Apparatus and method for sample collection

Abstract

Provided herein are devices and methods for collecting biological samples. The apparatus may include a lid, a puncturable container including a reagent for processing or holding a biological sample, and a container including a puncturing device. When the lid is engaged with the opening of the container, the piercer may be capable of piercing the pierceable container, thereby releasing the agent of the pierceable container into the container. The method may include collecting a biological sample using the device. The method may include determining an analyte of a biological sample.

Description

[0001] Cross-references

[0002] This application claims the benefit of U.S. Provisional Application No. 63 / 354,883, filed on June 23, 2022, which is incorporated herein by reference in its entirety. Background Art

[0003] Disease detection is a key component for providing treatment to patients, and early detection can improve outcomes. Collecting biological samples from a subject (e.g., a patient) can allow disease detection of the subject's biological fluids or tissues. Sample collection can occur at a time or location different from the location where the sample analysis is performed. The sample may need to maintain its integrity prior to analysis in order to provide accurate actionable data. Summary of the invention

[0004] Provided herein are devices and methods for collecting biological samples from objects. Biological samples collected from objects may include nucleic acids, polypeptides, or other biomolecules or analytes. The presence of these biomolecules or analytes may indicate the genotype state, phenotypic state, or other characteristics of the object. However, when collecting samples and before analyzing samples, biomolecules or analytes may degrade or otherwise react, so that the collected samples and the analyzed samples may include differences. Therefore, it is desirable to improve the preservation of biomolecules or analytes in samples. The devices and methods provided herein may be applicable to collecting and preserving samples from objects.

[0005] In one aspect, the present disclosure provides a device for collecting a biological sample from a subject, the device comprising: a container comprising a piercer extending across a longitudinal axis of the container toward an opening of the container; and a lid comprising a pierceable container comprising a reagent for processing or preserving the biological sample, wherein the device is configured so that when the lid is engaged with the container to position the lid near the opening, the piercer pierces the pierceable container to release the reagent into the container.

[0006] In some embodiments, the piercer pierces the container when the cap or container is rotated.

[0007] In some embodiments, engagement of the lid with the container for positioning the lid proximate the opening and movement of the lid toward the container or movement of the container toward the lid closes the container.

[0008] In some embodiments, the lid is configured to be attached to the container. In some embodiments, the lid is configured to be attached to the container at least in part by applying pressure to the lid toward the container or applying pressure to the container toward the lid when the lid is near the opening. In some embodiments, the lid is configured to be attached to the container at least in part by rotating the lid or the container when the lid is near the opening. In some embodiments, the attachment of the lid to the container creates a leak-resistant, leak-proof, or airtight compartment.

[0009] In some embodiments, the lid and the container each include threads, wherein the threads of the lid and the threads of the container are configured to connect together to close the container.

[0010] In some embodiments, the piercer comprises a rod, wherein the top of the rod comprises a sharp protrusion. In some embodiments, the piercer comprises a plurality of sharp protrusions. In some embodiments, the rod is disposed on the surface of the container. In some embodiments, the rod is disposed on the bottom surface of the container.

[0011] In some embodiments, the pierceable container is configured such that a pierceable surface of the pierceable container is exposed on a bottom surface of the lid.

[0012] In some embodiments, the cover includes solid surfaces at a top surface and side surfaces of the cover.

[0013] In some embodiments, the reagent is configured to maintain the integrity of an analyte in the biological sample in response to release of the reagent into the container. In some embodiments, the analyte comprises a nucleic acid, a polypeptide, a lipid, or a carbohydrate.

[0014] In some embodiments, the sharp protrusion is located above the plane of the opening. In some embodiments, the sharp protrusion is configured to protrude into the container.

[0015] In some embodiments, the container comprises a tube. In some embodiments, the container comprises a flat bottom or a substantially flat bottom. In some embodiments, the container comprises a rounded bottom or a substantially rounded bottom.

[0016] In some embodiments, the pierceable container comprises a bag.

[0017] In some embodiments, the reagent comprises an enzyme, an enzyme inhibitor, a chelating agent, a buffer, or a combination thereof. In some embodiments, the chelating agent comprises ethylenediaminetetraacetic acid (EDTA).

[0018] In some embodiments, the biological sample comprises a urine sample.

[0019] In another aspect, the present disclosure provides a method for collecting a biological sample from a subject, the method comprising: (a) providing a container comprising a piercer extending across a longitudinal axis of the container toward an opening of the container, wherein the container comprises a biological sample; (b) engaging a lid with the container to position the lid proximate the opening, wherein the lid comprises a pierceable container comprising a reagent for processing or preserving the biological sample; and (c) when engaging the lid with the container, causing the lid or the container to perform a closing movement, thereby piercing the pierceable container with the piercer to release the reagent into the container.

[0020] In some embodiments, the closing motion comprises rotating the container or lid.

[0021] In some embodiments, the closing motion includes applying pressure to the lid toward the container or applying pressure to the container toward the lid.

[0022] In some embodiments, the method further comprises closing the container at least in part by rotating the lid or the container.

[0023] In some embodiments, the method further comprises closing the container at least in part by applying pressure to the lid or the container.

[0024] In some embodiments, the method further comprises attaching a lid to the container.

[0025] In some embodiments, attachment of the lid to the container creates a leak-resistant, leak-proof, or airtight compartment.

[0026] In some embodiments, the cap and the container each include threads, and the method further includes coupling the threads of the cap and the threads of the container together, thereby closing the container.

[0027] In some embodiments, the piercer comprises a rod, wherein the top of the rod comprises a sharp protrusion. In some embodiments, the piercer comprises a plurality of sharp protrusions. In some embodiments, the rod is disposed on the surface of the container. In some embodiments, the rod is disposed on the bottom surface of the container.

[0028] In some embodiments, the pierceable container is configured such that a pierceable surface of the pierceable container is exposed on a bottom surface of the lid.

[0029] In some embodiments, the cover includes solid surfaces at a top surface and side surfaces of the cover.

[0030] In some embodiments, the method further comprises mixing the reagent and the biological sample together in response to the release of the reagent into the container. In some embodiments, the reagent is configured to maintain the integrity of the analyte in the biological sample in response to the mixing.

[0031] In some embodiments, the analyte comprises a nucleic acid, a polypeptide, a lipid, or a carbohydrate. In some embodiments, the method further comprises determining the analyte.

[0032] In some embodiments, the sharp protrusion is located above the plane of the container opening. In some embodiments, the sharp protrusion protrudes into the container.

[0033] In some embodiments, the container comprises a tube. In some embodiments, the container comprises a flat bottom or a substantially flat bottom. In some embodiments, the container comprises a rounded bottom or a substantially rounded bottom. In some embodiments, the pierceable container comprises a bag.

[0034] In some embodiments, the reagent comprises an enzyme, an enzyme inhibitor, a chelating agent, a buffer, or a combination thereof. In some embodiments, the chelating agent comprises ethylenediaminetetraacetic acid (EDTA).

[0035] In some embodiments, the method further comprises providing the biological sample to a container prior to (a).

[0036] In some embodiments, the subject has or is suspected of having a disease, disorder, genetic disorder, or genetic aberration.

[0037] In some embodiments, the disease comprises cancer. In some embodiments, the cancer comprises genitourinary cancer. In some embodiments, genitourinary cancer comprises bladder cancer, prostate cancer, kidney or renal cancer, penile cancer, testicular cancer, or urethral cancer.

[0038] In some embodiments, the biological sample comprises a urine sample.

[0039] Another aspect of the present disclosure provides a non-transitory computer-readable medium including machine-executable code that, when executed by one or more computer processors, implements any of the methods described above or elsewhere herein.

[0040] Another aspect of the present disclosure provides a system comprising one or more computer processors and a computer memory coupled to the one or more computer processors. The computer memory includes machine executable code that, when executed by the one or more computer processors, implements any method described above or elsewhere herein.

[0041] Additional aspects and advantages of the present disclosure will become apparent to those skilled in the art from the following detailed description, in which only illustrative embodiments of the present disclosure are shown and described. As will be appreciated, the present disclosure is capable of other, different embodiments, and its several details are capable of modification in various obvious respects, all without departing from the disclosure. Therefore, the drawings and description are to be regarded as illustrative in nature, and not restrictive.

[0042] Incorporation by reference

[0043] All publications, patents, and patent applications mentioned in this specification are incorporated herein by reference to the same extent as if each individual publication, patent, or patent application was specifically and individually indicated to be incorporated by reference. If a publication, patent, or patent application incorporated by reference contradicts the disclosure contained in the specification, the specification is intended to supersede and / or take precedence over any such contradictory material. BRIEF DESCRIPTION OF THE DRAWINGS

[0044] The novel features of the present invention are set forth with particularity in the appended claims. A better understanding of the features and advantages of the present invention will be obtained by reference to the following detailed description of illustrative embodiments in which the principles of the present invention are utilized, and the accompanying drawings (also referred to herein as "Figures"), in which:

[0045] Figure 1A-1B An example of an apparatus for collecting a biological sample is shown, including a view of an open configuration ( Figure 1A ) and the closed configuration view ( Figure 1B ).

[0046] Figure 2A-2F An example of a device for collecting a biological sample is shown, including example dimensions of the device ( Figure 2A ), the container's view ( Figure 2B ) and various views of the lid ( Figure 2C-2F ).

[0047] Figure 3A-3C An example of an apparatus for collecting a biological sample is shown, including a side view ( Figure 3A )、Cross-sectional side view( Figure 3B ) and oblique view ( Figure 3C ).

[0048] Figure 4A-4D An example of a cover for use in an apparatus for collecting a biological sample is shown, including a side view of the cover ( Figure 4A ), a cross-sectional side view of a lid within a closed container ( Figure 4B )、Top view of the lid( Figure 4C ) and oblique view of the cover ( Figure 4D ).

[0049] Figure 5A-5E An example of a container for use in an apparatus for collecting a biological sample is shown, including a side view ( Figure 5A )、Cross-sectional side view( Figure 5B )、Bottom view( Figure 5C )、Top view( Figure 5D ) and oblique view ( Figure 5E ).

[0050] Figure 6A-6C An example of an apparatus for collecting a biological sample is shown, including a view of an open configuration ( Fig. 6A ), closed configuration view ( Figure 6B ) and a top view of the container in an open configuration ( Figure 6C ).

[0051] Figure 7 A computer system 701 is shown that is programmed or otherwise configured to implement the methods of the present disclosure. DETAILED DESCRIPTION

[0052] Although various embodiments of the present invention have been shown and described herein, it will be apparent to those skilled in the art that these embodiments are provided by way of example only. Many variations, changes and substitutions may occur to those skilled in the art without departing from the present invention. It should be understood that various alternatives to the embodiments of the present invention described herein may be employed.

[0053] As used in the specification and claims, the singular forms "a", "an", and "the" include plural references unless the context clearly dictates otherwise. For example, the term "nucleic acid" includes a plurality of nucleic acids, including mixtures thereof.

[0054] As used herein, the term "subject" generally refers to an entity or medium with testable or detectable information. The object can be a person, an individual, or a patient. The object can be a vertebrate, such as, for example, a mammal. Non-limiting examples of mammals include humans, apes, farm animals, sports animals, rodents, and pets. The object can be a person suffering from a disease, illness, or condition (e.g., cancer) or suspected of having a disease, illness, or condition (e.g., cancer). The object can show symptoms indicating the health, physiological state, or condition of the object, such as cancer or other diseases, illnesses, or conditions of the object. As an alternative, the object can be asymptomatic for such health or physiological state or condition.

[0055] As used herein, the term "sample" generally refers to a biological sample obtained or derived from one or more subjects. A biological sample can be a cell-free biological sample or a substantially cell-free biological sample, or can be processed or fractionated to produce a cell-free biological sample. For example, a cell-free biological sample can include cell-free RNA (cfRNA), cell-free deoxyribonucleic acid (cfDNA), cell-free fetal DNA (cffDNA), proteins, antibodies, plasma, serum, urine, saliva, amniotic fluid, and derivatives thereof. An ethylenediaminetetraacetic acid (EDTA) collection tube, a cell-free RNA collection tube (e.g., RNA Complete ) or cell-free DNA collection tubes (e.g., Cell-Free DNA DNA ) obtains or derives a cell-free biological sample from a subject. The cell-free biological sample can be derived from a whole blood sample by fractionation (e.g., by differential centrifugation). The biological sample or its derivative can contain cells. For example, the biological sample can be a blood sample or its derivative (e.g., blood collected by a collection tube or blood drop).

[0056] As used herein, the term "cell-free sample" generally refers to a biological sample that is substantially free of intact cells. A cell-free sample can be derived from a biological sample that is itself substantially free of cells, or can be derived from a sample from which cells have been removed. Non-limiting examples of cell-free samples include samples derived from blood, serum, plasma, urine, semen, sputum, feces, ductal exudate, lymph fluid, and recovered lavage fluid.

[0057] As used herein, the term "nucleic acid" generally refers to a polymeric form of nucleotides of any length, whether deoxyribonucleotides (dNTPs) or ribonucleotides (rNTPs), or analogs thereof. Nucleic acids can have any three-dimensional structure and can perform any known or unknown function. Non-limiting examples of nucleic acids include deoxyribonucleic acid (DNA), ribonucleic acid (RNA), coding regions or non-coding regions of genes or gene fragments, sites (locus) defined from linkage analysis, exons, introns, messenger RNA (mRNA), transfer RNA, ribosomal RNA, short interfering RNA (siRNA), short hairpin RNA (shRNA), microRNA (miRNA), ribozymes, cDNA, recombinant nucleic acids, branched nucleic acids, plasmids, vectors, isolated DNA of any sequence, isolated RNA of any sequence, nucleic acid probes and primers. Nucleic acids can include one or more modified nucleotides, such as methylated nucleotides and nucleotide analogs. If present, the nucleotide structure can be modified before or after nucleic acid assembly. The nucleotide sequence of nucleic acids can be interrupted by non-nucleotide components. Nucleic acids can be further modified after polymerization, such as by conjugating or combining with a reporter.

[0058] As used herein, the term "target nucleic acid" generally refers to a nucleic acid molecule in a starting nucleic acid molecule population having a nucleotide sequence, the presence, amount and / or sequence of which or one or more changes therein need to be determined. The target nucleic acid can be any type of nucleic acid, including DNA, RNA and the like. As used herein, the term "target ribonucleic acid (RNA)" generally refers to a target nucleic acid as RNA. As used herein, the term "target deoxyribonucleic acid (DNA)" generally refers to a target nucleic acid as DNA.

[0059] As used herein, the term "amplification" generally refers to increasing the size or quantity of a nucleic acid molecule. A nucleic acid molecule can be single-stranded or double-stranded. Amplification can include generating one or more copies or "amplification products" of a nucleic acid molecule. For example, amplification can be performed by extension (e.g., primer extension) or connection. Amplification can include performing a primer extension reaction to generate a chain complementary to a single-stranded nucleic acid molecule, and generating one or more copies of the chain and / or single-stranded nucleic acid molecule in some cases. The term "DNA amplification" generally refers to generating one or more copies or "amplified DNA products" of a DNA molecule. The term "reverse transcription amplification" generally refers to generating deoxyribonucleic acid (DNA) from a ribonucleic acid (RNA) template via the action of a reverse transcriptase.

[0060] Disease detection is a key component for providing treatment to patients, and early detection can improve outcomes. Collecting biological samples from a subject (e.g., a patient) can allow disease detection of the subject's biological fluids or tissues. Sample collection can occur at a time or location different from the location where the sample analysis is performed. The sample may need to maintain its integrity prior to analysis in order to provide accurate actionable data.

[0061] Provided herein are devices and methods for collecting biological samples from objects. Biological samples collected from objects may include nucleic acids, polypeptides, or other biomolecules or analytes. The presence of these biomolecules or analytes may indicate the genotype state, phenotypic state, or other characteristics of the object. However, when collecting samples and before analyzing samples, biomolecules or analytes may degrade or otherwise react, so that the collected samples and the analyzed samples may include differences. Therefore, it is desirable to improve the preservation of biomolecules or analytes in samples. The devices and methods provided herein may be applicable to collecting and preserving samples from objects.

[0062] The device and method provided herein can be used to collect and preserve samples to allow the preserved samples to be transported to the analysis location. The sample can then be processed so that one or more types of analytes can be analyzed. One or more types of analytes can include DNA or RNA, such as cfDNA or cfRNA. One or more analytes can be cfDNA, germline DNA, and cfRNA. One or more types of analytes can include proteins. One or more types of analytes can include metabolites. Compared to samples that have not been subjected to the device and method of the present disclosure, the device and method can allow detection or determination of improved diagnosis or prognosis of an object.

[0063] The present invention provides a device for collecting a urine sample from a subject, the device comprising: a container, the container comprising a piercer extending across the longitudinal axis of the container toward an opening of the container; and a lid, the lid comprising a pierceable container, the pierceable container comprising a reagent for processing or preserving the urine sample, wherein the device is configured so that when the container is engaged with the lid to position the lid near the opening, the piercer pierces the pierceable container to release the reagent into the container.

[0064] Provided herein is a method for collecting a urine sample from a subject, the method comprising: (a) providing a container comprising a piercer extending across a longitudinal axis of the container toward an opening of the container, wherein the container comprises a urine sample; (b) engaging the container with a lid so that the lid is disposed proximate the opening, wherein the lid comprises a pierceable container comprising a reagent for processing or preserving the urine sample; and (c) when the container is engaged with the lid, causing the lid or container to perform a closing movement, the closing movement causing the piercer to pierce the pierceable container to release the reagent into the container.

[0065] In some embodiments, the device or method includes a container. The container can be configured to hold a sample that has been added to the container. The container can include a tube. The container can include a rounded bottom. The container can include a flat bottom. The container can include a bottom with a small ridge. The small ridge can allow the container to be stably placed on a flat surface, or can allow an instrument to be connected to the container. The piercer can be directly fixed to the container. The container can include a circular opening. The container can include a surface for attaching a label, or can include a surface on which writing or drawing can be performed. For example, the container can include a matte surface. The matte surface can allow handwriting or other marks that are less visible (or less clear) on a transparent container to be visible on the container. The label can be a separate component, such as a sticker that can be added to the container, or the label can be printed, engraved, etched, or otherwise added directly to the container. For example, the container can have a location for filling in the name of the object from which the sample is derived. Similarly, the container can have a location for indicating a room number, a doctor's name, or other information about the medical provider. In addition, the container can include an indication location for adding information related to the date and time of collecting the sample. This can allow the sample to be tracked as it is distributed to other individuals for processing. For example, date and time information can allow a medical provider to track when a sample was provided.

[0066] The container may include threads to connect with the lid and allow the lid to be screwed onto the container. The threads may be single threads. The threads may be double threads. The threads on the container may be spaced apart, have a width or pitch, so as to connect with the threads on the lid.

[0067] The volume of the container can be at least 10 mL, 15 mL, 20 mL, 25 mL, 30 mL, 40 mL, 50 mL, 55 mL, 60 mL, 65 mL, 70 mL, 75 mL, 80 mL, 85 mL, 90 mL, 95 mL, 100 mL, 110 mL, 120 mL, 130 mL, 140 mL, 150 mL, 160 mL, 170 mL, 180 mL, 190 mL, 200 mL or more. The volume of the container may be no more than 10 mL, 15 mL, 20 mL, 25 mL, 30 mL, 40 mL, 50 mL, 55 mL, 60 mL, 65 mL, 70 mL, 75 mL, 80 mL, 85 mL, 90 mL, 95 mL, 100 mL, 110 mL, 120 mL, 130 mL, 140 mL, 150 mL, 160 mL, 170 mL, 180 mL, 190 mL, 200 mL or less.

[0068] In some embodiments, the device or method includes a piercer. The piercer may include a piercing rod. The piercer may include a sharp object configured to pierce a pierceable container. The sharp object may be arranged in various directions relative to the piercing rod. For example, the piercing rod may be arranged along a vertical axis, and the sharp object may be directly fixed on the top of the piercing rod, with its sharp edge in line with the vertical axis. For example, the piercing rod may be arranged along a vertical axis, and the sharp object may be directly fixed on the top of the piercing rod, with its sharp edge at an angle to the vertical axis. The piercer may include a plurality of sharp objects. The sharp object may include a sharp edge along the vertical axis or at an angle to the vertical axis. The piercer may be fixed to the bottom surface of the container or another surface of the container, and may extend to different planes toward the opening of the container. The piercer may extend to the plane of the opening of the container. The piercer may extend beyond the plane of the opening of the container.

[0069] In some embodiments, the device or method includes a lid. The lid may include a circular lid. The lid may be configured to accommodate or include a pierceable container. For example, the lid may include a compartment that protrudes vertically into the container. The additional compartment may accommodate a pierceable container. The volume of the compartment may be at least 1 mL, 2 mL, 3 mL, 4 mL, 5 mL, 6 mL, 7 mL, 8 mL, 9 mL, 10 mL, 11 mL, 12 mL, 13 mL, 14 mL, 15 mL, 16 mL, 17 mL, 18 mL, 19 mL, 20 mL or more. The volume of the compartment may be no more than 1 mL, 2 mL, 3 mL, 4 mL, 5 mL, 6 mL, 7 mL, 8 mL, 9 mL, 10 mL, 11 mL, 12 mL, 13 mL, 14 mL, 15 mL, 16 mL, 17 mL, 18 mL, 19 mL, 20 mL or less.

[0070] The bottom of the lid can allow the pierceable container to be exposed (e.g., so that the pierceable surface of the pierceable container is exposed) and can be pierced by a piercer. The lid can be allowed to be attached to the container. For example, the lid can include a thread, and there can be a corresponding thread on the container to allow the lid to rotate or be screwed onto the container, thereby closing the container (e.g., to provide anti-leakage, leak-proof and / or airtight sealing). The lid can include a single thread. The lid can include a double thread. The thread on the lid can be spaced apart, have a width or a pitch, to be connected with the thread on the container. The lid can include a gasket to allow a leakproof container to be produced once the lid is attached to the container. When pressure is applied to the lid toward the container, the lid can be attached to the container. The lid can be configured to close a variety of different types of containers.

[0071] In some embodiments, the device or method includes a pierceable container. The pierceable container can be a compartment attached to a lid having a closure such as a membrane, a seal, or a lid; or the pierceable container can be an adapter attached to a lid into which a bottle or bag can fit. The pierceable container can have different diameter sizes and different protrusion lengths into the container. For example, the pierceable container can have a maximum diameter and a minimum protrusion length, such as Figure 1A As another example, the pierceable container may have a medium diameter and a medium protrusion length, such as Figure 2C As shown. The pierceable container may include a flexible material. The pierceable container may include a pierceable surface that can be pierced so that liquid in the pierceable container can leave the pierceable container. The pierceable container may include multiple pierceable surfaces. The pierceable container may include only one pierceable surface.

[0072] The volume of the pierceable container can be at least 1 mL, 2 mL, 3 mL, 4 mL, 5 mL, 6 mL, 7 mL, 8 mL, 9 mL, 10 mL, 11 mL, 12 mL, 13 mL, 14 mL, 15 mL, 16 mL, 17 mL, 18 mL, 19 mL, 20 mL or more. The volume of the pierceable container can be no more than 1 mL, 2 mL, 3 mL, 4 mL, 5 mL, 6 mL, 7 mL, 8 mL, 9 mL, 10 mL, 11 mL, 12 mL, 13 mL, 14 mL, 15 mL, 16 mL, 17 mL, 18 mL, 19 mL, 20 mL or less.

[0073] Figure 1A-1B An example of an apparatus for collecting a biological sample is shown, including a view of an open configuration ( Figure 1A ) and the closed configuration view ( Figure 1B ).

[0074] Figure 1AAn example of a device for collecting biological samples in an open configuration is shown. The container 101 may include a piercing rod 105, which is fixed to the bottom surface of the container and extends along a vertical axis. A piercer 110 is attached to the top of the piercing rod 105. The piercer 110 may include one or more sharp objects or edges. These edges may extend beyond the plane or opening of the container 101. The device may include a lid 120, which may be used to close the container 101. The lid may include a pierceable container 125, which is attached to the lid 120 or is part of the lid 120. The pierceable container may be exposed at the bottom of the lid so that when the lid 120 is brought to the opening of the container 101, the pierceable container 125 is near the piercer 110. When the lid 120 is attached to the container 101, the piercer 110 contacts the pierceable container 125 and pierces the pierceable surface of the pierceable container 125. After piercing the pierceable container, the contents of the pierceable container may be able to exit the pierceable container. With the help of gravity, the contents of the pierceable container may exit the pierceable container 125 and enter the container 101 and mix with the existing contents of the container (e.g., urine sample). Thus, closing the container 101 with the lid 120 may create a leak-resistant, leak-proof, airtight, or otherwise stable container including a sample, and at the same time allow for the addition of a reagent that may help preserve or stabilize the sample in the container.

[0075] Figure 1B An example of a device for collecting a biological sample is shown in a closed configuration. Lid 120 has been attached to container 101. Piercer 110 is now in direct contact with pierceable container 125 and pierces pierceable container 125. When the container is closed, the contents of pierceable container 125 exit pierceable container 125 and flow into closed container 101. The contents in container 101 can now mix with the existing contents in the pierceable container, thereby allowing the introduction of reagents into container 101 while the container is closed.

[0076] Figure 2A-2F An example of a device for collecting a biological sample is shown, including example dimensions of the device ( Figure 2A ), the container's view ( Figure 2B ) and various views of the lid ( Figure 2C-2F ). The container 201 including the piercing rod / piercer 205 is closed with a lid 220 including the pierceable container 210. The piercer 205 extends into the pierceable container 210 and allows any reagent to be released into the container.

[0077] Figure 2A Example dimensions for the device are shown. Figure 2BAlternative angles of container 201 are shown. Container 201 is shown with threads on the upper portion, which allows connection with lid 210 and allows the lid to be screwed onto the container. Lid 210 has threads to allow the container to be closed. The piercer is fixed to the inner bottom surface of the container and has a single tip capable of piercing the pierceable container. The container can be transparent to allow the fluid in the container to be visible. This can allow a user to identify the container as containing fluid. In addition, the color of the fluid can indicate the type of fluid or the presence of an agent. The container can also include text or markings that allow identification of the sample or identification of a specific patient or user from which the sample is derived.

[0078] Figure 2C Alternative angles of the lid 210 are shown. The lid 210 includes threads to allow connection with a container so that the container can be closed. The additional lid 210 includes an open space to allow insertion of a pierceable container. The pierceable container can be interchangeable with the lid and allows for a modular design, where a universal lid can be used and different pierceable containers can be added to the lid based on the desired application. In some embodiments, the lid 210 can be used directly as a pierceable container, using a pierceable membrane or seal or lid to close the pink opening.

[0079] Figure 2D Another angle of the cover 210 is shown. As described above, the cover 210 includes a hollow cylinder that can be filled with a pierceable container. The outside of the cylinder can be made of the same material as the cover and can be a hard object that cannot be pierced by the piercer or piercing rod. When properly oriented, the outside of the cylinder should not contact the piercer, but should wrap around the piercer so that it contacts the object placed in the opening created by the cylinder.

[0080] Figure 2E Shown with Figure 2D Similar angles, where a cylinder or other shape is filled with a pierceable container or reagent. Now, this lid 210 can be used to add reagents to a closed container when the lid is engaged with the container. Figure 2F A cross section of the lid is shown. The cylinder may have a solid wall surrounding the reagent / pierceable container, with only one open end.

[0081] Figure 3A-3C An example of an apparatus for collecting a biological sample is shown, including a side view ( Figure 3A )、Cross-sectional side view( Figure 3B ) and oblique view ( Figure 3C ).

[0082] Figure 3AAn example exterior of a collection device is shown. As shown, the device may include a label or location of the device for writing or adding information related to the sample. As shown, the device may have a location for filling in the name of the subject from whom the sample was derived. Similarly, the device may have a location for indicating a room number, a doctor's name, or other information about the medical provider. In addition, the device may include an indicated location for adding information related to the date and time the sample was collected.

[0083] Figure 3B A cross-sectional view of an example device with example dimensions is shown. A container 301 including a piercing rod / piercer 305 is closed with a lid 320 including a pierceable container 310. The piercer 305 extends into the pierceable container 310 and allows any agent to be released into the container. Figure 2A Compared to the single-pronged piercer depicted in Figure 3B The piercer depicted in is a multi-pronged piercer. Figure 3C An oblique view of a closure device with a lid 320 and a container 301 is shown.

[0084] Figure 4A-4D An example of a cover for use in an apparatus for collecting a biological sample is shown, including a side view of the cover ( Figure 4A ), a cross-sectional side view of a lid within a closed container ( Figure 4B )、Top view of the lid( Figure 4C ) and oblique view of the cover ( Figure 4D ).

[0085] Figure 4A Example dimensions of an example lid are provided. The dimensions of the diameter of the circular top of the lid, the diameter of the bottom protruding into the container, the height of the top, the total height of the lid including the bottom protruding into the container, and the height of the rim of the lid are all shown.

[0086] Figure 4B Example dimensions of an example lid are provided. The dimensions of the inner diameter of the circular top of the lid, the inner diameter of the bottom protruding into the container, the height of the bottom protruding into the container, and the diameter of the interior of the lid that contacts the container (e.g., from the threads of the lid) are all shown. In addition, the volume of the lid bottom that can accommodate a pierceable container can be at least 10 mL.

[0087] Figure 4C A top view of the cover is shown, indicating the size of the diameter of the cover.

[0088] Figure 5A-5E An example of a container for use in an apparatus for collecting a biological sample is shown, including a side view ( Figure 5A )、Cross-sectional side view( Figure 5B )、Bottom view( Figure 5C )、Top view( Figure 5D ) and oblique view ( Figure 5E ).

[0089] Figure 5A The inner diameter of the container, the outer diameter of the container including the thread, the outer diameter of the container not including the thread, the height of the container and the example dimensions of the height of the threaded portion of the container that can contact the lid are shown. The thread for contacting the lid and being screwed on the lid can be a double thread. This can allow for firm contact with the lid to prevent the lid from being accidentally removed. The container can also have an area with a matte surface. Writing tools (e.g., pens, pencils, etc.) can be used to write on the matte surface to provide information about the sample produced by the object or other individuals.

[0090] Figure 5B A cross-sectional view of a container with dimensions of the inner diameter of the container, the height of the threaded cup portion, and the height of the piercing rod / piercer is shown. The dimensions of the container can be such that the lid can be tightly coupled to the threads of the cup. Specifically, the threads of the container are designed to specifically couple with the threads on the lid to minimize the lid from slipping off the container. Figure 5B The example container shown in can hold a volume greater than 90 mL.

[0091] Figure 5C A bottom view of an example container is shown. As shown, the bottom can have three evenly spaced ridges. This can allow the container to be evenly placed on a surface or interface with an instrument.

[0092] Figure 5D A top view of an example container is shown. The piercer / piercing rod may be in an "x" shape.

[0093] Figure 5E An oblique view of an example container is shown. As shown, the piercer / piercing rod may have a raised tip at the end of the "x" and a slightly lower height in the middle of the "x".

[0094] Figure 6A-6C An example of an apparatus for collecting a biological sample is shown, including a view of an open configuration ( Fig. 6A ), closed configuration view ( Figure 6B ) and a top view of the container in an open configuration ( Figure 6C ). Figure 6A-6C Shown based on Figure 3A-3C , Figure 4A-4C and Figure 5A-5E Photograph of an example device with schematic diagram shown in .

[0095] In some embodiments, a sample from a subject may be obtained or collected. The subject may have cancer or be suspected of having cancer. Cancer may be specific or derived from an organ or other region of the subject. For example, cancer may include breast cancer, lung cancer, prostate cancer, colorectal cancer, melanoma, bladder cancer, non-Hodgkin's lymphoma, kidney cancer, endometrial cancer, leukemia, pancreatic cancer, thyroid cancer and liver cancer and any combination thereof. Cancer may include hormone-sensitive prostate cancer (HSPC), castration-resistant prostate cancer (CRPC), metastatic prostate cancer and combinations thereof.

[0096] Urine samples may include nucleic acids. Urine samples may be processed to obtain cell-free deoxyribonucleic acid (cfDNA) samples or cell-free ribonucleic acid (cfRNA) samples. Biological samples may include genomic DNA or germline DNA (gDNA). Nucleic acids may be DNA (e.g., double-stranded DNA, single-stranded DNA, single-stranded DNA hairpins, cDNA, genomic DNA, germline DNA, circulating tumor DNA (ctDNA), cell-free DNA (cfDNA)), RNA (e.g., cfRNA, mRNA, cRNA, miRNA, siRNA, miRNA, snoRNA, piRNA, tiRNA, snRNA) or DNA / RNA hybrids. In some cases, samples may include RNA and DNA. For example, samples may include cfDNA and cfRNA, and cfDNA and cfRNA may be analyzed. Urine samples may include polypeptides, lipids, or carbohydrates. Polypeptides, lipids, or carbohydrates may be stored or separated for further analysis. Polypeptides, lipids, or carbohydrates may be degraded or denatured so that the sample is rich in nucleic acids.

[0097] In some embodiments, the pierceable container includes one or more reagents. The reagent can stabilize the nucleic acid molecules, analytes, tissues or cells in the sample. The reagent can minimize the degradation of the biological sample before the assay. Additional reagents can include enzymes, enzyme inhibitors, buffer salts or chelating agents. For example, the reagent can include ethylenediaminetetraacetic acid (EDTA) or another chemical substance. The reagent can include a nuclease inhibitor.

[0098] The biological sample may be subjected to additional reactions or conditions prior to the assay. For example, the biological sample may be subjected to conditions sufficient to separate, enrich, extract, deplete, or amplify nucleic acids (such as cfDNA molecules or cfRNA molecules).

[0099] The methods disclosed herein may include performing one or more enrichment reactions on one or more nucleic acid molecules in a sample. Using the apparatus and methods provided herein can retain nucleic acids or prevent nucleic acid degradation, and allow additional nucleic acids compared to samples not subjected to the apparatus and methods provided herein. Therefore, the output of the enrichment reaction can be improved by using the apparatus and methods of the present disclosure. The enrichment reaction may include contacting the sample with one or more beads or bead groups. The enrichment reaction may include one or more hybridization reactions. For example, the enrichment reaction may include contacting the sample with one or more capture probes or bait molecules that hybridize with nucleic acid molecules of a biological sample. The enrichment reaction may include differential amplification of a group of nucleic acid molecules. The enrichment reaction may enrich multiple gene loci or sequences corresponding to gene loci.

[0100] The methods disclosed herein may include performing one or more separation or purification reactions on one or more nucleic acid molecules in a sample. The use of the apparatus and methods provided herein may retain nucleic acids or prevent nucleic acid degradation, and allow additional nucleic acids compared to samples not subjected to the apparatus and methods provided herein. Therefore, the output of the separation or purification reaction may be improved by using the apparatus and methods of the present disclosure. The separation or purification reaction may include contacting the sample with one or more beads or bead groups. The separation or purification reaction may include one or more hybridization reactions, enrichment reactions, amplification reactions, sequencing reactions, or combinations thereof. The separation or purification reaction may include the use of one or more separators. The one or more separators may include a magnetic separator. The separation or purification reaction may include separating the nucleic acid molecules bound to the beads from the nucleic acid molecules without the beads. The separation or purification reaction may include separating the nucleic acid molecules hybridized with the capture probe from the nucleic acid molecules without the capture probe. The separation reaction may include removing or separating one group of nucleic acid molecules from another group of nucleic acids.

[0101] The methods disclosed herein can include performing an extraction reaction on one or more nucleic acids in a biological sample. The extraction reaction can lyse cells or disrupt the interaction of nucleic acids with cells, thereby separating, purifying, enriching nucleic acids, or subjecting them to other reactions. Using the apparatus and methods provided herein can retain nucleic acids or prevent nucleic acid degradation, and allow additional nucleic acids to be compared to samples that have not been subjected to the apparatus and methods provided herein. Therefore, the output of the extraction reaction can be improved by using the apparatus and methods of the present disclosure.

[0102] The methods disclosed herein may include amplification or extension reaction of a sample or a nucleic acid derived from a sample. The amplification reaction may include polymerase chain reaction (PCR). The amplification reaction may include PCR-based amplification, non-PCR-based amplification, or a combination thereof. One or more PCR-based amplifications may include PCR, quantitative PCR (qPCR), nested PCR, linear amplification, or a combination thereof. One or more non-PCR-based amplifications may include multiple displacement amplification (MDA), transcription-mediated amplification (TMA), nucleic acid sequence-based amplification (NASBA), strand displacement amplification (SDA), real-time SDA, rolling circle amplification, ring-to-ring amplification, or a combination thereof. The amplification reaction may include isothermal amplification. The use of the apparatus and methods provided herein may retain nucleic acids or prevent nucleic acid degradation, and allow additional nucleic acids compared to samples that have not been subjected to the apparatus and methods provided herein. Therefore, the output of the amplification or extension reaction may be improved by using the apparatus or methods of the present disclosure. The methods disclosed herein may include mass spectrometry of a sample or an analyte (e.g., DNA, RNA, protein, and / or metabolite) derived from a sample.

[0103] In some embodiments, the nucleic acid can undergo a sequencing reaction. The sequencing reaction can be used for DNA, RNA or other nucleic acid molecules. Examples of sequencing reactions that can be used include capillary sequencing, next generation sequencing, Sanger sequencing, sequencing by synthesis, single molecule nanopore sequencing, sequencing by ligation, hybridization sequencing, nanopore current restriction sequencing or a combination thereof. Sequencing by synthesis can include reversible terminator sequencing, progressive single molecule sequencing, sequential nucleotide flow sequencing or a combination thereof. Sequential nucleotide flow sequencing can include pyrophosphate sequencing, pH-mediated sequencing, semiconductor sequencing or a combination thereof. The sequencing reaction can include whole genome sequencing, whole exome sequencing, low-throughput whole genome sequencing, targeted sequencing, methylation-aware sequencing, enzymatic methylation sequencing, bisulfite methylation sequencing. The sequencing reaction can be transcriptome sequencing, mRNA-seq, totalRNA-seq, smallRNA-seq, exosome sequencing or a combination thereof. A combination of sequencing reactions can be used in the methods provided herein. For example, a sample can undergo whole genome sequencing and whole transcriptome sequencing. Because a sample may include multiple types of nucleic acids (eg, RNA and DNA), sequencing reactions specific for DNA or RNA may be used to obtain sequence reads associated with the nucleic acid type.

[0104] Nucleic acid sequencing can generate sequencing read data. Sequencing reads can be processed to generate quality-improved data. Sequencing reads with quality scores can be generated. The quality score can indicate the accuracy of the sequence read or the level or signal above the noise threshold of a given base recognition. The quality score can be used to filter the sequencing reads. For example, sequencing reads that do not meet a specific quality score threshold can be removed. Sequencing reads can be processed to generate a consensus sequence or a consensus base recognition. A given nucleic acid (or nucleic acid fragment) can be sequenced, and errors may be generated in the sequence due to reactions before or during sequencing. For example, amplification or PCR may generate errors in the amplicon, making the sequence different from the parent sequence. Error correction can be performed using sample barcodes or molecular barcodes. Error correction can include identifying sequence reads that cannot be verified with other sequences from the same sample or the same original parent molecule. The use of barcodes can allow the identification of the same parent or sample. In addition, sequence reads can be processed by performing single-stranded consensus sequence recognition or double-stranded consensus sequence recognition, thereby reducing or suppressing errors.

[0105] In some embodiments, the apparatus and methods of the present disclosure may allow for improved accuracy, sensitivity, or specificity of detection of the presence of a molecule in a sample compared to a sample that has not been preserved or stabilized using the methods or apparatus disclosed herein. For example, the apparatus and methods may include improving detection of the presence of a molecule in a subject sample with an accuracy of at least about 60%, at least about 70%, at least about 75%, at least about 80%, at least about 85%, at least about 90%, at least about 95%, at least about 98%, or at least about 99%, compared to a sample that has not been preserved or stabilized using the methods or apparatus disclosed herein. The apparatus and methods may include detecting the presence of a molecule in a subject sample with a sensitivity of at least about 60%, at least about 70%, at least about 75%, at least about 80%, at least about 85%, at least about 90%, at least about 95%, at least about 98%, or at least about 99%, compared to a sample that has not been preserved or stabilized using the methods or apparatus disclosed herein. The devices and methods may include detecting the presence of a molecule in a sample from a subject with a specificity of at least about 60%, at least about 70%, at least about 75%, at least about 80%, at least about 85%, at least about 90%, at least about 95%, at least about 98%, or at least about 99%, compared to a sample that has not been preserved or stabilized using the methods or devices disclosed herein.

[0106] The present disclosure provides computer systems programmed to implement the disclosed methods. Figure 7 A computer system 701 is shown that is programmed or otherwise configured to, for example, collect a biological sample from a subject.

[0107] Computer system 701 can coordinate various aspects of the analysis, calculation and generation of the present disclosure, such as, for example, collecting biological samples of subjects. Computer system 701 can be a user's electronic device or a computer system remotely located relative to the electronic device. The electronic device can be a mobile electronic device.

[0108] The computer system 701 includes a central processing unit (CPU, also referred to herein as a "processor" and "computer processor") 705, which may be a single-core or multi-core processor, or multiple processors for parallel processing. The computer system 701 also includes a memory or storage location 710 (e.g., random access memory, read-only memory, flash memory), an electronic storage unit 715 (e.g., a hard disk), a communication interface 720 (e.g., a network adapter) for communicating with one or more other systems, and peripherals 725, such as cache, other memory, data storage, and / or an electronic display adapter. The memory 710, the storage unit 715, the interface 720, and the peripherals 725 communicate with the CPU 705 via a communication bus (solid lines) (such as a motherboard). The storage unit 715 may be a data storage unit (or data repository) for storing data. The computer system 701 may be operably coupled to a computer network ("network") 730 via the communication interface 720. The network 730 may be the Internet, an internetwork, and / or an extranet, or an intranet and / or an extranet in communication with the Internet.

[0109] In some cases, network 730 is a telecommunications and / or data network. Network 730 may include one or more computer servers that can implement distributed computing, such as cloud computing. For example, one or more computer servers can implement cloud computing through network 730 ("cloud") to perform various aspects of analysis, calculation, and generation of the present disclosure, such as, for example, collecting biological samples of an object. Such cloud computing can be provided by cloud computing platforms such as Amazon Web Services (AWS), Microsoft Azure, Google Cloud Platform, and IBM Cloud. In some cases, with the help of computer system 701, network 730 can implement a peer-to-peer network, which can enable devices coupled to computer system 701 to act as clients or servers.

[0110] The CPU 705 may include one or more computer processors and / or one or more graphics processing units (GPUs). The CPU 705 may execute a series of machine-readable instructions, which may be embodied in a program or software. The instructions may be stored in a memory location such as memory 710. The instructions may be directed to the CPU 705, which may then be programmed or otherwise configured to implement the methods of the present disclosure. Examples of operations performed by the CPU 705 may include fetching, decoding, executing, and writing back.

[0111] CPU 705 may be part of a circuit such as an integrated circuit. One or more other components of system 701 may be included in the circuit. In some cases, the circuit is an application specific integrated circuit (ASIC).

[0112] Storage unit 715 can store files, such as drivers, libraries, and saved programs. Storage unit 715 can store user data, such as user preferences and user programs. In some cases, computer system 701 may include one or more additional data storage units located external to computer system 701, such as located on a remote server that communicates with computer system 701 via an intranet or the Internet.

[0113] Computer system 701 may communicate with one or more remote computer systems via network 730. For example, computer system 701 may communicate with a user's remote computer system. Examples of remote computer systems include personal computers (e.g., portable PCs), tablets or tablet computers (e.g., iPad, Galaxy Tab), phones, smartphones (e.g. iPhone, Android-enabled devices, ) or a personal digital assistant. Users can access computer system 701 via network 730.

[0114] The methods described herein may be implemented by machine (e.g., computer processor) executable code stored in an electronic storage location (such as, for example, memory 710 or electronic storage unit 715) of computer system 701. Machine executable or machine readable code may be provided in the form of software. During use, processor 705 may execute the code. In some cases, the code may be retrieved from storage unit 715 and stored in memory 710 for ready access by processor 705. In some cases, electronic storage unit 715 may be removed and machine executable instructions may be stored in memory 710.

[0115] The code may be pre-compiled and configured for use with a machine having a processor suitable for executing the code, or may be compiled at run time. The code may be provided in a programming language which may be selected to enable the code to be executed in a pre-compiled or compiled form.

[0116] Aspects of the systems and methods provided herein, such as computer system 701, can be embodied in programming. Various aspects of the technology can be considered as "products" or "manufactures", which are usually in the form of machine (or processor) executable code and / or related data, which are carried or embodied in a type of machine-readable medium. Machine executable code can be stored in an electronic storage unit such as a memory (e.g., read-only memory, random access memory, flash memory) or a hard disk. "Storage" type media can include any or all tangible memories of a computer, processor, etc., or its related modules, such as various semiconductor memories, tape drives, disk drives, etc., which can provide non-transient storage for software programming at any time. All or part of the software can sometimes communicate through the Internet or various other telecommunications networks. For example, such communication can load software from one computer or processor to another computer or processor, such as from a management server or host computer to a computer platform of an application server. Therefore, another type of medium that can carry software elements includes light waves, radio waves, and electromagnetic waves, such as waves used by crossing physical interfaces between local devices, by wired and optical fiber fixed telephone networks, and by various air links. Physical elements that carry such waves (such as wired or wireless links, fiber optic links, etc.) can also be considered media that carry the software. As used herein, unless limited to non-transitory, tangible "storage" media, terms such as computer or machine "readable media" refer to any medium that participates in providing instructions to a processor for execution.

[0117] Thus, machine-readable media (such as computer executable code) can take a variety of forms, including but not limited to tangible storage media, carrier media, or physical transmission media. Non-volatile storage media include, for example, optical or magnetic disks, such as any storage device or the like in any computer, such as can be used to implement the database shown in the figure, etc. Volatile storage media include dynamic memory, such as the main memory of such a computer platform. Tangible transmission media include coaxial cables; copper wires and optical fibers, including wires that make up the bus within a computer system. Carrier transmission media can take the form of electrical or electromagnetic signals or sound or light waves, such as those generated during radio frequency (RF) and infrared (IR) data communications. Thus, common forms of computer-readable media include, for example: floppy disks, flexible disks, hard disks, magnetic tapes, any other magnetic media, CD-ROMs, DVDs or DVD-ROMs, any other optical media, punched card tapes, any other physical storage media with a pattern of holes, RAMs, ROMs, PROMs and EPROMs, FLASH-EPROMs, any other memory chips or cassettes, carriers that transmit data or instructions, cables or links that transmit such carriers, or any other media from which a computer can read programming code and / or data. Many of these forms of computer readable media may be involved in carrying one or more sequences of one or more instructions to a processor for execution.

[0118] Computer system 701 may include or communicate with electronic display 735 including user interface (UI) 740 for performing methods such as, for example, collecting a biological sample of a subject. Examples of UI include, but are not limited to, graphical user interfaces (GUIs) and web-based user interfaces.

[0119] The methods and systems of the present disclosure may be implemented by one or more algorithms. The algorithms may be implemented by software when executed by the central processing unit 705. The algorithms may, for example, collect a biological sample of a subject.

[0120] Although preferred embodiments of the present invention have been shown and described herein, it will be apparent to those skilled in the art that these embodiments are provided by way of example only. The present invention is not intended to be limited by the specific examples provided in the specification. Although the present invention has been described with reference to the above description, the description and illustration of the embodiments herein are not intended to be interpreted in a limiting sense. Those skilled in the art will now conceive of many variations, changes and substitutions without departing from the present invention. In addition, it should be understood that all aspects of the present invention are not limited to the specific descriptions, configurations or relative proportions described herein, which depend on various conditions and variables. It should be understood that in practicing the present invention, various alternatives to the embodiments of the present invention described herein may be adopted. Therefore, the present invention should also cover any such alternatives, modifications, variations or equivalents. The appended claims are intended to define the scope of the present invention, and thus cover methods and structures within the scope of these claims and their equivalents.

Claims

1. A device for collecting a biological sample from a subject, the device comprising: a container comprising a piercer extending across a longitudinal axis of the container toward an opening of the container; as well as a cover comprising a pierceable container comprising a reagent for processing or preserving the biological sample, Wherein the apparatus is configured such that when the lid is engaged with the container to position the lid adjacent the opening, the piercer pierces the pierceable container to release the agent into the container.

2. The device of claim 1, wherein the piercer pierces the pierceable container when the lid or the container is rotated.

3. The apparatus of claim 1, wherein the engagement of the lid with the container for positioning the lid adjacent the opening and movement of the lid toward the container or movement of the container toward the lid closes the container. The apparatus of claim 1 , wherein the lid is configured to be attached to the container.

5. The apparatus of claim 4, wherein the lid is configured to attach to the container at least in part by applying pressure to the lid toward the container or to the container toward the lid when the lid is adjacent the opening.

6. The apparatus of claim 4, wherein the lid is configured to be attached to the container at least in part by rotating the lid or the container when the lid is adjacent the opening.

7. The apparatus of claim 4, wherein said attachment of said lid to said container creates a leak-resistant, leak-proof or airtight compartment.

8. The apparatus of claim 1, wherein the cap and the container each include threads, wherein the threads of the cap and the threads of the container are configured to connect together to close the container.

9. The device of claim 1, wherein the piercer comprises a rod, wherein a top of the rod comprises a sharp protrusion.

10. The device of claim 9, wherein the piercer comprises a plurality of sharp protrusions.

11. The apparatus of claim 9, wherein the rod is disposed on a surface of the container.

12. The apparatus of claim 11, wherein the rod is disposed on a bottom surface of the container.

13. The device of claim 1, wherein the pierceable container is configured such that a pierceable surface of the pierceable container is exposed on a bottom surface of the lid.

14. The apparatus of claim 1, wherein the cover comprises solid surfaces at a top surface and side surfaces of the cover.

15. The device of claim 1, wherein the reagent is configured to maintain the integrity of an analyte in the biological sample in response to the release of the reagent into the container.

16. The apparatus of claim 15, wherein the analyte comprises a nucleic acid, a polypeptide, a lipid, or a carbohydrate.

17. The apparatus of claim 1, wherein the sharp protrusion is above the plane of the opening.

18. The apparatus of claim 1, wherein the sharp protrusion is configured to protrude into the container.

19. The apparatus of claim 1, wherein the container comprises a tube.

20. The apparatus of claim 1, wherein the container comprises a flat bottom or a substantially flat bottom.

21. The apparatus of claim 1, wherein the container comprises a circular bottom or a substantially circular bottom.

22. The device of claim 1, wherein the pierceable container comprises a bag.

23. The apparatus of claim 1, wherein the reagent comprises an enzyme, an enzyme inhibitor, a chelator, a buffer, or a combination thereof.

24. The apparatus of claim 23, wherein the chelating agent comprises ethylenediaminetetraacetic acid (EDTA).

25. The apparatus of any one of claims 1-24, wherein the biological sample comprises a urine sample.

26. A method for collecting a biological sample from a subject, the method comprising: (a) providing a container comprising a piercer extending across a longitudinal axis of the container toward an opening of the container, wherein the container comprises the biological sample; (b) engaging a cover with the container to position the cover adjacent the opening, wherein the cover comprises a pierceable container comprising a reagent for processing or preserving the biological specimen; and (c) when the lid is engaged with the container, causing the lid or the container to perform a closing movement, thereby piercing the pierceable container by the piercer to release the agent into the container.

27. The method of claim 26, wherein the closing motion comprises rotating the container or the lid.

28. The method of claim 26, wherein the closing motion comprises applying pressure to the lid toward the container or applying pressure to the container toward the lid.

29. The method of claim 26, further comprising closing the container at least in part by rotating the lid or the container.

30. The method of claim 26, further comprising closing the container at least in part by applying pressure to the lid or the container.

31. The method of claim 26, further comprising attaching the lid to the container.

32. The method of claim 26, wherein the attachment of the lid to the container creates a leak-resistant, leak-proof, or airtight compartment.

33. The method of claim 26, wherein the cap and the container each include threads, and wherein the method further comprises coupling the threads of the cap and the threads of the container together, thereby closing the container.

34. The method of claim 26, wherein the piercer comprises a rod, wherein a top of the rod comprises a sharp protrusion.

35. The method of claim 34, wherein the piercer comprises a plurality of sharp protrusions.

36. The method of claim 34, wherein the rod is disposed on a surface of the container.

37. The method of claim 36, wherein the rod is disposed on a bottom surface of the container.

38. The method of claim 26, wherein the pierceable container is configured such that a pierceable surface of the pierceable container is exposed on a bottom surface of the lid.

39. The method of claim 26, wherein the cover comprises solid surfaces at a top surface and side surfaces of the cover.

40. The method of claim 26, further comprising mixing the reagent and the biological specimen together in response to the releasing of the reagent into the container.

41. The method of claim 40, wherein the reagent is configured to maintain the integrity of the analyte in the biological sample in response to the mixing.

42. The method of claim 41, wherein the analyte comprises a nucleic acid, a polypeptide, a lipid, or a carbohydrate.

43. The method of claim 42, further comprising measuring the analyte.

44. The method of claim 26, wherein the sharp protrusion is located above the plane of the container opening.

45. The method of claim 26, wherein the sharp protrusions protrude into the container.

46. ​​The method of claim 26, wherein the container comprises a tube.

47. The method of claim 26, wherein the container comprises a flat bottom or a substantially flat bottom.

48. The method of claim 26, wherein the container comprises a circular bottom or a substantially circular bottom.

49. The method of claim 26, wherein the pierceable container comprises a bag.

50. The method of claim 26, wherein the reagent comprises an enzyme, an enzyme inhibitor, a chelating agent, a buffer, or a combination thereof.

51. The method of claim 50, wherein the chelating agent comprises ethylenediaminetetraacetic acid (EDTA).

52. The method of claim 26, further comprising providing the biological sample to the container.

53. The method of claim 26, wherein the subject has or is suspected of having a disease, disorder, genetic disorder, or genetic aberration.

54. The method of claim 53, wherein the disease comprises cancer.

55. The method of claim 54, wherein the cancer comprises a genitourinary cancer.

56. The method of claim 55, wherein the genitourinary cancer comprises bladder cancer, prostate cancer, kidney or renal cancer, penile cancer, testicular cancer, or urethral cancer.

57. A system comprising one or more computer processors and a computer memory coupled to the one or more computer processors, the computer memory comprising machine executable code that, when executed by the one or more computer processors, implements a method for collecting a biological sample from a subject, the method comprising: (a) providing a container comprising a piercer extending across a longitudinal axis of the container toward an opening of the container, wherein the container comprises the biological sample; (b) engaging a cover with the container to position the cover adjacent the opening, wherein the cover comprises a pierceable container comprising a reagent for processing or preserving the biological specimen; and (c) when the lid is engaged with the container, causing the lid or the container to perform a closing movement, thereby piercing the pierceable container by the piercer to release the agent into the container.

58. The system of claim 57, wherein the biological sample comprises a urine sample.

59. A non-transitory computer readable medium comprising machine executable code which, when executed by one or more computer processors, implements a method for collecting a biological sample from a subject, the method comprising: (a) providing a container comprising a piercer extending across a longitudinal axis of the container toward an opening of the container, wherein the container comprises the biological sample; (b) engaging a cover with the container to position the cover adjacent the opening, wherein the cover comprises a pierceable container comprising a reagent for processing or preserving the biological specimen; and (c) when the lid is engaged with the container, causing the lid or the container to perform a closing movement, thereby piercing the pierceable container by the piercer to release the agent into the container.

60. The non-transitory computer readable medium of claim 59, wherein the biological sample comprises a urine sample.

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