# US 12,180,540 B2 · Optimization of multigene analysis of tumor samples > Agents: this data is available as JSON from the patentgrep API and MCP server — see https://patentgrep.com/llms.txt - Number: US 12,180,540 B2 - Document ID: US12180540B2 - Status: Granted - Kind: B2 - Application number: 17/812,415 - Filed: 2022-07-13 - Published: 2023-05-11 - Granted: 2024-12-31 - Earliest claimed: 2010-12-30 - Assignees: Foundation Medicine, Inc. - Applicants: Foundation Medicine, Inc. - Inventors: Doron Lipson; Geoffrey Alan Otto; Alexander Nevin Parker; Philip James Stephens; Sean R. Downing; Mirna Jarosz; Mikhail G. Shapiro; Roman Yelensky - Web page: https://patentgrep.com/patent/US12180540B2 ## CPC - C12Q 1/6827: for detection of mutation or polymorphism - C12Q 1/6874: involving nucleic acid arrays, e.g. sequencing by hybridisation - G16B 20/00: ICT specially adapted for functional genomics or proteomics, e.g. genotype-phenotype associations - G16B 20/10: Ploidy or copy number detection - G16B 20/20: Allele or variant detection, e.g. single nucleotide polymorphism [SNP] detection - G16B 30/00: ICT specially adapted for sequence analysis involving nucleotides or amino acids - G16B 30/10: Sequence alignment; Homology search - C12Q 1/6886: for cancer (immunoassay for cancer G01N33/575) - C12Q 2537/143: Multiplexing, i.e. use of multiple primers or probes in a single reaction, usually for simultaneously analyse of multiple analysis - C12Q 2537/149: Sequential reactions - 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 - G16B: BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY ## 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. ## Claims ### Claim 1 A method of separating targeted nucleic acid molecules from a sample, comprising: combining, in the same solution, at least two different bait sets and a library comprising a plurality of nucleic acid molecules to form a plurality of nucleic acid hybrids, wherein the at least two different bait sets each comprise one or more bait molecules comprising a binding entity and a sequence configured to capture a target sequence, wherein the nucleic acid hybrids comprise a target nucleic acid molecule and a bait molecule, and wherein the at least two different bait sets comprise: a first bait set comprising a bait molecule comprising a sequence configured to capture a target sequence comprising a point mutation, and a second bait set comprising a bait molecule comprising a sequence configured to capture a target sequence comprising a structural breakpoint; and separating the plurality of nucleic acid hybrids from a remainder of the library. ### Claim 2 (depends on 1) The method of claim 1, further comprising sequencing target nucleic acid molecules in the plurality of nucleic acid hybrids separated from the remainder of the library. ### Claim 3 (depends on 2) The method of claim 2, wherein the target sequence comprising the point mutation is sequenced at a first sequencing depth and the target sequence comprising the structural breakpoint is sequenced at a second sequencing depth, and wherein the first sequencing depth differs from the second sequencing depth by at least a 2-fold. ### Claim 4 (depends on 2) The method of claim 2, wherein the sequencing is next generation sequencing. ### Claim 5 (depends on 1) The method of claim 1, wherein the plurality of nucleic acid molecules comprises DNA molecules. ### Claim 6 (depends on 1) The method of claim 1, further comprising amplifying target nucleic acid molecules in the plurality of nucleic acid hybrids. ### Claim 7 (depends on 1) The method of claim 1, comprising attaching sequencing adapters to the plurality of nucleic acid molecules in the library. ### Claim 8 (depends on 7) The method of claim 7, wherein the sequencing adapters comprise a barcode sequence. ### Claim 9 (depends on 1) The method of claim 1, wherein the plurality of nucleic acid molecules comprises cDNA molecules derived from RNA molecules. ### Claim 10 (depends on 1) The method of claim 1, wherein the structural breakpoint comprises an in-frame deletion of one or more codons, an intragenic deletion, and intragenic insertion, deletion of a full gene, an inversion, an interchromosomal translocation, a tandem duplication, a gene fusion, or a genomic rearrangement that comprises an intron sequence. ### Claim 11 (depends on 1) The method of claim 1, wherein the structural breakpoint is an exon-exon junction. ### Claim 12 (depends on 1) The method of claim 1, wherein the binding entity comprises biotin. ### Claim 13 (depends on 1) The method of claim 1, wherein the point mutation or the structural breakpoint is associated with a cancerous phenotype. ### Claim 14 (depends on 13) The method of claim 13, wherein the cancerous phenotype comprises a cancer risk, a cancer progression, a clinical outcome or responsiveness to therapy, or a resistance to cancer treatment. ### Claim 15 (depends on 1) The method of claim 1, wherein the size of the nucleic acid molecules in the plurality of nucleic acid molecules is 600 bp or less. ### Claim 16 (depends on 1) The method of claim 1, wherein the size of the sequence of the bait molecules is about 100 to about 300 bases. ### Claim 17 (depends on 1) The method of claim 1, wherein the plurality of nucleic acid hybrids are separated from a remainder of the library using a plurality of beads. ### Claim 18 (depends on 17) The method of claim 17, wherein the binding entity comprises biotin and the beads in the plurality of beads are coated with streptavidin. ### Claim 19 (depends on 1) The method of claim 1, wherein the at least two different bait sets and the library are combined in solution. ### Claim 20 A method of separating targeted nucleic acid molecules from a sample, comprising: combining, in the same solution, at least two different bait sets and a library comprising a plurality of nucleic acid molecules to form a plurality of nucleic acid hybrids, wherein the at least two different bait sets each comprise one or more bait molecules comprising a binding entity and a sequence configured to capture a target sequence, and wherein the plurality of nucleic acid hybrids comprises: a first nucleic acid hybrid comprising a bait molecule from the first bait set and a target nucleic acid molecule comprising a point mutation, and a second nucleic acid hybrid comprising a bait molecule from the second bait set and a target nucleic acid molecule comprising a structural breakpoint; and separating the plurality of nucleic acid hybrids from a remainder of the library.