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

Ellrott, Kyle; Bailey, Matthew H; Saksena, Gordon; Covington, Kyle R; Kandoth, Cyriac; Stewart, Chip; Hess, Julian; Ma, Singer; Chiotti, Kami E; McLellan, Michael; Sofia, Heidi J; Hutter, Carolyn; Getz, Gad; Wheeler, David; Ding, Li (2018). Scalable Open Science Approach for Mutation Calling of Tumor Exomes Using Multiple Genomic Pipelines. Cell systems, 6(3), 271-281.e7. Elsevier 10.1016/j.cels.2018.03.002

[img]
Preview
Text
1-s2.0-S2405471218300966-main.pdf - Published Version
Available under License Creative Commons: Attribution (CC-BY).

Download (2MB) | Preview

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.

Item Type:

Journal Article (Original Article)

Division/Institute:

04 Faculty of Medicine > Pre-clinic Human Medicine > BioMedical Research (DBMR) > DBMR Forschung Mu35 > Forschungsgruppe Präzisionsonkologie
04 Faculty of Medicine > Pre-clinic Human Medicine > BioMedical Research (DBMR) > DBMR Forschung Mu35 > Forschungsgruppe Präzisionsonkologie

Subjects:

600 Technology > 610 Medicine & health

ISSN:

2405-4712

Publisher:

Elsevier

Language:

English

Submitter:

Marla Rittiner

Date Deposited:

01 Oct 2019 13:31

Last Modified:

23 Oct 2019 22:22

Publisher DOI:

10.1016/j.cels.2018.03.002

PubMed ID:

29596782

Additional Information:

Mark Rubin (Direktor DBMR) ist Collaborator in dieser Publikation.

Uncontrolled Keywords:

PanCanAtlas project TCGA large-scale open science pan-cancer reproducible computing somatic mutation calling

BORIS DOI:

10.7892/boris.126391

URI:

https://boris.unibe.ch/id/eprint/126391

Actions (login required)

Edit item Edit item
Provide Feedback