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US 9,340,830 B2Granted
Optimization of multigene analysis of tumor samples
AssigneeFoundation Medicine, Inc.
InventorsDoron Lipson, Geoffrey Alan Otto, Alexander N. Parker, Philip James Stephens, Sean R. Downing, Mima Jarosz, Mikhail G. Shapiro, Roman Yelensky
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Abstract
A method of analyzing a tumor sample comprising: (a) acquiring a library comprising a plurality of tumor members from a tumor sample; (b) contacting the library with a bait set to provide selected members; (c) acquiring a read for a subgenomic interval from a tumor member from said library; (d) aligning said read; and (e) assigning a nucleotide value (e.g., calling a mutation) from said read for the preselected nucleotide position, thereby analyzing said tumor sample.
Claims85
A method of analyzing a tumor sample for a somatic mutation, comprising:
- (a) acquiring a library comprising a plurality of tumor members from the tumor sample;
- (b) contacting the library with at least two bait sets to provide selected tumor members, wherein said bait sets hydridize with the tumor members, thereby providing a library catch;
- (c) sequencing by a next generation sequencing method a subgenomic interval comprising the somatic mutation from a tumor member from said library or library catch, thereby acquiring a read for the subgenomic interval;
- (d) aligning said read by an alignment method;
- and
- (e) assigning a nucleotide value from said read for a preselected nucleotide position,
- thereby analyzing said tumor sample,
- wherein the at least two bait sets of step (b) are chosen from two of the following bait sets:
- (i) a first bait set that selects a high-level target chosen from one or more tumor nucleic acid molecules that comprise a subgenomic interval comprising a somatic mutation that appears at a frequency of about 5% or less of the cells from the tumor sample;
- (ii) a second bait set that selects a mid-level target chosen from one or more tumor nucleic acid molecules that comprise a subgenomic interval comprising a somatic mutation that appears at a frequency of about 10% or higher of the cells from the tumor sample;
- (iii) a third bait set that selects a low-level target chosen from one or more nucleic acid molecules that comprise a subgenomic interval chosen from one or more of:
- a) a pharmacogenomic (PGx) single nucleotide polymorphism (SNP) that distinguishes the ability of a patient to metabolize different drugs,
- b) a plurality of genomic SNPs that uniquely identify (fingerprint) a patient, or
- c) a genomic SNP or locus that is used to assess copy number gains or losses of genomic DNA and loss-of-heterozygosity (LOH);
- (iv) a fourth bait set that selects a nucleic acid molecule that comprises an intron sequence that detects a structural breakpoint;
- or
- (v) a fifth bait set that selects a one-copy deletion of several terminal exons, wherein each bait set of said plurality has a unique preselected efficiency for selection for its target as compared with the other bait sets in the plurality.
14 more elements
A method of analyzing a tumor sample for a somatic mutation, comprising:
- (a) acquiring a library comprising a plurality of tumor members from the tumor sample;
- (b) contacting the library with at least two bait sets to provide selected tumor members, wherein said bait sets hybridize with the tumor members, thereby providing a library catch;
- (c) sequencing by a next generation sequencing method a subgenomic interval comprising the somatic mutation from a tumor member from said library catch, thereby acquiring a read for the subgenomic interval;
- thereby analyzing said tumor sample for the somatic mutation,
- wherein the at least two bait sets of step (b) are chosen from two of the following bait sets:
- (i) a first bait set that selects a high-level target chosen from one or more tumor nucleic acid molecules that comprise a subgenomic interval comprising a somatic mutation that appears at a frequency of about 5% or less of the cells from the tumor sample;
- (ii) a second bait set that selects a mid-level target chosen from one or more tumor nucleic acid molecules that comprise a subgenomic interval comprising a somatic mutation that appears at a frequency of about 10% or higher of the cells from the tumor sample;
- (iii) a third bait set that selects a low-level target chosen from one or more nucleic acid molecules that comprise a subgenomic interval chosen from one or more of:
- a) a pharmacogenomic (PGx) single nucleotide polymorphism (SNP) that distinguishes the ability of a patient to metabolize different drugs,
- b) a plurality of genomic SNPs that uniquely identify (fingerprint) a patient, or
- c) a genomic SNP or locus that is used to assess copy number gains or losses of genomic DNA and loss-of-heterozygosity (LOH);
- (iv) a fourth bait set that selects a nucleic acid molecule that comprises an intron sequence that detects a structural breakpoint;
- or
- (v) a fifth bait set that selects a one-copy deletion of several terminal exons,
- wherein each bait set of said plurality has a unique preselected efficiency for selection for its target as compared with the other bait sets in the plurality.
12 more elements
Dependencies are inferred from the claim text.