Comparison of prospective and retrospective methods for haplotype inference in case-control studies

Genetic Epidemiology
Glen A Satten, Michael P Epstein

Abstract

We compare bias and power of three methods for haplotype inference on disease risk using unphased genotype data from a case-control study. We examine the prospective score test of Schaid et al., a novel modification of the prospective estimating equations of Zhao et al. and the retrospective likelihood of Epstein and Satten. We find that all three approaches are roughly comparable when the haplotype effect on disease odds follows a multiplicative model. However, for dominant and recessive models of haplotype effect, the retrospective-likelihood method has increased efficiency with respect to the prospective methods. As all three methods assume haplotype frequencies are in Hardy-Weinberg Equilibrium (HWE), we compare the robustness of each procedure to departures from HWE. We find the prospective methods are robust to departure from HWE, while the retrospective-likelihood method is biased for dominant and recessive models of haplotype effect. To remedy this limitation of the retrospective-likelihood method, we propose a modification that allows for a non-negative fixation index (common to all haplotype pairs) and show it dramatically reduces the bias of the retrospective likelihood when HWE is violated.

References

Jan 16, 2002·American Journal of Human Genetics·Daniel J SchaidGregory A Poland
Oct 18, 2002·Genetic Epidemiology·Richard W Morris, Norman L Kaplan
Nov 25, 2003·American Journal of Human Genetics·Michael P Epstein, Glen A Satten

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Citations

Aug 3, 2006·European Journal of Human Genetics : EJHG·Duncan C Thomas, Daniel O Stram
May 31, 2006·Prostate Cancer and Prostatic Diseases·L R KiddR A Kittles
Oct 27, 2005·Bioinformatics·Jing Li, Tao Jiang
Mar 18, 2008·Biostatistics·Andrea S FoulkesXiaohong Li
Sep 16, 2009·BMC Genetics·Hae-Won UhHans C van Houwelingen
Feb 3, 2006·BMC Genetics·Andrew S Allen, Glen A Satten
May 10, 2008·BMC Proceedings·Robert P IgoKatrina A B Goddard
May 12, 2009·Journal of the American Statistical Association·Yi-Hau ChenRaymond J Carroll
Mar 21, 2007·Environmental Health Perspectives·Karen K SteinbergGlen A Satten
Jan 5, 2007·Proceedings of the American Thoracic Society·Edwin K Silverman
Jan 1, 2008·The International Journal of Biostatistics·Samiran SinhaGad Rennert
Dec 19, 2014·BMC Proceedings·Swati Biswas, Charalampos Papachristou
Feb 17, 2009·Genetic Epidemiology·Jinbo ChenMelissa L Wilson
Apr 6, 2007·Genetic Epidemiology·W James GaudermanDavid V Conti
Mar 11, 2006·Genetic Epidemiology·Nianjun LiuHongyu Zhao
Jan 31, 2006·Annals of Human Genetics·Daniel J Schaid
Jan 26, 2008·Biometrical Journal. Biometrische Zeitschrift·Xiaowu Chen, Zhaohai Li
Dec 21, 2005·American Journal of Human Genetics·Jung-Ying TzengChuhsing Kate Hsiao
Jan 24, 2014·Journal of Human Genetics·Anthony Y C KukYaning Yang
Feb 3, 2007·Genetic Epidemiology·Maria De Iorio, Claudio J Verzilli
Oct 20, 2007·Genetic Epidemiology·Andrew S Allen, Glen A Satten

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