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Scalable open science approach for mutation calling of tumor exomes using multiple genomic pipelines

Title: Scalable open science approach for mutation calling of tumor exomes using multiple genomic pipelines
Authors: Ellrott, K
Bailey, MH
Saksena, G
Covington, KR
Kandoth, C
Stewart, C
Hess, J
Ma, S
Chiotti, KE
McLellan, M
Sofia, HJ
Hutter, C
Getz, G
Wheeler, D
Ding, L
Item Type: Journal Article
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.
Issue Date: 28-Mar-2018
Date of Acceptance: 1-Mar-2018
URI: http://hdl.handle.net/10044/1/71273
DOI: https://doi.org/10.1016/j.cels.2018.03.002
ISSN: 2405-4712
Publisher: Elsevier (Cell Press)
Start Page: 271
End Page: 281
Journal / Book Title: Cell Systems
Volume: 6
Issue: 3
Copyright Statement: © 2018 The Authors. This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/).
Sponsor/Funder: SAIC-F-Frederick, Inc
Leidos Biomedical Research, Inc.
Funder's Grant Number: TCGA Pilot Program
Keywords: Science & Technology
Life Sciences & Biomedicine
Biochemistry & Molecular Biology
Cell Biology
PanCanAtlas project
open science
reproducible computing
somatic mutation calling
MC3 Working Group
Cancer Genome Atlas Research Network
Publication Status: Published
Open Access location: https://www.cell.com/cell-systems/fulltext/S2405-4712(18)30096-6?_returnURL=https:%2F%2Flinkinghub.elsevier.com%2Fretrieve%2Fpii%2FS2405471218300966%3Fshowall%3Dtrue
Online Publication Date: 2018-03-28
Appears in Collections:Department of Surgery and Cancer