title: Conpair: concordance and contamination estimator for matched tumor-normal pairs.
abstract: 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.
  
  
  
  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.
  
  
  
  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.
authors.affiliation: New York Genome Center, New York, NY 10013, USA.
authors.forename: Ewa A
authors.initials: EA
authors.lastname: Bergmann
authors.affiliation: New York Genome Center, New York, NY 10013, USA.
authors.forename: Bo-Juen
authors.initials: BJ
authors.lastname: Chen
authors.affiliation: New York Genome Center, New York, NY 10013, USA.
authors.forename: Kanika
authors.initials: K
authors.lastname: Arora
authors.affiliation: New York Genome Center, New York, NY 10013, USA.
authors.forename: Vladimir
authors.initials: V
authors.lastname: Vacic
authors.affiliation: New York Genome Center, New York, NY 10013, USA.
authors.forename: Michael C
authors.initials: MC
authors.lastname: Zody
mesh_terms: D000465:Algorithms; D003198:Computer Simulation; D004273:DNA, Neoplasm; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D009369:Neoplasms / Q000473:pathology
chemical_list: D004273:DNA, Neoplasm