PT  - JOURNAL ARTICLE
AU  - Brian K Mannakee
AU  - Uthra Balaji
AU  - Agnieszka K. Witkiewicz
AU  - Ryan N. Gutenkunst
AU  - Erik S. Knudsen
TI  - Sensitive and specific post-call filtering of genetic variants in xenograft and primary tumors
AID  - 10.1101/187468
DP  - 2017 Jan 01
TA  - bioRxiv
PG  - 187468
4099  - http://biorxiv.org/content/early/2017/09/12/187468.short
4100  - http://biorxiv.org/content/early/2017/09/12/187468.full
AB  - Motivation Tumor genome sequencing offers great promise for guiding research and therapy, but spurious variant calls can arise from multiple sources. Mouse contamination can generate many spurious calls when sequencing patient-derived xenografts (PDXs). Paralogous genome sequences can also generate spurious calls when sequencing any tumor. We developed a BLAST-based algorithm, MAPEX, to identify and filter out spurious calls from both these sources.Results When calling variants from xenografts, MAPEX has similar sensitivity and specificity to more complex algorithms. When applied to any tumor, MAPEX also automatically flags calls that potentially arise from paralogous sequences. Our implementation, mapexr, runs quickly and easily on a desktocomputer. MAPEX is thus a useful addition to almost any pipeline for calling genetic variants in tumors.