Scalable Open Science Approach for Mutation Calling of Tumor Exomes Using Multiple Genomic Pipelines

Kyle Ellrott; Matthew H Bailey; Gordon Saksena; Kyle R Covington; Cyriac Kandoth; Chip Stewart; Julian Hess; Singer Ma; Kami E Chiotti; Michael McLellan; Heidi J Sofia; Carolyn Hutter; Gad Getz; David Wheeler; Li Ding

doi:10.1016/j.cels.2018.03.002

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Scalable Open Science Approach for Mutation Calling of Tumor Exomes Using Multiple Genomic Pipelines

Journal article

Open access

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Scalable Open Science Approach for Mutation Calling of Tumor Exomes Using Multiple Genomic Pipelines

Kyle Ellrott, Matthew H Bailey, Gordon Saksena, Kyle R Covington, Cyriac Kandoth, Chip Stewart, Julian Hess, Singer Ma, Kami E Chiotti, Michael McLellan, …

Cell systems, Vol.6(3), pp.271-281.e7

03/28/2018

DOI: 10.1016/j.cels.2018.03.002

PMCID: PMC6075717

PMID: 29596782

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Abstract

The Cancer Genome Atlas (TCGA) cancer genomics dataset includes over 10,000 tumor-normal exome pairs across 33 different cancer types, in total >400 TB of raw data files requiring analysis. Here we describe the Multi-Center Mutation Calling in Multiple Cancers project, our effort to generate a comprehensive encyclopedia of somatic mutation calls for the TCGA data to enable robust cross-tumor-type analyses. Our approach accounts for variance and batch effects introduced by the rapid advancement of DNA extraction, hybridization-capture, sequencing, and analysis methods over time. We present best practices for applying an ensemble of seven mutation-calling algorithms with scoring and artifact filtering. The dataset created by this analysis includes 3.5 million somatic variants and forms the basis for PanCan Atlas papers. The results have been made available to the research community along with the methods used to generate them. This project is the result of collaboration from a number of institutes and demonstrates how team science drives extremely large genomics projects.

Algorithms

Mutation

Software

Exome

Genomics - methods

High-Throughput Nucleotide Sequencing - methods

Humans

Information Dissemination - methods

Neoplasms - genetics

Sequence Analysis, DNA - methods

Whole Exome Sequencing - methods

Details

Title: Subtitle: Scalable Open Science Approach for Mutation Calling of Tumor Exomes Using Multiple Genomic Pipelines
Creators: Kyle Ellrott - Oregon Health & Science University
Matthew H Bailey - Washington University in St. Louis
Gordon Saksena - Massachusetts Institute of Technology
Kyle R Covington - Baylor College of Medicine
Cyriac Kandoth - Memorial Sloan Kettering Cancer Center
Chip Stewart - Massachusetts Institute of Technology
Julian Hess - Massachusetts Institute of Technology
Singer Ma - DNAnexus, 1975 W EL Camino Real, Suite 204, Mountain View, CA 94040, USA.
Kami E Chiotti - Oregon Health & Science University
Michael McLellan - Washington University in St. Louis
Heidi J Sofia - National Institutes of Health
Carolyn Hutter - National Institutes of Health
Gad Getz - Harvard University
David Wheeler - Baylor College of Medicine
Li Ding - Washington University in St. Louis
Contributors: MC3 Working Group (Contributor)
Cancer Genome Atlas Research Network (Contributor)
Deqin Ma (Contributor) - University of Iowa, Pathology
Mohammed M Milhem (Contributor) - University of Iowa, Internal Medicine
Aaron D Bossler (Contributor) - University of Iowa, Pathology
Resource Type: Journal article
Publication Details: Cell systems, Vol.6(3), pp.271-281.e7
DOI: 10.1016/j.cels.2018.03.002
PMID: 29596782
PMCID: PMC6075717
NLM abbreviation: Cell Syst
ISSN: 2405-4712
eISSN: 2405-4720
Grant note: U24 CA143843 / NCI NIH HHS U24 CA210957 / NCI NIH HHS U54 HG003079 / NHGRI NIH HHS P30 CA016672 / NCI NIH HHS HHSN261201400007C / NCI NIH HHS U24 CA143883 / NCI NIH HHS U24 CA210990 / NCI NIH HHS U24 CA143799 / NCI NIH HHS R01 CA180778 / NCI NIH HHS R01 CA183793 / NCI NIH HHS U24 CA143867 / NCI NIH HHS U24 CA143858 / NCI NIH HHS U54 HG007990 / NHGRI NIH HHS U24 CA143882 / NCI NIH HHS U54 HG003067 / NHGRI NIH HHS U24 CA143845 / NCI NIH HHS U24 CA143835 / NCI NIH HHS U54 HG003273 / NHGRI NIH HHS U24 CA143840 / NCI NIH HHS U24 CA211006 / NCI NIH HHS U24 CA144025 / NCI NIH HHS U24 CA143866 / NCI NIH HHS U24 CA210950 / NCI NIH HHS U24 CA210949 / NCI NIH HHS U24 CA143848 / NCI NIH HHS R01 CA163722 / NCI NIH HHS U01 HG006517 / NHGRI NIH HHS
Language: English
Date published: 03/28/2018
Academic Unit: Hematology, Oncology, and Blood & Marrow Transplantation; Pathology; Internal Medicine
Record Identifier: 9984185166002771

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