Sensitive and specific post-call filtering of genetic variants in xenograft and primary tumors
作者： Ryan N. Gutenkunst , Brian K Mannakee , Agnieszka K. Witkiewicz , Uthra Balaji , Erik S. Knudsen
DOI: 10.1101/187468
关键词:
摘要: Tumor genome sequencing offers great promise for guiding research and therapy, but spurious variant calls can arise from multiple sources. Mouse contamination generate many when patient-derived xenografts (PDXs). Paralogous sequences also any tumor. We developed a BLAST-based algorithm, MAPEX, to identify filter out both these When calling variants xenografts, MAPEX has similar sensitivity specificity more complex algorithms. applied tumor, automatically flags that potentially paralogous sequences. Our implementation, mapexr, runs quickly easily on desktop computer. is thus useful addition almost pipeline genetic in tumors.
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