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

Jeremy Goecks, Bassel F. El-Rayes, Shishir K. Maithel, H. Jean Khoury, James Taylor, Michael R. Rossi

Research output: Contribution to journalArticle

5 Citations (Scopus)

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 exome pipeline and tumor gene expression from the transcriptome pipeline to identify deleterious and druggable mutations in all genes and in highly expressed genes. These pipelines are integrated into the popular Web platform Galaxy at http://usegalaxy.org/cancer to make them accessible and reproducible, thereby providing an approach for doing standardized, distributed analyses in clinical studies. We have used our pipeline to identify similarities and differences between pancreatic adenocarcinoma cancer cell lines and primary tumors.

Original languageEnglish (US)
Pages (from-to)392-403
Number of pages12
JournalCancer Medicine
Volume4
Issue number3
DOIs
StatePublished - Mar 1 2015
Externally publishedYes

Fingerprint

Tumor Cell Line
Pancreatic Neoplasms
Exome
Genome
Transcriptome
Neoplasms
Mutation
Galaxies
Gene Expression
Gene Fusion
Gene Expression Profiling
Pharmaceutical Preparations
Genes
Adenocarcinoma
Databases

Keywords

  • Analysis pipelines
  • Bioinformatics
  • Galaxy
  • Genomic tumor profiles
  • Pancreatic cancer

ASJC Scopus subject areas

  • Oncology
  • Radiology Nuclear Medicine and imaging
  • Cancer Research

Cite this

Open pipelines for integrated tumor genome profiles reveal differences between pancreatic cancer tumors and cell lines. / Goecks, Jeremy; El-Rayes, Bassel F.; Maithel, Shishir K.; Khoury, H. Jean; Taylor, James; Rossi, Michael R.

In: Cancer Medicine, Vol. 4, No. 3, 01.03.2015, p. 392-403.

Research output: Contribution to journalArticle

Goecks, Jeremy ; El-Rayes, Bassel F. ; Maithel, Shishir K. ; Khoury, H. Jean ; Taylor, James ; Rossi, Michael R. / Open pipelines for integrated tumor genome profiles reveal differences between pancreatic cancer tumors and cell lines. In: Cancer Medicine. 2015 ; Vol. 4, No. 3. pp. 392-403.
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