Device and method for sample collection

Abstract

This specification provides a device and a method for collecting a biological sample. The device may include a cap, a pierceable container containing a reagent for processing or storing the biological sample, and a container with a piercer. When the cap is engaged with the opening of the container, the piercer can pierce the pierceable container, thereby releasing the reagent in the pierceable container into the container. The method may include the step of using a device for collecting a biological sample. The method may include the step of assaying an analyte of the biological sample.

Description

Technical Field

[0001] Cross-reference This application claims the benefit of U.S. Provisional Application No. 63 / 354,883, filed Jun. 23, 2022, which is hereby incorporated by reference in its entirety.

Background Art

[0002] The detection of diseases is a very important factor in providing treatment to patients, and early detection can improve the outcome. By collecting a biological sample from a subject (e.g., a patient), it may be possible to detect a disease in the biological fluid or tissue of the subject. Sampling may be performed at a different time or location than when the sample is analyzed. In order to provide accurate and valid data, the sample may need to maintain its integrity prior to analysis.

Summary of the Invention

[0003] Devices and methods for collecting a biological sample from a subject are provided herein. The biological sample collected from the subject may contain nucleic acids, polypeptides, or other biomolecules or analytes. The presence of these biomolecules or analytes may indicate the genotype, phenotype, or other characteristics of the subject. However, prior to sample collection and analysis, the biomolecules or analytes may undergo degradation or other reactions such that the collected sample and the analyzed sample do not match. Accordingly, there is a need for sample collection devices and methods that can improve the preservation of biomolecules or analytes in the sample. The devices and methods provided herein may be suitable for the collection and preservation of samples from a subject.

[0004] In one aspect, the present disclosure provides a device for collecting a biological sample of interest, the device comprising: a container having a cannula extending along a longitudinal axis of the container towards an opening of the container; and a cap comprising a pierceable container containing a reagent for treating or protecting the biological sample, wherein when the cap is engaged with the container and disposed adjacent to the opening, the cannula is configured to pierce the pierceable container to release the reagent into the container.

[0005] In some embodiments, the cannula pierces the pierceable container when the cap or the container is rotated.

[0006] In some embodiments, closing of the container is effected by engaging the cap with the container and disposing the cap adjacent to the opening, and moving the cap towards the container or moving the container towards the cap.

[0007] In some embodiments, the cap is configured to be attached to the container. In some embodiments, the cap is configured to be at least partially attached to the container by applying pressure to the cap in the direction of the container or applying pressure to the container in the direction of the cap when the cap is adjacent to the opening. In some embodiments, the cap is configured to be at least partially attached to the container by rotating the cap or the container when the cap is adjacent to the opening. In some embodiments, attaching the cap to the container creates a leak-resistant, leak-proof, or airtight compartment.

[0008] In some embodiments, the cap and the container each comprise a threaded portion, and the threaded portions of the cap and the container are configured to close the container by engaging with each other.

[0009] In some embodiments, the puncture device comprises a rod, and the upper part of the rod is provided with a sharp protrusion. In some embodiments, the puncture device 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.

[0010] In some embodiments, the pierceable container is configured such that the pierceable surface of the pierceable container is exposed on the bottom surface of the cap.

[0011] In some embodiments, the cap comprises a solid surface on the upper and side surfaces of the cap.

[0012] In some embodiments, the reagent is configured to maintain the integrity of the analyte in the biological sample in response to releasing the reagent into the container. In some embodiments, the analyte comprises nucleic acid, polypeptide, lipid, or carbohydrate.

[0013] 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.

[0014] 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 circular bottom or a substantially circular bottom.

[0015] In some embodiments, the pierceable container comprises a pouch.

[0016] 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).

[0017] In some embodiments, the biological sample comprises a urine sample.

[0018] In another aspect, the present disclosure provides a method for collecting a biological sample of interest, the method comprising: (a) providing a container comprising a cannula extending towards an opening of the container along a longitudinal axis of the container, the container containing a biological sample; (b) engaging a cap with the container and disposing the cap adjacent to the opening, the cap comprising a pierceable container containing a reagent for treating or protecting the biological sample; and (c) when the cap is engaged with the container, causing a closing operation on the cap or the container to cause the cannula to pierce the pierceable container and release the reagent into the container.

[0019] In some embodiments, the closing operation comprises rotating the container or the cap.

[0020] In some embodiments, the closing operation comprises applying pressure to the cap in the direction of the container or applying pressure to the container in the direction of the cap.

[0021] In some embodiments, the method further comprises at least partially closing the container by rotating the cap or the container.

[0022] In some embodiments, the method further comprises at least partially closing the container by applying pressure to the cap or the container.

[0023] In some embodiments, the method further comprises attaching the cap to the container.

[0024] In some embodiments, attaching the cap to the container creates a leak-resistant, leak-proof, or airtight compartment.

[0025] In some embodiments, the cap and the container each comprise a threaded portion, and the method further comprises closing the container by joining the threaded portion of the cap and the threaded portion of the container together.

[0026] In some embodiments, the piercer comprises a rod, and the upper part 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.

[0027] In some embodiments, the pierceable container is configured such that the pierceable surface of the pierceable container is exposed on the bottom surface of the cap.

[0028] In some embodiments, the cap comprises a solid surface on the upper surface and the side surface of the cap.

[0029] In some embodiments, the method further comprises a step of mixing the reagent and the biological sample together in response to releasing 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 step.

[0030] In some embodiments, the analyte comprises nucleic acid, polypeptide, lipid, or carbohydrate. In some embodiments, the method further comprises a step of assaying the analyte.

[0031] 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.

[0032] 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 circular bottom or a substantially circular bottom. In some embodiments, the pierceable container comprises a pouch.

[0033] 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).

[0034] In some embodiments, the method further includes, prior to step (a), supplying a biological sample to a container.

[0035] In some embodiments, the subject has or is suspected of having a disease, disorder, genetic disorder, or genetic abnormality.

[0036] In some embodiments, the disease includes cancer. In some embodiments, the cancer includes genitourinary cancer. In some embodiments, the genitourinary cancer includes bladder cancer, prostate cancer, kidney or renal cancer, penile cancer, testicular cancer, or urethral cancer.

[0037] In some embodiments, the biological sample includes a urine sample.

[0038] 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 in this specification.

[0039] Another aspect of the present disclosure provides a system including one or more computer processors and a computer memory coupled to the computer processors. The computer memory includes machine-executable code that, when executed by one or more computer processors, implements any of the methods described above or elsewhere in this specification.

[0040] Further aspects and advantages of the present disclosure will become readily apparent to those skilled in the art from the following detailed description, which illustrates only exemplary embodiments of the present disclosure. As will be understood, the present disclosure is capable of other and different embodiments, and some of its details are capable of modification in various obvious respects without departing from the present disclosure. Accordingly, the drawings and description are to be regarded as illustrative in nature and not as restrictive.

[0041] Incorporation by reference All publications, patents, and patent applications mentioned in this specification are hereby incorporated by reference into this specification to the same extent as if each individual publication, patent, or patent application was specifically and individually indicated to be incorporated by reference. To the extent that the publications and patents or patent applications incorporated by reference conflict with the present disclosure contained herein, this specification is intended to supersede and / or take precedence over any such conflicting materials.

Brief Description of the Drawings

[0042] The novel features of the invention are set forth in detail in the appended claims. The features and advantages of the invention will be better understood from the following detailed description which describes exemplary embodiments in which the principles of the invention are utilized, and from the appended drawings (also referred to herein as "figures" and "FIGs").

[0043]

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DETAILED DESCRIPTION OF THE INVENTION

[0044] Although various embodiments of the present invention have been shown and described herein, it will be apparent to those skilled in the art that such embodiments are provided by way of example only. Those skilled in the art can conceive of numerous variations, modifications, and substitutions without departing from the present invention. It should be understood that various alternative forms to the embodiments of the present invention described herein may be used.

[0045] As used in this specification and the claims, the singular forms "a", "an", and "the" include plural referents unless the context clearly dictates otherwise. For example, the term "nucleic acid" includes a plurality of nucleic acids including mixtures thereof.

[0046] As used herein, the term "subject" generally refers to an entity or medium having testable or detectable information. The subject can be a human, an individual, or a patient. The subject can be a vertebrate such as, for example, a mammal. Non-limiting examples of mammals include humans, monkeys, domestic animals, sport animals, rodents, and pets. The subject can be a human having or suspected of having a disease, disorder, or illness (e.g., cancer). The subject may exhibit symptoms indicative of the subject's health status, physiological state, or disease such as cancer or other disease, disorder, or illness. Alternatively, the subject may be asymptomatic with respect to such health status or physiological state or disease.

[0047] As used herein, the term "sample" generally refers to a biological sample obtained or derived from one or more subjects. The biological sample may be a cell-free or substantially cell-free biological sample, or may be processed or fractionated to generate a cell-free biological sample. For example, cell-free biological samples can include cell-free ribonucleic acid (cfRNA), cell-free deoxyribonucleic acid (cfDNA), cell-free fetal DNA (cffDNA), proteins, antibodies, plasma, serum, urine, saliva, amniotic fluid, and derivatives thereof. Cell-free biological samples can be obtained or derived from a subject using an ethylenediaminetetraacetic acid (EDTA) collection tube, a cell-free RNA collection tube (e.g., Streck® RNA Complete BCT®), or a cell-free DNA collection tube (e.g., Streck® Cell-Free DNA BCT®). Cell-free biological samples can be derived from whole blood samples by fractionation (e.g., by fractionation centrifugation). A biological sample or a derivative thereof may contain cells. For example, a biological sample can be a blood sample (e.g., blood collected by a blood collection tube or a small amount of blood) or a derivative thereof.

[0048] 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 cell-free or from a sample from which cells have been removed. Non-limiting examples of cell-free samples include those derived from blood, serum, plasma, urine, semen, sputum, feces, ductal exudate, lymph fluid, and recovered wash fluid.

[0049] As used herein, the term "nucleic acid" generally refers to a polymeric form of nucleotides of any length, i.e., either 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), the coding or non-coding regions of genes or gene fragments, loci defined from linkage analysis, exons, introns, messenger RNA (mRNA), transfer RNA, ribosomal RNA, small interfering RNA (siRNA), small 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 contain one or more modified nucleotides such as methylated nucleotides and nucleotide analogs. When included, modifications to the nucleotide structure can be made before or after assembly of the nucleic acid. The nucleotide sequence of a nucleic acid can be interrupted by non-nucleotide components. Nucleic acids can be further modified after multimerization, such as by conjugation or binding to a reporter agent.

[0050] As used herein, the term "target nucleic acid" generally refers to a nucleic acid molecule in a starting population of nucleic acid molecules having a nucleotide sequence for which it is desired to determine the presence, amount, and / or sequence, or one or more changes therein. The target nucleic acid can be any type of nucleic acid, including DNA, RNA, and their analogs. As used herein, "target ribonucleic acid (RNA)" generally refers to a target nucleic acid that is RNA. As used herein, "target deoxyribonucleic acid (DNA)" generally refers to a target nucleic acid that is DNA.

[0051] As used herein, the terms "amplify" and "amplification" generally refer to increasing the size or amount of a nucleic acid molecule. The nucleic acid molecule can be single-stranded or double-stranded. Amplification can include generating one or more copies or "amplification products" of the nucleic acid molecule. Amplification can be performed, for example, by extension (e.g., primer extension) or ligation. Amplification can include performing a primer extension reaction to generate a strand complementary to a single-stranded nucleic acid molecule and, optionally, generating one or more copies of the strand and / or the single-stranded nucleic acid molecule. The term "DNA amplification" generally refers to generating one or more copies of a DNA molecule or "amplified DNA product". The term "reverse transcription amplification" generally refers to generating deoxyribonucleic acid (DNA) from a ribonucleic acid (RNA) template by the action of reverse transcriptase.

[0052] The detection of disease is a very important element in providing treatment to a patient, and early detection may improve the outcome. By collecting a biological sample from a subject (e.g., a patient), it may be possible to detect a disease in the biological fluid or tissue of the subject. Sampling may be performed at a different time or location than where the sample is analyzed. The sample may need to maintain its integrity prior to analysis in order to provide accurate and valid data.

[0053] This specification provides devices and methods for collecting a biological sample from a subject. The biological sample collected from the subject can contain nucleic acids, polypeptides, or other biomolecules or analytes. The presence of these biomolecules or analytes can indicate the genotype state, phenotype state, or other characteristics of the subject. However, prior to sample collection and analysis, the biomolecules or analytes may undergo degradation or other reactions such that the collected sample and the analyzed sample do not match. Accordingly, there is a need for sample collection devices and methods that can improve the preservation of biomolecules or analytes in the sample. The devices and methods provided herein may be suitable for the collection and preservation of samples from a subject.

[0054] The devices and methods provided herein can be used for collecting and preserving a sample and can make the preserved sample transportable to an analysis location. The sample can then be processed to enable the analysis of one or more types of analytes. The one or more types of analytes can include DNA or RNA, such as cfDNA or cfRNA. The one or more analytes can be cfDNA, germline DNA, and cfRNA. The one or more types of analytes can include proteins. The one or more types of analytes can include metabolites. The present devices and methods may enable an improvement in the detection or determination of the diagnosis or prognosis of a subject as compared to samples to which the devices and methods of the present disclosure are not applied.

[0055] This specification provides a device for collecting a urine sample from a subject, the device comprising: a container having a cannula extending along a longitudinal axis of the container towards an opening of the container; and a cap comprising a pierceable container containing a reagent for treating or protecting the urine sample, wherein when the container is engaged with the cap and the cap is disposed adjacent to the opening, the cannula is configured to pierce the pierceable container to release the reagent into the container.

[0056] This specification provides a method for collecting a urine sample of interest, the method comprising: (a) providing a container, the container comprising a puncture device extending towards an opening of the container along a longitudinal axis of the container, the container containing the urine sample; (b) engaging the container with a cap such that the cap is disposed adjacent to the opening, the cap comprising a pierceable container containing a reagent for treating or protecting a biological sample; and (c) upon engaging the container with the cap, causing a closing operation to be performed on the cap or the container, the closing operation causing the puncture device to pierce the pierceable container and thereby release the reagent into the container.

[0057] In some embodiments, the device or method includes a container. The container may be configured to hold a sample added to the container. The container may comprise a tube. The container may comprise a circular bottom. The container may comprise a flat bottom. The container may comprise a bottom having a small protrusion. The small protrusion may enable the container to rest stably on a flat surface or may enable an instrument to engage with the container. The puncture device may be directly fixed to the container. The container may comprise a circular opening. The container may comprise a surface for affixing a label or a surface on which writing or drawing can be done. For example, the container may comprise a matte surface. The matte surface may make visible (or legible) pen marks and other markings that would otherwise be difficult to see (or read) on a transparent container. The label may be a separate component, such as a sticker that can be added to the container, or the label may be printed, engraved, etched, or otherwise added directly to the container. For example, the container may be provided with a location for entering the name of the subject from whom the sample is derived. Similarly, the container may be provided with a location for displaying room number, doctor's name, or other information regarding the healthcare provider. Further, the container may be provided with a display location for adding information regarding the date and time when the sample was obtained. This may enable tracking of the sample when the sample is supplied to other individuals for processing. For example, the date and time information may enable a healthcare provider to track when the sample was provided.

[0058] The container may comprise a threaded portion for joining with the cap and enabling screwing the cap onto the container. The threaded portion may be a single threaded portion. The threaded portion may be a double threaded portion. The threaded portion on the container may have a spacing, width, or thread pitch such that it joins with the threaded portion on the cap.

[0059] The volume of the container may 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 a volume greater than that. The volume of the container may be 10 mL or less, 15 mL or less, 20 mL or less, 25 mL or less, 30 mL or less, 40 mL or less, 50 mL or less, 55 mL or less, 60 mL or less, 65 mL or less, 70 mL or less, 75 mL or less, 80 mL or less, 85 mL or less, 90 mL or less, 95 mL or less, 100 mL or less, 110 mL or less, 120 mL or less, 130 mL or less, 140 mL or less, 150 mL or less, 160 mL or less, 170 mL or less, 180 mL or less, 190 mL or less, 200 mL or less, or a volume less than that.

[0060] In some embodiments, the device or method comprises a piercer. The piercer may comprise a piercing rod. The piercer may comprise a sharp instrument configured to pierce a pierceable container. The sharp instrument may be arranged in various directions with respect to the piercing rod. For example, the piercing rod may be arranged along a vertical axis, and the sharp instrument may be directly fixed to the upper part of the piercing rod such that the sharp edge coincides with the vertical axis. For example, the piercing rod may be arranged along a vertical axis, and the sharp instrument may be directly fixed to the upper part of the piercing rod with the sharp edge angled from the vertical axis. The piercer may comprise a plurality of sharp instruments. The sharp instrument may comprise a sharp edge along or angled with respect 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 in different planes towards the opening of the container. The piercer may extend in the plane of the opening of the container. The piercer may extend beyond the plane of the opening of the container.

[0061] In some embodiments, the device or method comprises a cap. The cap may comprise a circular cap. The cap may be configured to hold or comprise a pierceable container. For example, the cap may comprise a section that projects vertically into the container. This additional section can hold the pierceable container. The volume of the section 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 section can be 1 mL or less, 2 mL or less, 3 mL or less, 4 mL or less, 5 mL or less, 6 mL or less, 7 mL or less, 8 mL or less, 9 mL or less, 10 mL or less, 11 mL or less, 12 mL or less, 13 mL or less, 14 mL or less, 15 mL or less, 16 mL or less, 17 mL or less, 18 mL or less, 19 mL or less, 20 mL or less, or less than that.

[0062] The bottom of the cap can expose a pierceable container (e.g., such that the pierceable surface of a pierceable container is exposed) and can be pierced by a piercer. The cap can be attachable to the container. For example, the cap can include a threaded portion (e.g., to provide leak resistance, leak prevention, and / or an airtight seal), and a corresponding threaded portion can be present on the container, enabling the cap to be rotated or screwed onto the container, thereby closing the container. The cap can include a single threaded portion. The cap can include a double threaded portion. The threaded portion on the cap can have a spacing, width, or number of threads that mates with the threaded portion on the container. The cap may include a gasket, such that when the cap is attached to the container, a leak-proof container can be created. The cap can be attached to the container when pressure is applied to the cap in the direction of the container. The cap can be configured to close a plurality of different types of containers.

[0063] In some embodiments, the device or method includes a pierceable container. The pierceable container can be a compartment attached to a cap having a closure such as a membrane, seal, or cap, or the pierceable container can be an adapter attached to the cap, into which a bottle or pouch can fit. The pierceable container can have various diameter sizes and various lengths of protrusion into the container. For example, the pierceable container can have a maximum diameter and a minimum length of protrusion, as shown in FIG. 1A. As another example, the pierceable container can have an intermediate diameter and an intermediate length of protrusion, as shown in FIG. 2C. The pierceable container can include a flexible material. The pierceable container can include a pierceable surface through which liquid inside the pierceable container can exit when the pierceable container is pierced. The pierceable container can include a plurality of pierceable surfaces. The pierceable container can include only one pierceable surface.

[0064] The pierceable container may have a volume of 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 pierceable container may have a volume of 1 mL or less, 2 mL or less, 3 mL or less, 4 mL or less, 5 mL or less, 6 mL or less, 7 mL or less, 8 mL or less, 9 mL or less, 10 mL or less, 11 mL or less, 12 mL or less, 13 mL or less, 14 mL or less, 15 mL or less, 16 mL or less, 17 mL or less, 18 mL or less, 19 mL or less, 20 mL or less, or less than that.

[0065] Figures 1A - 1B are diagrams showing an example of a device for collecting a biological sample, including a diagram of an open configuration (Figure 1A) and a diagram of a closed configuration (Figure 1B).

[0066] Figure 1A shows an example of a device for biological sample collection in an open configuration. The container (101) may include a puncture rod (105) that is fixed to the bottom surface of the container and extends along a vertical axis. A puncturer (110) is attached to the upper part of the puncture rod (105). The puncturer (110) may include one or more sharp instruments or sharp blades. These blades may extend beyond the plane or opening of the container (101). The device may include a cap (120) that can be used to close the container (101). The cap may include a pierceable container (125) that is attached to or is part of the cap (120). The pierceable container may be exposed at the bottom of the cap such that when the cap (120) is carried to the opening of the container (101), the pierceable container (125) is adjacent to the puncturer (110). When the cap (120) is attached to the container (101), the puncturer (110) contacts the pierceable container (125) and pierces through the pierceable surface of the pierceable container (125). When the pierceable container is pierced, the contents of the pierceable container can be discharged from the pierceable container. With the aid of gravity, the contents of the pierceable container exit the pierceable container (125), enter the container (101), and can be mixed with the existing contents of the container (e.g., urine sample). Thus, by closing the container (101) with the cap (120), a leak-resistant, leak-proof, airtight, or otherwise stable container containing the sample can be created, and at the same time, it becomes possible to add reagents that can help protect or stabilize the sample in the container.

[0067] Figure 1B shows an example of a device for biological sample collection in a closed configuration. The cap (120) is attached to the container (101). Here, the puncturer (110) directly contacts the pierceable container (125) and pierces the pierceable container (125). When the container is closed, the contents of the pierceable container (125) exit the pierceable container (125) and flow into the closed container (101). Here, the contents in the container (101) can be mixed with the existing contents in the pierceable container, and at the same time as the container is closed, it becomes possible to introduce a reagent into the container (101).

[0068] Figures 2A - 2F show an example of a device for collecting a biological sample, including an exemplary dimension of the device (Figure 2A), a view of the container (Figure 2B), and various views of the cap (Figures 2C - 2F). A container (201) with a puncture rod / puncture device (205) is closed by a cap (220) with a pierceable container (210). The puncture device (205) extends into the pierceable container (210) and can release any reagent into the container.

[0069] Figure 2A shows exemplary dimensions of the device. Figure 2B shows an alternative angle of the container (201). The container (201) is shown to have a threaded portion at the top that enables joining with the cap (210) and screwing the cap onto the container. The cap (210) has a threaded portion for closing the container. The puncture device is fixed to the inner bottom surface of the container and has a single tip that can pierce the pierceable container. The container may be transparent so that the fluid inside the container can be seen. This may enable the user to identify the container as containing fluid. Further, the color of the fluid may indicate the type of fluid or the presence or absence of a reagent. The container may also include words or markings that enable identification of the sample, or the specific patient or user from whom the sample was derived.

[0070] Figure 2C shows an alternative angle of the cap (210). The cap (210) has a threaded portion that enables joining with the container so that the container can be closed. An additional cap (210) has an open space that enables insertion of the pierceable container. The pierceable container may be replaceable, enabling a modular design. In a modular design, a common cap may be used and different pierceable containers may be added to the cap based on the desired application. In some embodiments, the cap (210) can be used directly as a pierceable container, together with a pierceable membrane or seal or cap for closing the puncture opening.

[0071] Figure 2D shows another angle of the cap (210). As described above, the cap (210) comprises a hollow cylinder that can fill a pierceable container. The outside of the cylinder can be made of the same material as the cap and can be hard enough not to be pierced by a piercer or a piercing rod. When properly oriented, the outside of the cylinder should cover the piercer so as not to contact the piercer but instead contact an object placed within the opening created by the cylinder.

[0072] Figure 2E shows an angle similar to Figure 2D, with a pierceable container or reagent filled in the cylinder or other shape. Here, this cap (210) can be used to add a reagent to a closed container when the cap is engaged with the container. Figure 2F shows a cross-section of the cap. The cylinder can have a solid wall surrounding a reagent container / pierceable container with only one open end.

[0073] Figures 3A - 3C show an example of a device for biological sample collection, including a side view (Figure 3A), a cross-sectional side view (Figure 3B), and a perspective view (Figure 3C).

[0074] Figure 3A shows an exemplary appearance of the collection device. As shown, the device may be provided with a label or a location on the device for writing or adding information regarding the sample. As shown, the device may be provided with a location for entering the name of the subject from whom the sample is derived. Similarly, the device may be provided with a location for displaying room number, doctor's name, or other information regarding the healthcare provider. Further, the device may be provided with a display location for adding information regarding the date and time when the sample was obtained.

[0075] Figure 3B shows a cross-sectional view of an exemplary device having exemplary dimensions. A container (301) comprising a piercing rod / piercer (305) is closed by a cap (320) comprising a pierceable container (310). The piercer (305) extends into the pierceable container (310) and can release any reagent into the container. The piercer depicted in Figure 3B is a multi-pronged piercer as opposed to the single pronged piercer depicted in Figure 2A. Figure 3C shows a perspective view of a closed device having a cap (320) and a container (301).

[0076] Figures 4A - 4D show an example of a cap for use in a device for biological sample collection, including a side view of the cap (Figure 4A), a cross-sectional side view of the cap inside a closed container (Figure 4B), a top view of the cap (Figure 4C), and a perspective view of the cap (Figure 4D).

[0077] Figure 4A shows exemplary dimensions of an exemplary cap. Dimensions of the diameter of the circular top of the cap, the diameter of the bottom protruding into the container, the height of the top, the overall height of the cap including the bottom protruding into the container, and the height of the cap lip are all shown.

[0078] Figure 4B shows exemplary dimensions of an exemplary cap. Dimensions of the inner diameter of the circular top of the cap, the inner diameter of the bottom protruding into the container, the height of the bottom protruding into the container, and the diameter of the inner part of the cap that contacts the container (e.g., from the threads of the cap) are all shown. Further, the volume of the bottom of the cap that can hold a pierceable container can be at least 10 mL.

[0079] Figure 4C is a top view of the cap and shows dimensions for the diameter of the cap.

[0080] Figures 5A - 5E show an example of a container for use in a device for biological sample collection, including a side view (Figure 5A), a cross-sectional side view (Figure 5B), a bottom view (Figure 5C), a top view (Figure 5D), and a perspective view (Figure 5E).

[0081] Figure 5A shows exemplary dimensions regarding the inner diameter of the container, the outer diameter of the container including the threaded portion, the outer diameter of the container excluding the threaded portion, the height of the container, and the height of the threaded portion of the container that can contact the cap. The threaded portion for contacting and screwing onto the cap can be a double-threaded portion. This enables strong contact with the cap and can prevent the cap from accidentally coming off. Further, the container can have a region with a matte surface. Information about a subject or a sample of another individual can be provided by writing on this matte surface with a writing instrument (e.g., a pen, a pencil, etc.).

[0082] Figure 5B shows a cross-sectional view of the container including the dimensions of the inner diameter of the container, the height of the portion of the cap having the threaded portion, and the height of the piercing rod / piercer. The dimensions of the container can be such that the cap can fit snugly with the threaded portion of the cap. Specifically, the threaded portion of the container is designed to specifically engage with the threaded portion of the cap so as to minimize the cap slipping off the container. The exemplary container shown in Figure 5B can hold a volume of more than 90 mL.

[0083] Figure 5C shows a bottom view of an exemplary container. As shown, the bottom can have three equally spaced raised portions. This can allow the container to rest horizontally on a surface or to engage with an instrument.

[0084] Figure 5D shows a top view of an exemplary container. The piercer / piercing rod can be in an "x" shape.

[0085] Figure 5E shows a perspective view of an exemplary container. As shown, the piercer / piercing rod can have raised points at the ends of the "x", and the center of the "x" is at a slightly lower height.

[0086] Figures 6A-6C show an example of a device for biological sample collection, including a diagram of an open configuration (Figure 6A), a diagram of a closed configuration (Figure 6B), and a top view of the container in the open configuration (Figure 6C). Figures 6A-6C show photographs of exemplary devices based on the schematic diagrams shown in Figures 3A-3C, 4A-4C, and 5A-5E.

[0087] In some embodiments, a sample can be obtained or collected from a subject. The subject has or is suspected of having cancer. The cancer can be specific to or originate in an organ or other area of the subject. For example, the cancer can include breast cancer, lung cancer, prostate cancer, colorectal cancer, melanoma, bladder cancer, non-Hodgkin lymphoma, kidney cancer, endometrial cancer, leukemia, pancreatic cancer, thyroid cancer, and liver cancer, as well as any combination thereof. The cancer can include hormone-sensitive prostate cancer (HSPC), castration-resistant prostate cancer (CRPC), metastatic prostate cancer, and combinations thereof.

[0088] A urine sample can contain nucleic acids. The urine sample can be processed to obtain a cell-free deoxyribonucleic acid (cfDNA) sample or a cell-free ribonucleic acid (cfRNA) sample. A biological sample can contain genomic DNA or germline DNA (gDNA). The nucleic acid can be DNA (e.g., double-stranded DNA, single-stranded DNA, single-stranded DNA hairpin, 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 a DNA / RNA hybrid. In some cases, the sample can contain both RNA and DNA. For example, the sample can contain cfDNA and cfRNA, and the cfDNA and cfRNA can be analyzed. A urine sample can contain polypeptides, lipids, or carbohydrates. The polypeptides, lipids, or carbohydrates can be protected or isolated for further analysis. The polypeptides, lipids, or carbohydrates can be degraded or denatured such that the sample is enriched with respect to nucleic acids.

[0089] In some embodiments, the pierceable container contains one or more reagents. The reagents can stabilize nucleic acid molecules, analytes, tissues, or cells in the sample. The reagents can minimize the degradation of biological samples prior to the assay. Additional reagents can include enzymes, enzyme inhibitors, buffer salts, or chelating agents. For example, the reagents can include ethylenediaminetetraacetic acid (EDTA) or another chemical substance. The reagents can include nuclease inhibitors.

[0090] Additional reactions or conditions can be applied to the biological sample prior to the assay. For example, sufficient conditions for the isolation, concentration, extraction, reduction, or amplification of nucleic acids such as cfDNA molecules or cfRNA molecules are applied to the biological sample.

[0091] The methods disclosed herein can include performing one or more concentration reactions on one or more nucleic acid molecules in a sample. By using the devices and methods provided herein, nucleic acids can be protected or nucleic acid degradation can be prevented, enabling the addition of nucleic acids as compared to samples to which the devices and methods provided herein were not applied. Thus, the amount of product of the concentration reaction can be improved by using the devices and methods of the present disclosure. The concentration reaction can include contacting the sample with one or more beads or bead sets. The concentration reaction may include one or more hybridization reactions. For example, the concentration reaction can include contacting the sample with one or more capture probes or bait molecules that hybridize to the nucleic acid molecules of the biological sample. The concentration reaction can include differentially amplifying a set of nucleic acid molecules. The concentration reaction can concentrate sequences corresponding to multiple loci or loci.

[0092] The methods disclosed herein may include performing one or more isolation or purification reactions on one or more nucleic acid molecules in a sample. By using the devices and methods provided herein, nucleic acids can be protected or nucleic acid degradation can be prevented, enabling the addition of nucleic acids as compared to samples to which the devices and methods provided herein were not applied. Thus, the amount of product of the isolation or purification reaction can be improved by using the devices and methods of the present disclosure. The isolation or purification reaction may include contacting the sample with one or more beads or bead sets. The isolation or purification reaction may include one or more hybridization reactions, concentration reactions, amplification reactions, sequencing reactions, or combinations thereof. The isolation or purification reaction may include using one or more separators. The one or more separators may include a magnetic separator. The isolation or purification reaction may include separating bead-bound nucleic acid molecules from non-bead-bound nucleic acid molecules. The isolation or purification reaction may include separating capture probe hybridized nucleic acid molecules from non-capture probe nucleic acid molecules. The isolation reaction may include removing or separating a nucleic acid population from another nucleic acid population.

[0093] The methods disclosed herein may include performing an extraction reaction on one or more nucleic acids in a biological sample. The extraction reaction may lyse the cells or disrupt the interaction between the nucleic acids and the cells such that the nucleic acids can be isolated, purified, concentrated, or other reactions can be applied to the nucleic acids. By using the devices and methods provided herein, nucleic acids can be protected or nucleic acid degradation can be prevented, enabling the addition of nucleic acids as compared to samples to which the devices and methods provided herein were not applied. Thus, the amount of product of the extraction reaction can be improved by using the devices and methods of the present disclosure.

[0094] The methods disclosed herein may include an amplification reaction or an extension reaction on a sample or nucleic acid derived from a sample. The amplification reaction may include a 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, circle-to-circle amplification, or a combination thereof. The amplification reaction may include isothermal amplification. By using the devices and methods provided herein, nucleic acids can be protected or degradation of nucleic acids can be prevented, and additional nucleic acids may be enabled as compared to samples to which the devices and methods provided herein were not applied. Thus, the amount of product of the amplification or extraction reaction may be improved by using the devices and methods of the present disclosure. The methods disclosed herein may include mass spectrometry measurements on a sample or an analyte derived from a sample (e.g., DNA, RNA, protein, and / or metabolite).

[0095] In some embodiments, nucleic acids can be subjected to a sequencing reaction. The sequencing reaction can be used on 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, sequencing by hybridization, sequencing by nanopore current restriction, or combinations thereof. Sequencing by synthesis can include reversible terminator sequencing, processive single molecule sequencing, sequential nucleotide flow sequencing, or combinations thereof. Sequential nucleotide flow sequencing can include pyrosequencing, pH-mediated sequencing, semiconductor sequencing, or combinations thereof. The sequencing reaction can include whole genome sequencing, whole exome sequencing, low-pass 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 combinations thereof. Combinations of sequencing reactions can be used in the methods provided herein. For example, whole genome sequencing and whole transcriptome sequencing can be applied to a sample. Since the sample can contain multiple types of nucleic acids (e.g., RNA and DNA), sequencing reactions specific to DNA or RNA can be used to obtain sequencing reads related to the nucleic acid type.

[0096] Nucleic acid sequencing can generate sequencing read data. The sequencing reads can be processed to generate improved quality data. The sequencing reads can be generated using quality scores. The quality scores can indicate the accuracy of the sequence reads for a given base call, or a level or signal above a nose threshold. The quality scores can be used to filter the sequencing reads. For example, sequencing reads that do not meet a specific quality score threshold can be removed. The sequencing reads can be processed to generate a consensus sequence or a consensus base call. A given nucleic acid (or nucleic acid fragment) can be sequenced, and errors can occur in the sequence due to reactions before or during sequencing. For example, errors can occur in amplicons such that the sequence is not identical to the parental sequence, such as by amplification or PCR. Error correction can be performed using sample barcodes or molecular barcodes. Error correction can include identifying sequence reads that do not corroborate with other sequences from the same sample or parental molecules of the same origin. Use of barcodes can enable identification of the same parent or sample. Additionally, the sequence reads can be processed by performing single-stranded consensus scoring or double-stranded consensus scoring, thereby reducing or suppressing errors.

[0097] In some embodiments, the devices and methods of the present disclosure can improve the accuracy, sensitivity, or specificity of detecting the presence of a molecule in a sample as compared to a sample that is not protected or stabilized using the methods or devices disclosed herein. For example, the devices and methods can include improving the detection of the presence of a molecule in a sample in a subject with 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% accuracy as compared to a sample that is not protected or stabilized using the methods or devices disclosed herein. The devices and methods can include detecting the presence of a molecule in a sample in a subject with 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% sensitivity as compared to a sample that is not protected or stabilized using the methods or devices disclosed herein. The device or method can include detecting the presence of a molecule in a sample in a subject with 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% specificity as compared to a sample that is not protected or stabilized using the methods or devices disclosed herein.

[0098] The present disclosure provides a computer system programmed to implement the methods of the present disclosure. FIG. 7 shows, for example, a computer system (701) programmed or otherwise configured to collect a biological sample from a subject.

[0099] A computer system (701) can regulate various aspects of the analysis, calculation, and generation of the present disclosure, such as the collection of a target biological sample. The computer system (701) can be a user's electronic device or a computer system located remotely from the electronic device. The electronic device can be a mobile electronic device.

[0100] The computer system (701) includes a central processing unit (CPU, also referred to herein as "processor" and "computer processor") (705) that can be a single-core processor or a multi-core processor, or multiple processors for parallel processing. The computer system (701) also includes a memory or memory location (710) (e.g., random access memory, read-only memory, flash memory), an electronic storage unit (715) (e.g., hard disk), a communication junction (720) (e.g., network adapter) for communicating with one or more other systems, and peripheral devices (725) such as a cache, other memory, data storage, and / or an electronic display adapter. The memory (710), storage unit (715), junction (720), and peripheral devices (725) communicate with the CPU (705) via a communication bus (solid line) such as a motherboard. The storage unit (715) can be a data storage unit (or data repository) for storing data. The computer system (701) can be operably coupled to a computer network ("network") (730) by the communication junction (720). The network (730) can be the Internet, the Internet and / or an extranet, or an intranet and / or an extranet that communicates with the Internet.

[0101] The network (730) may, in some cases, be a telecommunications and / or data network. The network (730) may include one or more computer servers that enable distributed computing such as cloud computing. For example, one or more computer servers may enable cloud computing through the network (730) (the "cloud") to perform various aspects of the analysis, calculation, and generation of the present disclosure, such as the collection of a biological sample of interest. Such cloud computing may be provided by a cloud computing platform such as Amazon Web Services (AWS), Microsoft Azure, Google Cloud Platform, IBM cloud, etc. The network (730) may, in some cases, implement a peer-to-peer network using the computer system (701) to enable a device coupled to the computer system (701) to function as a client or a server.

[0102] The CPU (705) may include one or more computer processors and / or one or more graphics processing units (GPUs). The CPU (705) can execute an array of machine-readable instructions that can be embodied in a program or software. The instructions can be stored in a memory location such as the memory (710). The instructions can be directed to the CPU (705), and the CPU (705) can then program or otherwise configure the CPU (705) to implement the methods of the present disclosure. Examples of operations performed by the CPU (705) include fetch, decode, execute, and write-back.

[0103] The CPU (705) may be part of a circuit such as an integrated circuit. One or more other components of the system (701) may be included in the circuit. In some cases, the circuit is an application-specific integrated circuit (ASIC).

[0104] The memory unit (715) can store files such as drivers, libraries, and stored programs. The memory unit (715) can store user data, such as user selections and user programs. The computer system (701) may include one or more additional data storage units external to the computer system (701), such as being located on a remote server that communicates with the computer system (701) via an intranet or the Internet in some cases.

[0105] The computer system (701) can communicate with one or more remote computer systems via the network (730). For example, the computer system (701) can communicate with a user's remote computer system. Examples of remote computer systems include personal computers (e.g., portable PCs), slate or tablet PCs (e.g., Apple® iPad®, Samsung® Galaxy Tab), telephones, smartphones (e.g., Apple® iPhone®, Android-enabled devices, Blackberry®), or personal digital assistants. The user can access the computer system (701) via the network (730).

[0106] The methods described herein may be implemented by machine (e.g., computer processor) executable code stored in an electronic memory location of a computer system (701), such as in a memory (710) or an electronic storage unit (715). The machine executable code or machine readable code may be provided in the form of software. In use, the code may be executed by a processor (705). In some cases, the code may be retrieved from the storage unit (715) and stored in the memory (710) for easy access by the processor (705). In some situations, the electronic storage unit (715) may be excluded and the machine executable instructions may be stored in the memory (710).

[0107] The code may be pre-compiled and configured for use on a machine having a processor adapted to execute the code, or may be compiled during runtime. The code may be supplied in a programming language selected to enable the code to be executed in a pre-compiled or as-compiled manner.

[0108] Aspects of the systems and methods provided herein, such as computer system (701), can be implemented in programming. Various aspects of the technology can typically be considered a "product" or "manufactured article" in the form of machine (or processor) executable code that is carried on or embodied in some type of machine-readable medium, and / or associated data. The machine executable code can be stored in an electronic memory unit such as a memory (e.g., read-only memory, random access memory, flash memory) or a hard disk. The "memory" type of medium can include any or all of tangible memories such as computers, processors, or their associated modules such as various semiconductor memories, tape drives, disk drives, etc., which can provide non-transitory storage devices for software programming as needed. All or part of the software can sometimes be communicated via the Internet or various other electrical communication networks. Such communication can enable, for example, the loading of software from one computer or processor to another, such as from an administrative server or host computer to an application server's computer platform. Thus, another type of medium that can carry software elements includes light, electrical, and electromagnetic waves such as those used over physical connections between local devices, via wired and optical terrestrial links, and through various air links. Physical elements that carry such waves, such as wired or wireless links, optical links, etc., can also be considered media that carry software. As used herein, unless limited to non-transitory and tangible "memory" media, terms such as computer or machine "readable media" refer to any medium involved in providing instructions to a processor for execution.

[0109] Thus, machine-readable media such as computer-executable code can take many forms including, but not limited to, tangible storage media, carrier wave media, or physical transmission media. Non-volatile storage media can include optical disks or magnetic disks such as any of the storage devices in any computer, such as those that can be used to implement, for example, the databases shown in the figures. Volatile storage media can include dynamic memory such as the main memory of such a computer platform. Tangible transmission media can include copper wire and optical fiber, including coaxial cable and wire with a bus within a computer system. Carrier wave transmission media can take the form of electrical or electromagnetic signals, or acoustic 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 tape, any other magnetic media, CD-ROM, DVD or DVD-ROM, any other optical media, punch cards, paper tape, any other physical storage media with patterns of holes, RAM, ROM, PROM and EPROM, FLASH-EPROM, any other memory chip or cartridge, carrier waves that carry data or instructions, cables or links that carry such carrier waves, or any other media that a computer can read programming code and / or data from. Many of these forms of computer-readable media can be involved in carrying one or more sequences of one or more instructions to a processor for execution.

[0110] A computer system (701) can include, or be communicable with, an electronic display (735) having a user interface (UI) (740) for performing methods such as, for example, collecting a biological sample of interest. Examples of UIs include, but are not limited to, graphical user interfaces (GUIs) and web-based user interfaces.

[0111] The methods and systems of the present disclosure can be implemented by one or more algorithms. The algorithms can be implemented by software when executed by a central processing unit (705). For example, a biological sample of interest can be collected.

[0112] Preferred embodiments of the present invention have been shown and described herein, but it will be apparent to those skilled in the art that such embodiments are provided by way of example only. The present invention is not intended to be limited by the specific examples provided herein. The present invention has been described with reference to the foregoing specification, but the description and illustration of the embodiments herein are not intended to be construed in a limiting sense. Those skilled in the art will envision numerous variations, modifications, and substitutions without departing from the present invention. Furthermore, it should be understood that all aspects of the present invention are not limited to the specific depictions, configurations, or relative ratios described herein, which depend on various conditions and variables. It should be understood that various alternative forms of the embodiments of the present invention described herein can be used in practicing the present invention. Accordingly, it is intended that the present invention encompass any such alternatives, modifications, variations, or equivalents. The following claims define the scope of the present invention, and it is intended that methods and structures within the scope of these claims and their equivalents be encompassed by the following claims.

Claims

1. A device for collecting a target biological sample, comprising: a container having a puncture device extending towards the opening of the container along the longitudinal axis of the container; a cap comprising a pierceable container containing a reagent for treating or protecting the biological sample; and when the cap is engaged with the container and disposed adjacent to the opening, the puncture device is configured to puncture the pierceable container to release the reagent into the container.

2. The device according to claim 1, wherein the puncture device punctures the pierceable container when the cap or the container is rotated.

3. The device according to claim 1, wherein when the cap is engaged with the container and disposed adjacent to the opening, and when the cap is moved towards the container or the container is moved towards the cap, the container closes.

4. The device according to claim 1, wherein the cap is configured to be attached to the container.

5. The device according to claim 4, wherein the cap is configured to be at least partially attached to the container by applying pressure to the cap in the direction of the container or applying pressure to the container in the direction of the cap when the cap is adjacent to the opening.

6. The device according to claim 4, wherein the cap is configured to be at least partially attached to the container by rotating the cap or the container when the cap is adjacent to the opening.

7. The device according to claim 4, wherein attaching the cap to the container creates a leak-resistant, leak-proof, or airtight compartment.

8. The device according to claim 1, wherein the cap and the container each comprise a threaded portion, and the threaded portions of the cap and the container are configured to engage with each other to close the container.

9. The device according to claim 1, wherein the puncture device comprises a rod, and the upper portion of the rod comprises a sharp protrusion.

10. The device according to claim 9, wherein the puncture device comprises a plurality of sharp protrusions.

11. The device according to claim 9, wherein the rod is disposed on the surface of the container.

12. The device according to claim 11, wherein the rod is disposed on the bottom surface of the container.

13. The device according to 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 cap.

14. The device according to claim 1, wherein the cap has solid surfaces on an upper surface and a side surface of the cap.

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

16. The device according to claim 15, wherein the analyte includes nucleic acid, polypeptide, lipid, or carbohydrate.

17. The device according to claim 1, wherein a sharp protrusion is located above a plane of the opening.

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

19. The device according to claim 1, wherein the container comprises a tube.

20. The device according to claim 1, wherein the container has a flat bottom or a substantially flat bottom.

21. The device according to claim 1, wherein the container has a circular bottom or a substantially circular bottom.

22. The device according to claim 1, wherein the pierceable container comprises a pouch.

23. The device according to claim 1, wherein the reagent includes an enzyme, an enzyme inhibitor, a chelating agent, a buffer, or a combination thereof.

24. The device according to claim 23, wherein the chelating agent includes ethylenediaminetetraacetic acid (EDTA).

25. The device according to any one of claims 1 to 24, wherein the biological sample includes a urine sample.

26. A method for collecting a biological sample of a subject, comprising: (a) providing a container, the container comprising a piercer extending toward an opening of the container along a longitudinal axis of the container, the container containing the biological sample; (b) engaging a cap with the container and disposing the cap adjacent to the opening, the cap comprising a pierceable container containing a reagent for treating or protecting the biological sample. (c) a step of discharging the reagent into the container by piercing the pierceable container with the piercer by causing the cap or the container to perform a closing operation when the cap is engaged with the container. A method comprising: **Claim 27** The method according to claim 26, wherein the closing operation includes rotating the container or the cap. **Claim 28** The method according to claim 26, wherein the closing operation includes applying pressure in the direction of the container to the cap or applying pressure in the direction of the cap to the container. **Claim 29** The method according to claim 26, further comprising a step of at least partially closing the container by rotating the cap or the container. **Claim 30** The method according to claim 26, further comprising a step of at least partially closing the container by applying pressure to the cap or the container. **Claim 31** The method according to claim 26, further comprising a step of attaching the cap to the container. **Claim 32** The method according to claim 26, wherein attaching the cap to the container creates a leak-resistant, leak-proof, or airtight compartment. **Claim 33** The method according to claim 26, wherein the cap and the container each have a threaded portion, and the method further comprises a step of closing the container by joining the threaded portion of the cap and the threaded portion of the container together. **Claim 34** The method according to claim 26, wherein the piercer includes a rod, and an upper portion of the rod has a sharp protrusion. **Claim 35** The method according to claim 34, wherein the piercer has a plurality of sharp protrusions. **Claim 36** The method according to claim 34, wherein the rod is disposed on a surface of the container. **Claim 37** The method according to claim 36, wherein the rod is disposed on a bottom surface of the container. **Claim 38** The method according to 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 cap. **Claim 39** The method according to claim 26, wherein the cap has a solid surface on an upper surface and a side surface of the cap. **Claim 40** The method according to claim 26, further comprising a step of mixing the reagent and the biological sample together in response to discharging the reagent into the container. **Claim 41** The method according to claim 40, wherein the reagent is configured to maintain the integrity of the analyte in the biological sample in response to the mixing step.

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

43. The method according to claim 42, further comprising the step of assaying the analyte.

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

45. The method according to claim 26, wherein the sharp protrusion protrudes into the container.

46. The method according to claim 26, wherein the container comprises a tube.

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

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

49. The method according to claim 26, wherein the pierceable container comprises a pouch.

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

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

52. The method according to claim 26, further comprising the step of supplying the biological sample to the container.

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

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

55. The method according to claim 54, wherein the cancer comprises urogenital cancer.

56. The method according to claim 55, wherein the urogenital cancer comprises bladder cancer, prostate cancer, kidney (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 computer processors, wherein the computer memory comprises machine-executable code that, when executed by the one or more computer processors, implements a method of collecting a biological sample from a subject, the method comprising a step of providing a container, wherein the container comprises a puncture device extending towards the opening of the container along the longitudinal axis of the container, and the container contains the biological sample; a step of engaging a cap with the container and disposing the cap adjacent to the opening, wherein the cap comprises a pierceable container containing a reagent for treating or protecting the biological sample; a system comprising a step of, when the cap is engaged with the container, causing the cap or the container to perform a closing operation, so that the puncture device pierces the pierceable container to release the reagent into the container.

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

59. A non-transitory computer-readable medium comprising machine-executable code that implements a method for collecting a target biological sample when executed by one or more computer processors, the method comprising: a step of providing a container, wherein the container comprises a puncture device extending towards the opening of the container along the longitudinal axis of the container, and the container contains the biological sample; a step of engaging a cap with the container and disposing the cap adjacent to the opening, wherein the cap comprises a pierceable container containing a reagent for treating or protecting the biological sample; a non-transitory computer-readable medium comprising a step of, when the cap is engaged with the container, causing the cap or the container to perform a closing operation, so that the puncture device pierces the pierceable container to release the reagent into the container.

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

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