Adjusted P Values for Genome-Wide Scans

Corresponding author: Theodore C. Lystig, Chalmers University of Technology, Eklandagatan 86, 412 96 Göteborg, Sweden., lystig{at}math.chalmers.se (E-mail)

Communicating editor: G. CHURCHILL

Genome-wide scans for quantitative trait loci (QTL) have traditionally been summarized with plots of logarithm of odds (LOD) scores. A valuable modification is to supplement such plots with an additional vertical axis displaying quantiles of adjusted P values and labeling local maxima of the LOD scores with location-specific adjusted P values. This provides a visible gradation of genome-wide significance for the LOD score curve, instead of the stark dichotomy that a single threshold yields. Adjusted P values give genome-wide significance of individual LOD scores and are obtained through a straightforward modification of the familiar algorithm for generating permutation-based thresholds.

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