Computational Analysis in Cancer Exome Sequencing
Exome sequencing in cancer is a powerful tool for identifying mutational events across the coding region of human genes. Here, we describe computational methods that use exome sequencing reads from cancer samples to identify somatic single nucleotide variants (SNVs), copy number alterations, and short insertions and deletions (InDels). We further describe analytical methods to generate lists of driver genes with more mutational events than expected by chance.
Key wordsCancer Single nucleotide variant Copy number variation Exome sequencing Gene burden InDels
This work was supported by the Yale SPORE in Skin Cancer funded by the National Cancer Institute grant number 1 P50 CA121974 (principal investigator, Ruth Halaban), the Melanoma Research Alliance (a Team award to Ruth Halaban and M.K.), The National Library of Medicine Training grant 5T15LM007056 (P.E.), Yale Comprehensive Cancer Center (M.K.), and Gilead Sciences, Inc. (M.K.).