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Bioinformatics. 2016 Oct 15;32(20):3196-3198. Epub 2016 Jun 26.

Conpair: concordance and contamination estimator for matched tumor-normal pairs.

Author information

1
New York Genome Center, New York, NY 10013, USA.

Abstract

MOTIVATION:

Sequencing of matched tumor and normal samples is the standard study design for reliable detection of somatic alterations. However, even very low levels of cross-sample contamination significantly impact calling of somatic mutations, because contaminant germline variants can be incorrectly interpreted as somatic. There are currently no sequence-only based methods that reliably estimate contamination levels in tumor samples, which frequently display copy number changes. As a solution, we developed Conpair, a tool for detection of sample swaps and cross-individual contamination in whole-genome and whole-exome tumor-normal sequencing experiments.

RESULTS:

On a ladder of in silico contaminated samples, we demonstrated that Conpair reliably measures contamination levels as low as 0.1%, even in presence of copy number changes. We also estimated contamination levels in glioblastoma WGS and WXS tumor-normal datasets from TCGA and showed that they strongly correlate with tumor-normal concordance, as well as with the number of germline variants called as somatic by several widely-used somatic callers.

AVAILABILITY AND IMPLEMENTATION:

The method is available at: https://github.com/nygenome/conpair CONTACT: egrabowska@gmail.com or mczody@nygenome.orgSupplementary information: Supplementary data are available at Bioinformatics online.

PMID:
27354699
PMCID:
PMC5048070
DOI:
10.1093/bioinformatics/btw389
[Indexed for MEDLINE]
Free PMC Article

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