Method for finding variants from targeted sequencing panels

Abstract

Provided herein is a method for identifying a sequence variant in an enriched sample. In certain embodiments, this method may comprise: (a) obtaining: (i) a plurality of sequence reads from a sample that has been enriched for a genomic region and (ii) a reference sequence for the genomic region; (b) assembling the sequence reads to obtain a plurality of discrete sequence assemblies that correspond to potential variants; (c) determining which of the potential variants are true and which are artifacts by examining the sequence reads that make up each of the discrete sequence assemblies; (d) optionally determining whether each of the true potential variants contains a mutation that is known to be associated with the reference sequence; and (e) outputting a report indicating whether the sample comprises a sequence variant.

What is claimed is: 
     
         1 . A method for identifying a sequence variant, comprising:
 (a) obtaining: (i) a plurality of sequence reads from a sample that has been enriched for a genomic region and (ii) a reference sequence for the genomic region;   (b) assembling the sequence reads to obtain a plurality of discrete sequence assemblies each of which corresponding to a potential variant;   (c) determining which of the potential variants are true and which are artifacts by examining the sequence reads that make up each of the discrete sequence assemblies;   (d) optionally determining whether each of the true potential variants contains a mutation that is known to be associated with the reference sequence; and   (e) outputting a report indicating whether said sample comprises a sequence variant.   
     
     
         2 . The method of  claim 1 , wherein the genomic region is associated with cancer. 
     
     
         3 . The method of  claim 1 , wherein the genomic region comprises at least a portion of at least one of the following genes: PIK3CA, NRAS, KRAS, JAK2, HRAS, FGFR3, FGFR1, EGFR, CDK4, BRAF, RET, PGDFRA, KIT and ERBB2. 
     
     
         4 . The method of  claim 1 , wherein the sequence variant is a low frequency sequence variant corresponding to a somatic mutation. 
     
     
         5 . The method of  claim 1 , wherein the genomic region is a region of the human genome. 
     
     
         6 . The method of  claim 1 , wherein the enriched genomic region is enriched from total DNA obtained from a clinical sample. 
     
     
         7 . The method of  claim 6 , wherein the clinical sample is a biopsy. 
     
     
         8 . The method of  claim 1 , wherein the report provides an indication of whether the sample contains a mutation, as well as available public information about the reference sequence. 
     
     
         9 . The method of  claim 1 , wherein said assembling comprises demarcating the region in each of the sequence reads where the sequence is deemed reliable. 
     
     
         10 . The method of  claim 1 , wherein said assembling uses graph theory. 
     
     
         11 . The method of  claim 10 , wherein said assembling is done using a minimal de-Bruijn sequence. 
     
     
         12 . The method of  claim 10 , wherein said assembling is done using a BEST theorem. 
     
     
         13 . The method of  claim 1 , wherein said determining comprises examining the quality of a sequence, the number of reads, the quality of base calls and their match to the reference sequence, to provide a score for each of said potential variants. 
     
     
         14 . The method of  claim 1 , wherein the reference sequence is annotated to identify mutations that are known in the art and where sequencing reads are likely to be. 
     
     
         15 . The method of  claim 1 , wherein said assembling uses sequences that are from said reference sequence and sequences that are local to said reference sequence in order to anchor the assemblies. 
     
     
         16 . The method of  claim 1 , wherein said method provides a probability for a variant call. 
     
     
         17 . A computer system comprising a memory comprising:
 (a) a database of sequence reads from a sample that has been enriched for a genomic region;   (b) a reference sequence for the genomic region; and   (c) an executable program for performing the method of  claim 1 .   
     
     
         18 . A computer readable storage medium comprising instructions for performing the method of  claim 1 . 
     
     
         19 . A method of identifying a variant sequence, comprising:
 a) inputting sequence information into a computer system comprising a program comprising instructions for performing the method of  claim 1 ;   b) executing the program; and   c) receiving an output from the computer system.