Kullback-Leibler divergence for detection of rare haplotype common disease association.

European Journal of Human Genetics : EJHG
Shili Lin

Abstract

Rare haplotypes may tag rare causal variants of common diseases; hence, detection of such rare haplotypes may also contribute to our understanding of complex disease etiology. Because rare haplotypes frequently result from common single-nucleotide polymorphisms (SNPs), focusing on rare haplotypes is much more economical compared with using rare single-nucleotide variants (SNVs) from sequencing, as SNPs are available and 'free' from already amassed genome-wide studies. Further, associated haplotypes may shed light on the underlying disease causal mechanism, a feat unmatched by SNV-based collapsing methods. In recent years, data mining approaches have been adapted to detect rare haplotype association. However, as they rely on an assumed underlying disease model and require the specification of a null haplotype, results can be erroneous if such assumptions are violated. In this paper, we present a haplotype association method based on Kullback-Leibler divergence (hapKL) for case-control samples. The idea is to compare haplotype frequencies for the cases versus the controls by computing symmetrical divergence measures. An important property of such measures is that both the frequencies and logarithms of the frequencies contribute i...Continue Reading

References

Jan 16, 2002·American Journal of Human Genetics·Daniel J SchaidGregory A Poland
Mar 12, 2005·Science·Robert J KleinJosephine Hoh
Aug 29, 2007·Investigative Ophthalmology & Visual Science·Kylee L SpencerJonathan L Haines
Feb 14, 2009·PLoS Genetics·Bo Eskerod Madsen, Sharon R Browning
Jul 9, 2009·European Journal of Human Genetics : EJHG·Jung-Ying Tzeng, Howard D Bondell
Oct 9, 2009·Nature·Teri A ManolioPeter M Visscher
Oct 23, 2009·Genetic Epidemiology·Xiaofeng ZhuRobert C Elston
Mar 17, 2011·PLoS Genetics·Benjamin M NealeMark J Daly
Jul 9, 2011·American Journal of Human Genetics·Michael C WuXihong Lin
Dec 14, 2011·Genetic Epidemiology·Carmen DeringAndreas Ziegler
Jun 19, 2012·Genetic Epidemiology·Wan-Yu LinNianjun Liu
Nov 26, 2013·Genetic Epidemiology·Swati BiswasShili Lin

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Citations

Oct 12, 2016·Scientific Reports·Andreas J HülsmeierThierry Hennet

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