# US 2023/0056549 A1 · Methods of determining a surgical margin and methods of use thereof > Agents: this data is available as JSON from the patentgrep API and MCP server — see https://patentgrep.com/llms.txt - Number: US 2023/0056549 A1 - Document ID: US20230056549A1 - Status: Published application - Kind: A1 - Application number: 17/981,082 - Filed: 2022-11-04 - Published: 2023-02-23 - Earliest claimed: 2020-06-08 - Assignees: 10x Genomics, Inc. - Applicants: 10x Genomics, Inc. - Inventors: Smritee Dadhwal - Web page: https://patentgrep.com/patent/US20230056549A1 ## CPC - C12N 15/1065: {Preparation or screening of tagged libraries, e.g. tagged microorganisms by STM-mutagenesis, tagged polynucleotides, gene tags} - C12Q 1/6841: In situ hybridisation - C12Q 1/6874: involving nucleic acid arrays, e.g. sequencing by hybridisation - C12N: MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA (microbiological testing media C12Q1/00) - C12Q: MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS (immunoassay G01N33/53); COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES ## Abstract Provided herein are methods of determining a surgical margin and the site and size of a tissue to be resected from a subject, and methods of use thereof. ## Claims ### Claim 1 A method of determining a surgical margin of a tissue to be resected in a subject, the method comprising: (a) contacting a tissue section obtained from the subject to a first substrate; (b) aligning the first substrate with a second substrate comprising an array, such that at least a portion of the biological sample is aligned with at least a portion of the array, wherein the array comprises a plurality of capture probes, wherein a capture probe of the plurality of capture probes comprises: (i) a spatial barcode and (ii) a capture domain; (c) permeabilizing the tissue section and hybridizing the analyte to the capture domain; (d) determining (i) all or a part of a nucleic acid sequence corresponding to the analyte hybridized to the capture domain or a complement thereof, and (ii) the spatial barcode or a complement thereof, and using the determined nucleic acid sequences of (i) and (ii) to identify the presence of the analyte at a location in the tissue section; and (e) comparing the presence of the analyte at the location in the tissue section to presence of the analyte at one or more different locations in the tissue section, thereby determining the surgical margin of the tissue to be resected from the subject based on the comparison. ### Claim 2 (depends on 1) The method of claim 1, wherein the presence of the analyte at the location in the tissue section is increased compared to the presence of the analyte at the different location in the tissue section that is a non-cancerous location and/or a non-tumor location. ### Claim 3 (depends on 1) The method of claim 1, wherein the presence of the analyte at the location in the tissue section is decreased compared to the presence of the analyte at the different location in the tissue section that is a non-cancerous location and/or a non-tumor location. ### Claim 4 (depends on 1) The method of claim 1, wherein the tissue to be resected comprises a tumor. ### Claim 5 (depends on 1) The method of claim 1, wherein the tissue to be resected is an infected tissue, a necrotic tissue, or a diseased tissue. ### Claim 6 (depends on 5) The method of claim 5, wherein the infected tissue is infected by a bacterium, a virus, a fungus, a parasite, and/or protozoa. ### Claim 7 (depends on 1) The method of claim 1, wherein the subject is suspected of or diagnosed as having cancer. ### Claim 8 (depends on 7) The method of claim 7, wherein the cancer is breast cancer. ### Claim 9 (depends on 1) The method of claim 1, wherein the analyte is ribonucleic acid (RNA) or deoxyribonucleic acid (DNA). ### Claim 10 (depends on 1) The method of claim 1, wherein step (d) comprises sequencing (i) all or a part of the nucleic acid sequence corresponding to the analyte specifically bound to the capture domain or a complement thereof, and (ii) the spatial barcode or a complement thereof. ### Claim 11 (depends on 1) The method of claim 1, wherein the capture probe further comprises one or more functional domains, a unique molecular identifier, a cleavage domain, or any combination thereof. ### Claim 12 (depends on 1) The method of claim 1, wherein comparing the presence of the analyte at the location in the tissue section to the presence of the analyte at one or more different locations in the tissue section further comprises determining the size and site of the tissue to be resected from the subject. ### Claim 13 (depends on 1) The method of claim 1, wherein the method results in a: reduced rate of re-excision of the tissue; and/or reduced rate of recurrence of the tissue abnormality in the subject. ### Claim 14 (depends on 1) The method of claim 1, further comprising administering a treatment of surgery to the subject after step (e). ### Claim 15 (depends on 1) The method of claim 1, wherein the tissue section was previously fixed and/or stained by hematoxylin and eosin, immunohistochemistry, and/or immunofluorescence. ### Claim 16 A method of determining a surgical margin of a tissue to be resected in a subject, the method comprising: (a) contacting a tissue section obtained from the subject to a first substrate; (b) contacting the tissue sample to a plurality of analyte capture agents, wherein an analyte capture agent of the plurality of analyte capture agents comprises: an analyte binding moiety that binds specifically to an analyte, an analyte binding moiety barcode, and an analyte capture sequence; (c) aligning the first substrate with a second substrate comprising an array, such that at least a portion of the biological sample is aligned with at least a portion of the array, wherein the array comprises a plurality of capture probes, wherein a capture probe of the plurality of capture probes comprises: (i) a spatial barcode and (ii) a capture domain; (d) permeabilizing the tissue section and hybridizing the analyte capture sequence to the capture domain; (e) determining (i) all or a part of a nucleic acid sequence corresponding to the analyte capture sequence hybridized to the capture domain or a complement thereof, and (ii) the spatial barcode or a complement thereof, and using the determined nucleic acid sequences of (i) and (ii) to identify the presence of the analyte at a location in the tissue section; and (f) comparing the presence of the analyte at the location in the tissue section to presence of the analyte at one or more different locations in the tissue section, thereby determining the surgical margin of the tissue to be resected from the subject based on the comparison. ### Claim 17 (depends on 16) The method of claim 16, wherein the presence of the analyte at the location in the tissue section is increased compared to the presence of the analyte at the different location in the tissue section that is a non-cancerous location and/or a non-tumor location. ### Claim 18 (depends on 16) The method of claim 16, wherein the presence of the analyte at the location in the tissue section is decreased compared to the presence of the analyte at the different location in the tissue section that is a non-cancerous location and/or a non-tumor location. ### Claim 19 (depends on 16) The method of claim 16, wherein the tissue to be resected comprises a tumor. ### Claim 20 (depends on 16) The method of claim 16, wherein the tissue to be resected is an infected tissue, a necrotic tissue, or a diseased tissue. ### Claim 21 (depends on 20) The method of claim 20, wherein the infected tissue is infected by a bacterium, a virus, a fungus, a parasite, and/or protozoa. ### Claim 22 (depends on 16) The method of claim 16, wherein the subject is suspected of or diagnosed as having cancer. ### Claim 23 (depends on 22) The method of claim 22, wherein the cancer is breast cancer. ### Claim 24 (depends on 16) The method of claim 16, wherein the analyte is a protein. ### Claim 25 (depends on 16) The method of claim 16, wherein step (e) comprises sequencing (i) all or a part of the nucleic acid sequence corresponding to the analyte capture sequence specifically bound to the capture domain or a complement thereof, and (ii) the spatial barcode or a complement thereof. ### Claim 26 (depends on 16) The method of claim 16, wherein the capture probe further comprises one or more functional domains, a unique molecular identifier, a cleavage domain, or any combination thereof. ### Claim 27 (depends on 16) The method of claim 16, wherein comparing the presence of the analyte at the location in the tissue section to the presence of the analyte at one or more different locations in the tissue section further comprises determining the size and site of the tissue to be resected from the subject. ### Claim 28 (depends on 16) The method of claim 16, wherein the method results in a: reduced rate of re-excision of the tissue; and/or reduced rate of recurrence of the tissue abnormality in the subject. ### Claim 29 (depends on 16) The method of claim 16, further comprising administering a treatment of surgery to the subject after step (f). ### Claim 30 (depends on 16) The method of claim 16, wherein the tissue section was previously fixed and/or stained by hematoxylin and eosin, immunohistochemistry, and/or immunofluorescence.