mapexr

mapexr filters spurious variant calls from tumor genome sequencing by using BLASTN-based post-variant-calling evaluation to remove calls arising from mouse contamination and paralogous sequences.

Key Features:

• BLASTN-Based Filtering: Uses BLASTN to assess alignment quality of reads supporting each variant and determines the fraction of reads that align best to the variant site.
• Mouse Contamination Detection: Identifies and filters variant calls resulting from mouse contamination in patient-derived xenografts.
• Paralogous Sequence Flagging: Flags potential variant calls arising from paralogous sequences in tumor genomes.
• Performance: Demonstrates sensitivity and specificity comparable to more complex algorithms when applied to xenografts.
• Implementation: Implemented as an R package.

Scientific Applications:

• Variant Call Refinement: Improves accuracy of variant calls in tumor genome sequencing by reducing false positives due to contamination and paralogy.
• Xenograft Sequencing: Applicable to patient-derived xenograft sequencing to remove mouse-derived variant calls.
• Cancer Research and Precision Medicine: Supports identification of genetic alterations relevant to cancer research and personalized therapy.

Methodology:

Performs post-variant-calling filtration using BLASTN to evaluate alignments of reads supporting each variant and retains variants whose supporting reads align optimally to the variant locus, reducing false positives from contamination or sequence similarity.