Scalable Open Science Approach for Mutation Calling of Tumor Exomes Using Multiple Genomic Pipelines
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No Canadian affiliation. An affiliation-only frame — the usual design — would never have seen this work. It is one of the works that make the case for inverting the frame.
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.
Fetched live from OpenAlex and de-inverted. Abstracts are not stored in this database: the inverted indexes are 8.6 GB of the frame’s 9.3 GB of text, and the host has 13 GB free.
The record
- Venue
- Cell Systems
- Topic
- Cancer Genomics and Diagnostics
- Field
- Biochemistry, Genetics and Molecular Biology
- Canadian institutions
- —
- Funders
- National Cancer InstituteNational Institutes of HealthBC Cancer FoundationInstituto Tecnológico de Costa RicaBroad InstituteUniversity of California, Santa CruzNational Human Genome Research InstituteMemorial Sloan-Kettering Cancer CenterNational Cancer Institute, Cairo UniversityVan Andel Research InstituteCancer Prevention and Research Institute of Texas
- Keywords
- GenomicsExome sequencingExomeComputational biologyComputer scienceScalabilityMetagenomicsGenomeDNA sequencingBiologyMutationData miningGeneticsDatabaseGene
- Has abstract in OpenAlex
- yes