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Genetic Epidemiology 34 : 816834 (2010) MaCH: Using Sequence and Genotype Data to Estimate Haplotypes
 

Summary: Genetic Epidemiology 34 : 816834 (2010)
MaCH: Using Sequence and Genotype Data to Estimate Haplotypes
and Unobserved Genotypes
Yun Li,1
Cristen J. Willer,2
Jun Ding,2
Paul Scheet,3
and Gonc-alo R. Abecasis2
1
Department of Genetics, Department of Biostatistics, University of North Carolina, Chapel Hill, North Carolina
2
Center for Statistical Genetics, Department of Biostatistics, University of Michigan School of Public Health, Ann Arbor, Michigan
3
Department of Epidemiology, University of Texas M.D. Anderson Cancer Center, Houston, Texas
Genome-wide association studies (GWAS) can identify common alleles that contribute to complex disease susceptibility.
Despite the large number of SNPs assessed in each study, the effects of most common SNPs must be evaluated indirectly
using either genotyped markers or haplotypes thereof as proxies. We have previously implemented a computationally
efficient Markov Chain framework for genotype imputation and haplotyping in the freely available MaCH software
package. The approach describes sampled chromosomes as mosaics of each other and uses available genotype and shotgun
sequence data to estimate unobserved genotypes and haplotypes, together with useful measures of the quality of these

  

Source: Abecasis, Goncalo - Department of Biostatistics, University of Michigan

 

Collections: Biology and Medicine; Mathematics