METHODS FOR ASSESSING CANCER
First Claim
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1. A method of monitoring cancer progression in a subject in need thereof, comprising:
- (a) determining the presence, absence, and/or amount of each of a subset of genes in a sample derived from a fluid sample in the subject, wherein the subset is determined by (i) performing targeted sequencing on a set of genes on a solid tissue sample from the subject wherein the solid tissue sample is known or suspected of comprising cancerous tissue;
(ii) determining a profile of genetic mutations for said set of genes based on the sequencing; and
(iii) selecting a subset of 2, 3, or 4 genes of the set of genes based on said profile for said set, wherein said subset is specific to said subject; and
(b) using the results of (a) to monitor progression of the cancer or lack thereof in the subject.
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Abstract
Provided herein are methods for assessing cancer, comprising analysis of sequence data from a set of cancer-related genes in a tumor sample from a subject, followed by monitoring of a subset of the set in circulating tumor-associated DNA in a fluid sample from the subject. Also provided are kits and systems for practicing any of them methods of the invention.
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Citations
78 Claims
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1. A method of monitoring cancer progression in a subject in need thereof, comprising:
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(a) determining the presence, absence, and/or amount of each of a subset of genes in a sample derived from a fluid sample in the subject, wherein the subset is determined by (i) performing targeted sequencing on a set of genes on a solid tissue sample from the subject wherein the solid tissue sample is known or suspected of comprising cancerous tissue;
(ii) determining a profile of genetic mutations for said set of genes based on the sequencing; and
(iii) selecting a subset of 2, 3, or 4 genes of the set of genes based on said profile for said set, wherein said subset is specific to said subject; and(b) using the results of (a) to monitor progression of the cancer or lack thereof in the subject. - View Dependent Claims (3, 6, 7, 8, 10, 13, 16, 17, 20, 23, 25, 71, 72, 73, 74, 75)
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48. A method of detecting a mutation in a target polynucleotide region, comprising:
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(a) selectively hybridizing an oligonucleotide primer to said target polynucleotide region, wherein said oligonucleotide primer comprises (i) a probe-binding region, and (ii) a template binding region that is at least 70% complementary to a template nucleic acid suspected of harboring a mutation, wherein a portion of said template binding region at least partially overlays a locus of said suspected mutation, and wherein said oligonucleotide primer upon hybridization to said template nucleic acid is extendable by a polymerase if said mutation is present but is not extendable by said polymerase if said mutation is not present; (b) extending said hybridized oligonucleotide primer to form an extension product; and (c) detecting said extension product, whereby wherein said detecting indicates the presence of said mutation. - View Dependent Claims (49, 50, 51, 53, 54, 60, 61, 64, 65, 66, 78)
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70. A method, comprising:
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(a) hybridizing a target-selective oligonucleotide (TSO) to a single-stranded DNA (ssDNA) fragment of an ssDNA library to create a hybridization product, wherein the TSO comprises (i) a region sequence that selectively is complementary to a single target genomic region and (ii) a second single-stranded adaptor sequence located at a first end of the TSO, wherein the ssDNA fragment comprises a second adaptor sequence attached to said ssDNA fragment via single-stranded ligation and further wherein said second adaptor sequence is different than said first adaptor sequence; and (b) amplifying the hybridization product to create a double stranded extension product.
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76. A method for assessing status of cancer in a subject, comprising:
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(a) obtaining a cell free plasma sample from said subject; (b) extracting targeted polynucleotides from said sample; (c) analyzing by digital sequencing said targeted polynucleotides to obtain a genetic profile for a set of genes; and
,(d) using said genetic profile to assess the status of the cancer in said subject. - View Dependent Claims (77)
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Specification