FineMAV: prioritizing candidate genetic variants driving local adaptations in human populations

Michał Szpak, Massimo Mezzavilla, Qasim Ayub, Yuan Chen, Yali Xue, Chris Tyler-Smith

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    5 Citations (Scopus)

    Abstract

    We present a new method, Fine-Mapping of Adaptive Variation (FineMAV), which combines population differentiation, derived allele frequency, and molecular functionality to prioritize positively selected candidate variants for functional follow-up. We calibrate and test FineMAV using eight experimentally validated "gold standard" positively selected variants and simulations. FineMAV has good sensitivity and a low false discovery rate. Applying FineMAV to the 1000 Genomes Project Phase 3 SNP dataset, we report many novel selected variants, including ones in TGM3 and PRSS53 associated with hair phenotypes that we validate using available independent data. FineMAV is widely applicable to sequence data from both human and other species.

    Original languageEnglish
    Article number5
    Number of pages18
    JournalGenome Biology
    Volume19
    Issue number1
    DOIs
    Publication statusPublished - 17 Jan 2018

    Keywords

    • FineMAV
    • Human evolution
    • Local adaptation
    • Positive selection
    • Selective sweep

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