Open pipelines for integrated tumor genome profiles reveal differences between pancreatic cancer tumors and cell lines.

ABSTRACT: We describe open, reproducible pipelines that create an integrated genomic profile of a cancer and use the profile to find mutations associated with disease and potentially useful drugs. These pipelines analyze high-throughput cancer exome and transcriptome sequence data together with public databases to find relevant mutations and drugs. The three pipelines that we have developed are: (1) an exome analysis pipeline, which uses whole or targeted tumor exome sequence data to produce a list of putative variants (no matched normal data are needed); (2) a transcriptome analysis pipeline that processes whole tumor transcriptome sequence (RNA-seq) data to compute gene expression and find potential gene fusions; and (3) an integrated variant analysis pipeline that uses the tumor variants from the

SUBMITTER: Goecks J 

PROVIDER: S-EPMC4380965 | biostudies-literature | 2015 Mar

REPOSITORIES: biostudies-literature