A hidden Markov modeling approach for admixture mapping based on case-control data

Genetic Epidemiology
Chun ZhangHongzhe Li

Abstract

Admixture mapping is potentially a powerful method for mapping genes for complex human diseases, when the disease frequency due to a particular disease-susceptible gene is different between founding populations of different ethnicity. The method tests for association of the allele ancestry with the disease. Since the markers used to define ancestral populations are not fully informative for the ancestry status, direct test of such association is not possible. In this report, we develop a unified hidden Markov model (HMM) framework for estimating the unobserved ancestry haplotypes across a chromosomal region based on marker haplotype or genotype data. The HMM efficiently utilizes all the marker data to infer the latent ancestry states at the putative disease locus. In this HMM modelling framework, we develop a likelihood test for association of allele ancestry and the disease risk based on case-control data. Existence of such association may imply linkage between the candidate locus and the disease locus. We evaluate by simulations how several factors affect the power of admixture mapping, including sample size, ethnicity relative risk, marker density, and the different admixture dynamics. Our simulation results indicate correct...Continue Reading

References

Dec 1, 1988·Proceedings of the National Academy of Sciences of the United States of America·R Chakraborty, K M Weiss
Dec 1, 1994·Annals of Neurology·A D Sadovnick
Jun 3, 2000·American Journal of Human Genetics·A P MorrisD J Balding
Jun 3, 2000·Genetics·J K PritchardP Donnelly
Jan 10, 2001·American Journal of Physical Anthropology·E J ParraM D Shriver
Mar 20, 2001·American Journal of Human Genetics·M StephensP Donnelly
Oct 9, 2001·American Journal of Human Genetics·M W SmithS J O'Brien
Feb 15, 2002·American Journal of Human Genetics·Heather E Collins-SchrammMichael F Seldin
Nov 19, 2002·Human Heredity·Benjamin A RybickiMichael C Iannuzzi

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Citations

Aug 10, 2006·Human Genetics·Xiaofeng ZhuRichard Cooper
Jul 14, 2005·Nature Reviews. Genetics·Michael W Smith, Stephen J O'Brien
Nov 21, 2007·PLoS Genetics·Rahul C DeoDavid Reich
May 1, 2007·Current Opinion in Genetics & Development·Michael F Seldin
Dec 21, 2006·American Journal of Physical Anthropology·Michael F SeldinMarta E Alarcon-Riquelme
Oct 30, 2010·Genetic Epidemiology·Hua TangStephanie J London
May 16, 2007·American Journal of Human Genetics·Xianyun MaoEsteban J Parra
Jun 15, 2007·American Journal of Human Genetics·Chao TianMichael F Seldin
Nov 13, 2004·American Journal of Human Genetics·Paul M McKeigue
May 18, 2007·Genetic Epidemiology·Geraldine Clarke, Alice S Whittemore
Oct 19, 2006·Human Heredity·Qiuying ShaShuanglin Zhang

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