Location-Dependent Empirical Thresholds for Quantitative Trait Mapping

G3: Genes, Genomes, Genetics

Benjamin McClosky¹  Steven Tanksley¹  Jason LaCombe¹ 

[1] Nature Source Genetics, Ithaca, New York 14850Nature Source Genetics, Ithaca, New York 14850Nature Source Genetics, Ithaca, New York 14850

关键词: QTL;    empirical threshold;    adjusted P-value;    local error rate;    multiple hypothesis testing;   

DOI  :  10.1534/g3.112.003517

学科分类：生物科学（综合）

来源: Genetics Society of America

【 摘 要 】

The Churchill-Doerge approach toward constructing empirical thresholds has received widespread use in the genetic mapping literature through the past 16 years. The method is valued for both its simplicity and its ability to preserve the genome-wide error rate at a prespecified level. However, the Churchill-Doerge method is not designed to maintain the local (comparison-wise) error rate at a constant level except in situations that are unlikely to occur in practice. In this article, we introduce the objective of preserving the local error rate at a constant level in the context of mapping quantitative trait loci in linkage populations. We derive a method that preserves the local error rate at a constant level, provide an application via simulation on a Hordeum vulgare population, and demonstrate evidence of the relationship between recombination and location bias. Furthermore, we indicate that this method is equivalent to the Churchill-Doerge method when several assumptions are satisfied.

【 授权许可】

Unknown