] Various embodiments of thermocycler instruments include a sample block 214, elements for heating and cooling 216, a heat exchanger 218, control system 220, and user interface 222. Various embodiments of a thermal block assembly according to the present teachings comprise components 214-218 of thermocycler instrument 200 of FIG. 2.

[0057] According to other embodiments of the present teachings, the thermal block assembly includes thermal electric devices such that substantial uniform heat transfer is provided throughout the thermal block assembly.

[0058] As mentioned above, detection of the target may include fluorescence detection, detection of positive or negative ions, pH detection, voltage detection, or current detection, for example. As such, a detection system, according to various embodiments described herein may include an optical system, an electrical detection system, an ion detection system, an illumination system, or a pH detection system, for example. According to various embodiments, the detection system may be integrated in the sample support device.Matter No. TP389518WO1

[0059] Referring to FIG. 3, as mentioned above, a system 300 may be used optically view, inspect, detect, or measure one or more biological targets contained in the partitions. Various configurations of an optical system 300 may be used to detect the various biological reactions run on the thermocycling system. Further, parallel optical systems similar to system 300 may be needed to detect the plurality of biological reactions based on the plurality of protocols run on a single thermocycler according to various embodiments described herein. In various embodiments of the present teachings, general system 300 may include multiple photodectors.

[0060] According to embodiments, system 300 is configured to detect, take images for, and / or collect data from, samples on the set of sample blocks simultaneously. System 300 can be configured to detect, take images for, and / or collect data from, samples on the set sample blocks concurrently throughout a PCR process or a melt detection process.

[0061] In some embodiments, the set of sample blocks 104 can be configured to receive a single sample support device 308 (e.g., sample holder, sample plate, or sample slide) therein. Within the single sample support device, samples corresponding to each of sample blocks can be heated or cooled according to independent protocols from the set of sample blocks 104. According to some embodiments, multiple blocks of the set of sample blocks 104 can be configured to receive a single sample support device 308 (e.g., sample holder, sample plate or sample slide).

[0062] Partitions can be included in a sample support device 308, which may be contained in a carrier. System 300 comprises an optical head or system 302. System 300 may further comprise a controller, computer, or processor 704 configured, for example, to operate various components of optical system 302 or to obtain and / or process data provided by system 300. For example, processor 404 (FIG. 4) may be used to obtain and / or process optical data provided by one or more photodetectors of optical system 302. In other embodiments, processor 404 may transmit data to one or more computing systems for further processing. Data may be transmitted from processor 404 to the computing systems, via a network, in some embodiments.

[0063] In certain embodiments, system 300 further comprises a thermal control system 306 comprising, for example, a thermocycler configured to perform a PCR procedure or protocol on at least some of the samples contained in sample support device 308. Systems 302, 306 may combined or coupled together into a single unit, for example, in order to perform a qPCR and / orMatter No. TP389518WO1a biological testing procedure or protocol on at least some of the samples contained in sample support device 308. In such embodiments, computer 304 may be used to control systems 302, 306 and / or to collect or process data provided or obtained by either or both systems 302, 306. In other embodiments, system 302 and system 306 may be independent units.

[0064] In certain embodiments, optical system 302 comprises a light source 310 and an associated excitation optic system 312 configured to illuminate at least some of samples contained in the partitions of sample support device 308. Excitation optical system 312 may include one or more lenses 314 and / or one or more filters 316 for conditioning light directed to the samples. Optical system 302 may further comprise a photodetector 320 and an associated emission optic system 322 configured to receive optical data emitted by at least some of samples contained in the partitions of sample support device 308. For example, when system 300 is configured to perform a qPCR protocol, the sample may contain fluorescent dyes that provide a fluorescent signal that varies according to an amount of target nucleotide sequence contained in various of the through-holes, wells, and / or chambers of sample support device 308. Emission optical system 322 may include one or more lenses 324 and / or one or more filters 326 for conditioning light directed to the samples.

[0065] According to various embodiments, optical system 302 may have a focal length of 13 mm and a working distance of 60 mm, where the working distance of the distance from the sample support device to the camera lens. Furthermore, in various embodiments, the overall system F-number is less than or equal to 3.

[0066] In the illustrated embodiment of FIG. 3, excitation / emission optical systems 312, 322 both comprise one or more common optical elements. For example, excitation / emission optical systems 312, 322 both comprise a beamsplitter 330 that reflects excitation light and transmits emission light from the samples to photodetector 320. In certain embodiments, excitation / emission optical systems 312, 322 both comprise a field lens (not shown) disposed between beamsplitter 330 and sample support device 308, which may be used improve optical performance, for example, to provide more even illumination and reading of light to and from the samples contained in sample support device 308. In certain embodiments, for example where even illumination is less critical, the common field lens may be omitted, as shown in theMatter No. TP389518WO1illustrated embodiment of FIG. 3. Omission of the field lens may help to reduce the size and complexity of optical system 302.

[0067] Those skilled in the art will recognize that the operations of the various embodiments may be implemented using hardware, software, firmware, or combinations thereof, as appropriate. For example, some processes can be carried out using processors or other digital circuitry under the control of software, firmware, or hard-wired logic. (The term “logic” herein refers to fixed hardware, programmable logic and / or an appropriate combination thereof, as would be recognized by one skilled in the art to carry out the recited functions.) Software and firmware can be stored on computer-readable media. Some other processes can be implemented using analog circuitry, as is well known to one of ordinary skill in the art. Additionally, memory or other storage, as well as communication components, may be employed in embodiments of the invention.

[0068] FIG. 4 is a block diagram that illustrates a computing system 400 that may be employed to carry out processing functionality, according to various embodiments, upon which embodiments of a thermocycler system (FIG. 4) may utilize. Thermal control of heating / cooling modules may be controlled by computing system 400. A user may use computing system 400 to control which thermal protocol is run for each sample block of the set of sample blocks. The user may control a thermocycler system locally or from over a network. Computing system 400 may also receive temperature information from various temperature sensors within a thermocycler system. According to various embodiments, the temperature sensors may be included on the sample blocks and heat sink. Further, optical sensors may also be controlled by computing system 400. According to various embodiments described herein, a thermocycler system may need a plurality of optical sensors to detect various results. The plurality of optical sensors is controlled by a computing system 400, for example. A biological analysis result may also be calculated by computing system 400. A biological analysis result may be a quantitation result of a target molecule in various embodiments.

[0069] Computing system 400 can include one or more processors, such as a processor 404. Processor 404 can be implemented using a general or special purpose processing engine such as,Matter No. TP389518WO1for example, a microprocessor, controller or other control logic. In this example, processor 404 is connected to a bus 402 or other communication medium.

[0070] Further, it should be appreciated that a computing system 400 of FIG. 4 may be embodied in any of a number of forms, such as a rack-mounted computer, mainframe, supercomputer, server, client, a desktop computer, a laptop computer, a tablet computer, handheld computing device (e.g., PDA, cell phone, smart phone, palmtop, etc.), cluster grid, netbook, embedded systems, or any other type of special or general purpose computing device as may be desirable or appropriate for a given application or environment. Additionally, a computing system 400 can include a conventional network system including a client / server environment and one or more database servers, or integration with LIS / LIMS infrastructure. A number of conventional network systems, including a local area network (LAN) or a wide area network (WAN), and including wireless and / or wired components, are known in the art. Additionally, client / server environments, database servers, and networks are well documented in the art.

[0071] Computing system 400 may include bus 402 or other communication mechanism for communicating information, and processor 404 coupled with bus 402 for processing information.

[0072] Computing system 400 also includes a memory 406, which can be a random-access memory (RAM) or other dynamic memory, coupled to bus 402 for storing instructions to be executed by processor 404. Memory 406 also may be used for storing temporary variables or other intermediate information during execution of instructions to be executed by processor 404. Computing system 400 further includes a read only memory (ROM) 408 or other static storage device coupled to bus 402 for storing static information and instructions for processor 404.

[0073] Computing system 400 may also include a storage device 410, such as a magnetic disk, optical disk, or solid-state drive (SSD) is provided and coupled to bus 402 for storing information and instructions. Storage device 410 may include a media drive and a removable storage interface. A media drive may include a drive or other mechanism to support fixed or removable storage media, such as a hard disk drive, a floppy disk drive, a magnetic tape drive, an optical disk drive, a CD or DVD drive (R or RW), flash drive, or other removable or fixed media drive. As these examples illustrate, the storage media may include a computer-readable storage medium having stored therein particular computer software, instructions, or data.Matter No. TP389518WO1

[0074] In alternative embodiments, storage device 410 may include other similar instrumentalities for allowing computer programs or other instructions or data to be loaded into computing system 400. Such instrumentalities may include, for example, a removable storage unit and an interface, such as a program cartridge and cartridge interface, a removable memory (for example, a flash memory or other removable memory module) and memory slot, and other removable storage units and interfaces that allow software and data to be transferred from the storage device 410 to computing system 400.

[0075] Computing system 400 can also include a communications interface 418.Communications interface 418 can be used to allow software and data to be transferred between computing system 400 and external devices. Examples of communications interface 418 can include a modem, a network interface (such as an Ethernet or other NIC card), a communications port (such as for example, a USB port, a RS-232C serial port), a PCMCIA slot and card, Bluetooth, etc. Software and data transferred via communications interface 418 are in the form of signals which can be electronic, electromagnetic, optical or other signals capable of being received by communications interface 418. These signals may be transmitted and received by communications interface 418 via a channel such as a wireless medium, wire or cable, fiber optics, or another communications medium. Some examples of a channel include a phone line, a cellular phone link, an RF link, a network interface, a local or wide area network, and other communications channels.

[0076] Computing system 400 may be coupled via bus 402 to a display 412, such as a cathode ray tube (CRT) or liquid crystal display (LCD), for displaying information to a computer user. An input device 414, including alphanumeric and other keys, is coupled to bus 402 for communicating information and command selections to processor 404, for example. An input device may also be a display, such as an LCD display, configured with touchscreen input capabilities. Another type of user input device is cursor control 416, such as a mouse, a trackball or cursor direction keys for communicating direction information and command selections to processor 404 and for controlling cursor movement on display 412. This input device typically has two degrees of freedom in two axes, a first axis (e.g., x) and a second axis (e.g., y), that allows the device to specify positions in a plane. A computing system 400 provides data processing and provides a level of confidence for such data. Consistent with certainMatter No. TP389518WO1implementations of embodiments of the present teachings, data processing and confidence values are provided by computing system 400 in response to processor 404 executing one or more sequences of one or more instructions contained in memory 406. Such instructions may be read into memory 406 from another computer-readable medium, such as storage device 410.Execution of the sequences of instructions contained in memory 406 causes processor 404 to perform the process states described herein. Alternatively, hard-wired circuitry may be used in place of or in combination with software instructions to implement embodiments of the present teachings. Thus, implementations of embodiments of the present teachings are not limited to any specific combination of hardware circuitry and software.

[0077] The term "computer-readable medium" and “computer program product” as used herein generally refers to any media that is involved in providing one or more sequences or one or more instructions to processor 404 for execution. Such instructions, generally referred to as “computer program code” (which may be grouped in the form of computer programs or other groupings), when executed, enable the computing system 400 to perform features or functions of embodiments of the present invention. These and other forms of computer-readable media may take many forms, including but not limited to, non-volatile media, volatile media, and transmission media. Non-volatile media includes, for example, solid state, optical or magnetic disks, such as storage device 410. Volatile media includes dynamic memory, such as memory 406. Transmission media includes coaxial cables, copper wire, and fiber optics, including the wires that comprise bus 402.

[0078] Common forms of computer-readable media include, for example, a floppy disk, a flexible disk, hard disk, magnetic tape, or any other magnetic medium, a CD-ROM, any other optical medium, punch cards, paper tape, any other physical medium with patterns of holes, a RAM, PROM, and EPROM, a FLASH-EPROM, any other memory sample support device or cartridge, a carrier wave as described hereinafter, or any other medium from which a computer can read.

[0079] Various forms of computer readable media may be involved in carrying one or more sequences of one or more instructions to processor 404 for execution. For example, the instructions may initially be carried on magnetic disk of a remote computer. The remoteMatter No. TP389518WO1computer can load the instructions into its dynamic memory and send the instructions over a telephone line using a modem. A modem local to computing system 400 can receive the data on the telephone line and use an infra-red transmitter to convert the data to an infra-red signal. An infra-red detector coupled to bus 402 can receive the data carried in the infra-red signal and place the data on bus 402. Bus 402 carries the data to memory 406, from which processor 404 retrieves and executes the instructions. The instructions received by memory 406 may optionally be stored on storage device 410 either before or after execution by processor 404.

[0080] It will be appreciated that, for clarity purposes, the above description has described embodiments of the invention with reference to different functional units and processors.However, it will be apparent that any suitable distribution of functionality between different functional units, processors or domains may be used without detracting from the invention. For example, functionality illustrated to be performed by separate processors or controllers may be performed by the same processor or controller. Hence, references to specific functional units are only to be seen as references to suitable means for providing the described functionality, rather than indicative of a strict logical or physical structure or organization.

[0081] FIG. 5A illustrates a graph of temperature of different zones of a known thermocycler. A zone is also referred to as a sample block within a set of sample blocks of a thermocycler system. FIG. 5B illustrates zones, or sample blocks, in a set of sample blocks corresponding to the temperature graph of FIG. 5 A. As illustrated in graph 500, six zones (Zl-Z6) each are a different temperature. However, the period of a set temperature is the same across zones Z1-Z6. In other words, the same protocol is being run across each zone, with a different temperature in each zone.

[0082] According to various embodiments described herein, several protocols with different set of steps including varying times and temperatures may be run in a thermocycler system. For example, a standard 40 cycle PCR protocol, a fast PCR protocol, and a thermal melt protocol may be run simultaneously in the same thermocycler system according to various embodiments of the present teachings.

[0083] FIGS. 6A-6M illustrate an example of a plurality of sample blocks of a set of sample blocks running independent thermal protocols according to various embodiments describedMatter No. TP389518WO1herein. In this example, a set of 12 sample blocks 600 are shown. Each sample block may be designated as a zone. Each sample block may run a different thermal protocol. For example, standard curve protocols may be run in zones 602, 604, 610, and 312. In zone 610, a longer hold time may be used in the standard curve protocol. In zones 306 and 308, a thermal melt curve protocol is run. In zones, 614 and 616, a presence-absence protocol is run. Further, in zones 618 and 620, a genotyping protocol is run. In zones 620 and 622, a comparative Ct protocol is run. In some embodiments, independent thermal protocol can include, at the same time point, one or more zones are undergoing temperature ramping, while one or more other zones may be undergoing cooling or temperature holding. Thermal protocol running in one zone does not affect thermal protocols in other zones.

[0084] Previously, the various protocols may be run in series or on different thermocyclers. However, according to various embodiments of the present teachings, a plurality of protocols may be run simultaneously on a single thermocycler system. In this example, there are 12 independent zones. However, it should be appreciated that a thermocycler system may have at least two zones. In various embodiments, a thermocycler system may have six zones or 12 zones. Each zone may be configured in a variety of ways.

[0085] For example, FIGS. 7A and 7B illustrate configurations of sample blocks of a set of sample blocks according to various embodiments of the present teachings. In FIG. 7A, each zone is configured to hold eight samples in a 2x4 configuration. In FIG. 7B, each zone is also configured to hold eight samples, but in a 1x8 configuration. In both FIGS. 7A and 7B, each zone is independent and different thermal protocols may be run in each zone.

[0086] FIG. 8 illustrates an exemplary flowchart of method 800 of biological analysis according to various embodiments of the present teachings. In step 802, a first biological sample is loaded into a first sample block and a second biological sample is loaded into a second sample block. Each sample block is thermally isolated by a thermal insulation material and / or an air gap. The thermal insulation material and / or air gap are sufficient for thermally isolating each sample block so that different temperatures may be run in different sample blocks of the set of sample blocks included in the thermocycler system. The type of thermal insulation is chosen to have a high thermal resistance. In various embodiments, the thermal insulation material has aMatter No. TP389518WO1thermal resistance of less than 0.02 W / mK. Examples of thermal insulation material are aerogels, polyurethane, and silicone gaskets.

[0087] In step 804, a biological reaction is initiated in the first biological sample using a first thermal protocol. The first biological sample is loaded into the first sample block. In step 806, a biological reaction is initiated in the second biological sample using a second thermal protocol. The second biological sample is loaded into the second sample block. The first and second thermal protocols are different. The thermal protocols may have different configurations of temperatures at different time intervals. In various embodiments, the thermal protocol may be a standard curve protocol, a thermal melt protocol, a comparative Ct protocol, or a genotyping protocol, for example.

[0088] The first and second sample blocks are included in a set of sample blocks in a single thermocycler system. In some embodiments, the first and second sample block may be adjacent blocks. The first and second sample blocks are separated by a thermal insulation material according to various embodiments of the present teachings. The thermal isolation provided by the thermal insulation material allows different temperatures to be applied to the plurality of biological samples in the set of sample blocks.

[0089] In the thermocycler system, a set of heating / cooling modules heat and cool the set of sample blocks. Associated with each sample block in the set of sample blocks is a heating / cooling module. Each heating / cooling module is configured to heat and cool its associated sample block based on the thermal protocol determined for the biological sample in the sample block. The control system is configured to control each heating / cooling module based on the desired thermal protocol.

[0090] In various embodiments, a single heatsink is disposed under the set of sample blocks. In other embodiments, a segmented heatsink may be used, where each heatsink segment corresponds to a sample block.

[0091] FIGS. 9 A and 9B illustrate a set of sample blocks according to various embodiments described herein. FIG. 9A shows a set of sample blocks in a thermocycler system. A magnified portion 902 of the set of sample blocks is shown in FIG. 9B. Each sample block contains aMatter No. TP389518WO1partition or set of partitions for loading the biological sample into. In the example shown in FIG.9B, each sample block includes eight partitions. Each partition may hold a microtube including the biological sample, for example.

[0092] According to various embodiments described herein, each sample block has an associated heating / cooling module as well as associated block sensors and heatsink sensors. A control system receives the temperatures measured to make adjustments to the heating / cooling modules to follow a determined protocol for the sample block.

[0093] In various embodiments described herein, independent temperature gradients may be implemented in each sample block of a set of sample blocks. Each sample block may also be referred to as a zone. FIGS. 10A and 10B illustrate various configurations of a sample block configured for gradient temperatures according to various embodiments described herein. FIG.10A illustrates three zones, where each zone may have eight different temperatures. In another example, FIG. 10B illustrates six zones, also capable of eight temperatures in each zone from using a temperature gradient.

[0094] FIG. 11 illustrates an exemplary schematic of a thermocycler system configured for gradient temperatures according to various embodiments described herein. According to various embodiments of the present teachings, similar to the embodiment shown in FIG. 1, a set of sample blocks 1104 are thermally isolated using thermal insulation material (not shown). Set of sample blocks 1104 includes six sample blocks. Each sample block has an associated set of block sensors 1102 to measure the temperature of each sample block. Also, similar to FIG. 1, a first interface material 116 is disposed between set of sample blocks 1104 and set of heating / cooling modules 1108. Each sample block has an associated two heating / cooling modules. Two heating / cooling modules are used to create the temperature gradient across each sample block. In this way, a temperature gradient can be varied independently in each sample block in the set of sample blocks. According to various embodiments described herein, a temperature gradient for each sample block in the set of sample blocks may be controlled to closely follow a determined thermal protocol for the biological sample included in a particular sample block. Moreover, a temperature gradient can be further refined and adjusted based in part on temperature measurements by sensors situated in the block and / or heat sink.Matter No. TP389518WO1

[0095] FIG. 12A illustrates six zones of a sample block using a temperature gradient configuration, such as the system illustrated in FIG. 11 , according to various embodiments described herein. Each sample block in a set of sample block may be referred to as a zone according to various embodiments described herein. Further, each individual partition may have a different temperature because of a temperature gradient.

[0096] FIG. 12B is a chart of the varying temperatures to create a temperature gradient in each of the zones of the set of sample blocks illustrated in FIG. 12A according to various embodiments described herein. As shown in the chart of FIG. 12B, each row of partitions in each zone has a different temperature.

[0097] FIG. 13 shows a cross-sectional view of a thermal block assembly with enhanced water management features, according to various embodiments. Thermal block assembly 1300 may include no isolation material other than air-gaps between sample blocks 1304 of different temperature zones. In some embodiments, thermal block assembly 1300 includes sample block 1304 coupled to sealed thermoelectric cooler (TEC) 1302, heatsink 1306 including heatsink water catchment area 1308, and airduct 1310 including airduct water catchment area 1312. In some embodiments, sample blocks 1304 may include all the features and configurations of sample blocks 104 as shown FIG. 1. In some embodiments, TEC 1302 can be sealed by a water resistant material. Examples of the water resistant material may include epoxy, roomtemperature vulcanizing (RTV) silicone, or a combination thereof. In some embodiments, thermal block assembly 1300 includes heatspreader 1314 disposed between TEC 1302 and heatsink 1306. Heatspreader 1314 may comprise copper. Heatsink 1306 may be disposed underneath heatspreader 1314. In various embodiments, heatspreader 1314 may be segmented with each segment corresponding to a sample block 1304. Airduct 1310, according to embodiments, is coupled to heatsink 1306. In some embodiments, heatsink 1306 is not segmented. In other embodiments, heatsink 1306 can be segmented with each heatsink segment corresponding to a heat spreader segment. Airduct 1310 may comprise a covering structure configured to direct and improve air flow through fins 1318 disposed under heatsink 1306, thereby enhancing the convection efficiency of heatsink 1306 and improving cooling with a fan (not shown).Matter No. TP389518WO1

[0098] In some embodiments, heatsink 1306 is segmented with each segment corresponding to a sample block. Each segment of the heatsink 1306 may include a plurality of fins disposed on the bottom surface thererof.

[0099] Condensation formed during the operation of thermal block assembly 1300 can be collected in heatsink water catchment area 1308 and, upon exceeding a threshold level, is directed through a drainage channel toward the airduct water catchment area 1312, thereby preventing accumulation of liquid near the TEC or thermal interfaces. In some embodiments, heatsink water catchment area 1308 is disposed at outer edges of heatsink 1306. According to various embodiments, the airduct water catchment area 1312 is disposed at a lower vertical level than the heatsink water catchment area 1308, such that liquid collected in the heatsink water catchment area flows to the airduct water catchment area under the force of gravity. In this manner, liquid is passively directed away from the heatsink and thermoelectric cooler without the need for active pumping or control mechanisms.

[0100] In some embodiments, as shown in FIG. 13, airduct water catchment areal312 has a larger volume capacity than the heatsink water catchment area 1308. This configuration allows the airduct water catchment area to receive and retain liquid transferred from the heatsink water catchment area, thereby reducing the likelihood of overflow near the heatsink or thermoelectric components and improving overall tolerance to condensation, spills, or seal degradation. In some embodiments, thermal block assembly 1300 includes drip-pan 1316 disposed on top of sample blocks 1304. Drip-pan 1316 is configured to enclose sub-assembly electronics components including a printed circuit board assembly (PCBA), a thermoelectric cooler (TEC), resistance temperature detector (RTD) wirings.

[0101] FIGS. 14A and 14B illustrate well geometry of the sample blocks, according to various embodiments. In some embodiments, wells 1402 include substantially uniform wall thickness around the well circumference. An all-around undercut geometry is implemented to wells 1402 to maintain the substantially uniform wall thickness of the well. As shown in FIG. 14B, well 1402 comprises gradient base 1404. In certain embodiments, the thickness of block material beneath well 1402 tapers from the block base toward the well cavity. This can be beneficial for improving thermal conductivity while minimizing overall block mass.Matter No. TP389518WO1

[0102] According to various embodiments, thermal block assembly 1300 may include multiple sample blocks 1304 (e.g., twelve blocks) to form a multi-zone thermal block assembly. As shown in FIGS. 15A and 15B, each sample block 1304 may include its own heatsink interface (heatsink base 1502) and may be independently secured to the heatsink.

[0103] In some embodiments, sample block 1304 does not include a full peripheral flange for sealing between adjacent blocks. Instead, individual wells are formed within discrete sample block 1304 that are isolated by an airgap from adjacent sample blocks. According to various embodiments, the width of the airgap is less than 5 mm including ranges of 0 to 1mm, 1 to 2 mm, 2 to 3mm, 3 to 4 mm, 4 to 5 mm and all ranges and values therebetween. In some embodiments, the width of the airgap is about 1 mm.

[0104] Further, the thermal block assembly 1300 is designed so that there is minimal contact between sample blocks 1304, according to various embodiments of the present teachings. As shown in FIG. 16, thermal block assembly 1300, in some embodiments, can comprise block clamp 1604 disposed across the middle section of each sample block 1304 configured to secure each sample block 1304 onto thermal block assembly 1300 such that it avoids physical contact between sample blocks 1304 via block clamp 1604, thereby preventing thermal crosstalk.

[0105] In certain embodiments, thermal cycler system 100 may include a heated or temperature controlled cover disposed above the thermal cycler assembly 1300. The heated cover or temperature controlled cover may be configured to prevent condensation above the samples loaded onto thermal cycler assembly 1300, thereby maintaining optical access to the samples. In various embodiments, the heated cover or temperature controlled cover is segmented with each segment corresponding to a sample block 1304, thereby reducing or minimizing thermal crosstalk between sample blocks 1304 via the heated cover or temperature controlled cover. In some embodiments, each segment of the heated cover or temperature controlled cover has its own heater and sensor, driven by an independent circuit driver. When the corresponding sample block 1304 drops to below ambient temperature, the heated cover or temperature controlled cover will drop its setpoint lower to enable the sample block to reach the setpoint faster.Matter No. TP389518WO1Examples

[0106] The following numbered examples are embodiments:1. A system for performing biological reactions, the system comprising:a set of sample blocks configured to have at least a first and a second sample block in the set, wherein each sample block is configured to receive a biological sample;a thermal insulation material disposed around each sample block in the set of sample blocks;a plurality of heating / cooling devices, wherein the plurality of heating / cooling devices includes at least a first set and a second set of heating / cooling devices, wherein the first set of heating / cooling devices is disposed to correspond to the first sample block, and the second set of heating / cooling devices is disposed to correspond to the second sample block;a control system configured to initiate biological reactions in a first biological sample of the first sample block and the second biological sample of the second sample block; anda detection system configured to detect biological reactions of the first and second biological samples.2. The system of example 1, further comprising:a plurality of thermal sensor sets comprising a first thermal sensor set and a second thermal sensor set, wherein the first thermal sensor set detects a temperature of the first sample block and the second thermal sensor set detects a temperature of the second sample block.3. The system of examples 1 or 2, wherein the control system is further configured to receive temperature information from the plurality of thermal sensor sets.4. The system of any of the examples 1 to 3, wherein the control system is further configured to run independent thermal protocols for each sample block of the set of sample blocks.Matter No. TP389518WO15. The system of any of the examples 1 to 4, wherein the thermal insulation material has a thermal resistance less than 0.02 W / mK.6. The system of any of the examples 1 to 5, wherein the thermal insulation material is an aerogel, and / or a polyurethane.7. The system of any of the examples 1 to 6, wherein the thermal insulation material includes an air gap.8. The system of any of the examples 1 to 7, wherein the heating / cooling devices are thermal electric cooling (TEC) / Peltier devices.9. The system of any of the examples 1 to 8, wherein the control system is further configured to adjust the heating / cooling devices based on the received temperature information from the plurality of thermal sensor sets.10. The system of any of the examples 1 to 9, wherein an area of the heating / cooling devices is larger than an area its respective sample block.11. The system of any of the examples 1 to 10, wherein each temperature sensor set of the plurality of temperature sensor sets is connected to a heat sink.12. A system for performing biological reactions, the system comprising:a set of sample blocks configured to have at least a first and a second sample block, wherein each sample block is configured to receive biological samples, wherein the first sample block is configured to receive a first biological sample and the second sample block is configured to receive a second biological sample;a thermal insulation material disposed around each sample block; anda plurality of heating / cooling devices,wherein the plurality of heating / cooling devices includes at least a first set and a second set of heating / cooling devices, wherein the first set of heating / cooling devices is disposed toMatter No. TP389518WO1correspond to the first sample block, and the second set of heating / cooling devices is disposed to correspond to the second sample block,wherein the first set of heating / cooling devices is configured to run a first thermal protocol and the second set of heating / cooling devices is configured to run a second thermal protocol, andwherein the first and second thermal protocols are different.13. The system of 12, further comprising:a detection system configured to detect biological reactions in the set of sample blocks.14. The system of examples 12 or 13, further comprising:a control system configured to run independent thermal protocols for each sample block of the set of sample blocks.15. The system of any of the examples 12 to 14, further comprising:a plurality of thermal sensor sets comprising a first thermal sensor set and a second thermal sensor set, wherein the first thermal sensor set detects a temperature of the first sample block and the second thermal sensor set detects a temperature of the second sample block.16. The system of examples 14 or 15, wherein the control system is further configured to receive temperature information from the plurality of thermal sensor sets.17. The system of any of the examples 12 to 16, wherein the thermal insulation material has a thermal resistance less than 0.02 W / mK.18. The system of any of the examples 12 to 17, wherein the thermal insulation material is an aerogel.19. The system of any of the examples 12 to 17, wherein the thermal insulation material is a polyurethane.20. The system of any of the examples 12 to 19, wherein the heating / cooling devices are thermal electric cooling (TEC) / Peltier devices.Matter No. TP389518WO121. The system of any of the examples 14 to 20, wherein the control system is further configured to adjust the heating / cooling devices based on the received temperature information from the plurality of thermal sensor sets.22. The system of any of the examples 12 to 21, wherein an area of the heating / cooling devices is larger than an area its respective sample block.23. The system of any of the examples 12 to 22, wherein each temperature sensor set of the plurality of temperature sensor sets is connected to a heat sink.24. The system of any of the examples 12 to 23, further comprising:a rubber block seal disposed between each sample block of the set, wherein the rubber block seal is configured to limit liquid exchange between each sample block.25. A method of running at least two thermal protocols on a biological sample in a set of sample blocks with at least two sample blocks, the method comprising:loading a first biological sample on a first sample block and a second biological sample on a second sample block, wherein the first and second sample blocks are thermally isolated by a thermal insulation material and / or an air gap;initiating a biological reaction in the first biological sample of the first sample block using a first set of heating / cooling devices controlled by a first thermal protocol; andinitiating a biological reaction in the second sample block using a second set of heating / cooling devices controlled by a second thermal protocol, wherein the first and second thermal protocols are different.26. The method of example 25, wherein initiating the biological reactions is by a control system configured to run independent thermal protocols for each sample block of the set of sample blocks.27. The method of examples 25 or 26, further comprising:Matter No. TP389518WO1receiving fluorescent emission data, by a detection system, from the first and second biological samples.28. The method of any of the examples 25 to 27, further comprising:detecting a temperature of the first sample block by a first thermal sensor set; anddetecting a temperature of the second sample block by a second thermal sensor set, wherein a plurality of thermal sensor sets includes the first and second thermal sensor sets.29. The method of any of the examples 25 to 28, wherein the thermal insulation material has a thermal resistance less than 0.02 W / mK.30. The method of any of the examples 25 to 29, wherein the thermal insulation material is an aerogel.31. The method of any of the examples 25 to 29, wherein the thermal insulation material is a polyurethane.32. The method of any of the examples 25 to 31 , wherein the heating / cooling devices are thermal electric cooling (TEC) / Peltier devices.33. The method of any of the examples 26 to 32, further comprising:adjusting the heating / cooling devices, by the control system, based on the received temperature information from the plurality of thermal sensor sets.34. The method of any of the examples 25 to 33, wherein an area of the heating / cooling devices is larger than an area its respective sample block.35. A method of optimizing a thermal protocol for a biological sample using a system according to examples 1-24, the method comprising:loading the biological sample on the set of sample blocks;initiating a biological reaction in the biological sample of the sample blocks concurrently, wherein each of the sample block is configured to perform a different thermal protocol;Matter No. TP389518WO1determining a best thermal protocol by comparing results of the biological reaction from each of the sample blocks.36. The method of example 35, wherein the thermal protocol includes a thermal protocol for polymerase chain reaction (PCR) or a melt process.37. The method of example 36, wherein optimizing the thermal protocol comprises optimizing parameters for the PCR , the parameters including an initial denaturation temperature, an initial denaturation duration, a denaturation temperature for amplification cycles, a denaturation for amplification cycles, an annealing temperature for amplification cycles, an annealing duration for amplification cycles, an extension temperature for amplification cycles, an extension duration for amplification cycles, a final extension temperature, a final extension duration, a final hold duration, a temperature ramp rate, melt temperatures, or any combination thereof.38. The method of any of examples 34-37, wherein the determining comprises comparing amplification curves generated by different thermal protocols, comparing Cqvalue variations for different thermal protocols, comparing sensitivity of sample level (lowest amount of sample need to detect) for different thermal protocols, comparing linearity of the sample input for different thermal protocols, comparing dynamic ranges of sample input generated by different thermal protocols , and / or comparing PCR efficiency of different thermal protocols.39. A thermal block assembly comprising:a plurality of sample blocks each include a plurality of sample wells having undercut sidewalls and gradient bases;a sealed thermoelectric cooler couple to each sample block;a heatsink including a water catchment area; anda drainage path configured to direct liquid away from the thermoelectric cooler.40. The thermal block assembly of example 39, wherein the plurality of sample blocks are configured to perform different thermal protocols independently.Matter No. TP389518WO141. The thermal block assembly of any of examples 39 and 40, wherein the heatsink water catchment area comprises a peripheral channel encircling the thermal block assembly.42. The thermal block assembly of any of examples 39-41, further comprising an airduct secured around the heatsink, wherein the air duct comprises a airduct water catchment area configured to receive liquid from the water catchment area of the heatsink.43. The thermal block assembly of example 42, wherein the air duct water catchment area is disposed at a lower vertical level than the water catchment area of the heatsink.44. The thermal block assembly of any of examples 39-43, wherein the heatsink comprises a plurality heatsink bases and each sample block interfaces with a heatsink base.45. The thermal block assembly of any of examples 39-44, wherein each sample well includes a wall having a substantially uniform thickness around a circumference of the well.46. The thermal block assembly of any of examples 39-45, wherein each sample well includes a gradient base such that a thickness of block material beneath the well tapers down between a sample block base and a well cavity.47. The thermal block assembly of any of examples 39-46, wherein an air gap is disposed between adjacent sample blocks to provide thermal isolation.48. The thermal block assembly of example 47, wherein the air gap is about 1 mm wide.49. The thermal block assembly of any of examples 39-48, wherein adjacent sample blocks are not joined by a continuous sealing member.51. A thermal block assembly comprising:Matter No. TP389518WO1a plurality of sample blocks each include a plurality of sample wells, wherein the sample blocks segment the thermal block assembly into a set of independent thermal zones; and a plurality of heating and cooling components configured to independently heat and cool at least two of the independent thermal zones such that each of the two independent thermal zones is capable of running an independent thermal protocol.52. The thermal block assembly of example 51 , wherein the heating and cooling components include a plurality of thermoelectric coolers with each thermoelectric cooler corresponding to a sample block.53. The thermal block assembly of any of examples 51 and 52, wherein the heating and cooling components include a segmented heatspreader with each segment of the heatspreader corresponding to a sample block.54. The thermal block assembly of example 53, wherein each segment of the heatspreader is separated from adjacent segments by an air gap.55. The thermal block assembly of any of examples 51-54, wherein the heating and cooling components includes a heatsink disposed under the heatspreader configured to dissipate heat from the sample blocks.56. The thermal block assembly of example 55, further comprising a plurality of fins disposed under the heatsink forming a plurality of air channels, and the air channels and fins are configured to improve a rate of heat dissipation and / or improve thermal uniformity for one or more of the sample blocks.57. The thermal block assembly of any of examples 51-56, wherein the at least two sample blocks are disposed adjacent to each other.58. The thermal block assembly of any of examples 51-57, wherein adjacent sample blocks of the plurality of sample blocks are separated by an air-gap.Matter No. TP389518WO159. The thermal block assembly of example 58, wherein the air-gap is about 1 mm wide.60. The thermal block assembly of any of examples 51-59, further comprising a heated cover disposed over the thermal block assembly, the heated cover is configured to prevent condensation over the sample block while maintaining optical access to samples disposed on the sample blocks.61. The thermal block assembly of example 60, wherein the heated cover is segmented such that each segment of the heated cover corresponds to a sample block.62. The thermal block assembly of example 61, wherein a temperature of each segment of the heated cover is independently controlled.

[0107] Although the present invention has been described with respect to certain exemplary embodiments, examples, and applications, it will be apparent to those skilled in the art that various modifications and changes may be made without departing from the invention.

Claims

Matter No. TP389518WO1CLAIMSWhat is claimed is:

1. A system for performing biological reactions, the system comprising:a set of sample blocks configured to have at least a first and a second sample block in the set, wherein each sample block is configured to receive a biological sample;air-gaps disposed around each sample block in the set of sample blocks;a plurality of heating / cooling devices, wherein the plurality of heating / cooling devices includes at least a first set and a second set of heating / cooling devices, wherein the first set of heating / cooling devices is disposed to correspond to the first sample block, and the second set of heating / cooling devices is disposed to correspond to the second sample block;a control system configured to initiate biological reactions in a first biological sample of the first sample block and the second biological sample of the second sample block; anda detection system configured to detect biological reactions of the first and second biological samples.

2. The system of claim 1, further comprising:a plurality of thermal sensor sets comprising a first thermal sensor set and a second thermal sensor set, wherein the first thermal sensor set detects a temperature of the first sample block and the second thermal sensor set detects a temperature of the second sample block.

3. The system of claims 1 or 2, wherein the control system is further configured to receive temperature information from the plurality of thermal sensor sets.

4. The system of any of the claims 1 to 3, wherein the control system is further configured to run independent thermal protocols for each sample block of the set of sample blocks.

5. The system of any of the claims 1 to 4, further comprising a thermal insulation material disposed around each sample blocks.Matter No. TP389518WO16. The system of claim 5, wherein the thermal insulation material has a thermal resistance less than 0.02 W / mK.

7. The system of any of claims 5 and 6, wherein the thermal insulation material includes an aerogel and or a polyurethane.

8. The system of any of the claims 1 to 7, wherein the heating / cooling devices are thermal electric cooling (TEC) / Peltier devices.

9. The system of any of the claims 1 to 8, wherein the control system is further configured to adjust the heating / cooling devices based on the received temperature information from the plurality of thermal sensor sets.

10. The system of any of the claims 1 to 9, wherein an area of the heating / cooling devices is larger than an area its respective sample block.

11. The system of any of the claims 1 to 10, wherein each temperature sensor set of the plurality of temperature sensor sets is connected to a heat sink.

12. A system for performing biological reactions, the system comprising:a set of sample blocks configured to have at least a first and a second sample block, wherein each sample block is configured to receive biological samples, wherein the first sample block is configured to receive a first biological sample and the second sample block is configured to receive a second biological sample;a thermal insulation material disposed around each sample block; anda plurality of heating / cooling devices,wherein the plurality of heating / cooling devices includes at least a first set and a second set of heating / cooling devices, wherein the first set of heating / cooling devices is disposed to correspond to the first sample block, and the second set of heating / cooling devices is disposed to correspond to the second sample block,wherein the first set of heating / cooling devices is configured to run a first thermal protocol and the second set of heating / cooling devices is configured to run a second thermal protocol, andMatter No. TP389518WO1wherein the first and second thermal protocols are different.

13. The system of 12, further comprising:a detection system configured to detect biological reactions in the set of sample blocks.

14. The system of claims 12 or 13, further comprising:a control system configured to run independent thermal protocols for each sample block of the set of sample blocks.

15. The system of any of the claims 12 to 14, further comprising:a plurality of thermal sensor sets comprising a first thermal sensor set and a second thermal sensor set, wherein the first thermal sensor set detects a temperature of the first sample block and the second thermal sensor set detects a temperature of the second sample block.

16. The system of claims 14 or 15, wherein the control system is further configured to receive temperature information from the plurality of thermal sensor sets.

17. The system of any of the claims 12 to 16, wherein the thermal insulation material has a thermal resistance less than 0.02 W / mK.

18. The system of any of the claims 12 to 17, wherein the thermal insulation material is an aerogel or a polyurethane.

19. The system of any of the claims 12 to 17, wherein the thermal insulation material is an air-gap disposed between adjacent sample blocks.

20. The system of any of the claims 12 to 19, wherein the heating / cooling devices are thermal electric cooling (TEC) / Peltier devices.

21. The system of any of the claims 14 to 20, wherein the control system is further configured to adjust the heating / cooling devices based on the received temperature information from the plurality of thermal sensor sets.Matter No. TP389518WO122. The system of any of the claims 12 to 21, wherein an area of the heating / cooling devices is larger than an area its respective sample block.

23. The system of any of the claims 12 to 22, wherein each temperature sensor set of the plurality of temperature sensor sets is connected to a heat sink.

24. The system of any of the claims 12 to 23, further comprising:a rubber block seal disposed between each sample block of the set, wherein the rubber block seal is configured to limit liquid exchange between each sample block.

25. A method of running at least two thermal protocols on a biological sample in a set of sample blocks with at least two sample blocks, the method comprising:loading a first biological sample on a first sample block and a second biological sample on a second sample block, wherein the first and second sample blocks are thermally isolated by a thermal insulation material;initiating a biological reaction in the first biological sample of the first sample block using a first set of heating / cooling devices controlled by a first thermal protocol; and initiating a biological reaction in the second sample block using a second set of heating / cooling devices controlled by a second thermal protocol, wherein the first and second thermal protocols are different.

26. The method of claim 25, wherein initiating the biological reactions is by a control system configured to run independent thermal protocols for each sample block of the set of sample blocks.

27. The method of claims 25 or 26, further comprising:receiving fluorescent emission data, by a detection system, from the first and second biological samples.

28. The method of any of the claims 25 to 27, further comprising:detecting a temperature of the first sample block by a first thermal sensor set; anddetecting a temperature of the second sample block by a second thermal sensor set, wherein a plurality of thermal sensor sets includes the first and second thermal sensor sets.Matter No. TP389518WO129. The method of any of the claims 25 to 28, wherein the thermal insulation material has a thermal resistance less than 0.02 W / mK.

30. The method of any of the claims 25 to 29, wherein the thermal insulation material is an aerogel.

31. The method of any of the claims 25 to 29, wherein the thermal insulation material is a polyurethane.

32. The method of any of the claims 25 to 31 , wherein the heating / cooling devices are thermal electric cooling (TEC) / Peltier devices.

33. The method of any of the claims 26 to 32, further comprising:adjusting the heating / cooling devices, by the control system, based on the received temperature information from the plurality of thermal sensor sets.

34. The method of any of the claims 25 to 33, wherein an area of the heating / cooling devices is larger than an area its respective sample block.

35. A method of optimizing a thermal protocol for a biological sample using a system according to any of claims 1-24, the method comprising:loading the biological sample on the set of sample blocks;initiating a biological reaction in the biological sample of the sample blocks concurrently, wherein each of the sample block is configured to perform a different thermal protocol;determining a best thermal protocol by comparing results of the biological reaction from each of the sample blocks.

36. The method of claim 35, wherein the thermal protocol includes a thermal protocol for polymerase chain reaction (PCR) or a melt process.

37. The method of claim 36, wherein optimizing the thermal protocol comprises optimizing parameters for the PCR , the parameters including an initial denaturation temperature, an initial denaturation duration, a denaturation temperature for amplification cycles, aMatter No. TP389518WO1denaturation for amplification cycles, an annealing temperature for amplification cycles, an annealing duration for amplification cycles, an extension temperature for amplification cycles, an extension duration for amplification cycles, a final extension temperature, a final extension duration, a final hold duration, a temperature ramp rate, melt temperatures, or any combination thereof.

38. The method of any of claims 34-37, wherein the determining comprises comparing amplification curves generated by different thermal protocols, comparing Cqvalue variations for different thermal protocols, comparing sensitivity of sample level (lowest amount of sample need to detect) for different thermal protocols, comparing linearity of the sample input for different thermal protocols, comparing dynamic ranges of sample input generated by different thermal protocols , and / or comparing PCR efficiency of different thermal protocols.

39. A thermal block assembly comprising:a plurality of sample blocks each include a plurality of sample wells, wherein the sample blocks segment the thermal block assembly into a set of independent thermal zones;a sealed thermoelectric cooler couple to each sample block;a heatsink including a water catchment area; anda drainage path configured to direct liquid away from the thermoelectric cooler.

40. The thermal block assembly of claim 39, wherein the plurality of sample blocks are configured to perform different thermal protocols independently.

41. The thermal block assembly of any of claims 39 and 40, wherein the heatsink water catchment area comprises a peripheral channel encircling the thermal block assembly.

42. The thermal block assembly of any of claims 39-41, further comprising an airduct secured around the heatsink, wherein the air duct comprises an airduct water catchment area configured to receive liquid from the water catchment area of the heatsink.

43. The thermal block assembly of claim 42, wherein the air duct water catchment area is disposed at a lower vertical level than the water catchment area of the heatsink.Matter No. TP389518WO144. The thermal block assembly of any of claims 39-43, wherein the heatsink comprises a plurality heatsink bases and each sample block interfaces with a heatsink base.

45. The thermal block assembly of any of claims 39-44, wherein each sample well includes a wall having a substantially uniform thickness around a circumference of the well.

46. The thermal block assembly of any of claims 39-45, wherein each sample well includes a gradient base such that a thickness of block material beneath the well tapers down between a sample block base and a well cavity.

47. The thermal block assembly of any of claims 39-46, wherein an air gap is disposed between adjacent sample blocks to provide thermal isolation.

48. The thermal block assembly of claim 47, wherein the air gap is about 1 mm wide.

49. The thermal block assembly of any of claims 39-48, wherein adjacent sample blocks are not joined by a continuous sealing member.

50. The thermal block assembly of any of claims 39-49, further comprising a block clamp disposed across a middle section of each sample block, configured to reduce physical contact between adjacent sample blocks.

51. A thermal block assembly comprising:a plurality of sample blocks each include a plurality of sample wells, wherein the sample blocks segment the thermal block assembly into a set of independent thermal zones; and a plurality of heating and cooling components configured to independently heat and cool at least two of the independent thermal zones such that each of the two independent thermal zones is capable of running an independent thermal protocol.Matter No. TP389518WO152. The thermal block assembly of claim 51 , wherein the heating and cooling components include a plurality of thermoelectric coolers with each thermoelectric cooler corresponding to a sample block.

53. The thermal block assembly of any of claims 51 and 52, wherein the heating and cooling components include a segmented heatspreader with each segment of the heatspreader corresponding to a sample block.

54. The thermal block assembly of claim 53, wherein each segment of the heatspreader is separated from adjacent segments by an air gap.

55. The thermal block assembly of any of claims 51-54, wherein the heating and cooling components includes a heatsink disposed under the heatspreader configured to dissipate heat from the sample blocks.

56. The thermal block assembly of claim 55, further comprising a plurality of fins disposed under the heatsink forming a plurality of air channels, and the air channels and fins are configured to improve a rate of heat dissipation and / or improve thermal uniformity for one or more of the sample blocks.

57. The thermal block assembly of any of claims 51-56, wherein the at least two sample blocks are disposed adjacent to each other.

58. The thermal block assembly of any of claims 51-57, wherein adjacent sample blocks of the plurality of sample blocks are separated by an air-gap.

59. The thermal block assembly of claim 58, wherein the air-gap is about 1 mm wide.

60. The thermal block assembly of any of claims 51-59, further comprising a heated cover disposed over the thermal block assembly, the heated cover is configured to preventMatter No. TP389518WO1condensation over the sample block while maintaining optical access to samples disposed on the sample blocks.

61. The thermal block assembly of claim 60, wherein the heated cover is segmented such that each segment of the heated cover corresponds to a sample block.

62. The thermal block assembly of claim 61, wherein a temperature of each segment of the heated cover is independently controlled.

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