Robust indices of Hardy-Weinberg disequilibrium for QTL fine mapping.
Hardy-Weinberg disequilibrium (HWD) measures have been proposed using dense markers to fine map a quantitative trait locus (QTL) to regions < approximately 1 cM. Earlier HWD measures may introduce bias in the fine mapping because they are dependent on marker allele frequencies across loci. Hence, HWD indices that do not depend on marker allele frequencies are desired for fine mapping. Based on our earlier work, here we present four new HWD indices that do not depend on marker allele frequencies. Two are for use when marker allele frequencies in a study population are known, and two are for use when marker allele frequencies in a study population are not known and are only known in the extreme samples. The new measures are a function of the genetic distance between the marker locus and a QTL. Through simulations, we investigated and compared the fine mapping performance of the new HWD measures with that of the earlier ones. Our results show that when marker allele frequencies vary across loci, the new measures presented here are more robust and powerful.
Deng
Hong-Wen
HW
Laboratory of Molecular and Statistical Genetics, College of Life Sciences, Hunan Normal University, Changsha, PR China. deng@creighton.edu
Li
Yu-Mei
YM
Li
Miao-Xin
MX
Liu
Peng-Yuan
PY
D002874:Chromosome Mapping / Q000379:methods*; D003198:Computer Simulation; D005819:Genetic Markers; D006801:Humans; D015810:Linkage Disequilibrium; D040641:Quantitative Trait Loci
D005819:Genetic Markers