Haplotype-based analysis: a summary of GAW16 Group 4 analysis.
In this summary article, we describe the contributions included in the haplotype-based analysis group (Group 4) at the Genetic Analysis Workshop 16, which was held in September 17-20, 2008. Our group applied a large number of haplotype-based methods in the context of genome-wide association studies. Two general approaches were applied: a two-stage approach that selected significant single-nucleotide polymorphisms (SNPs) in the first stage and then created haplotypes in the second stage and genome-wide analysis of smaller sets of SNPs selected by sliding windows or estimating haplotype blocks. Genome-wide haplotype analyses performed in these ways were feasible. The presence of the very strong chromosome 6 association in the North American Rheumatoid Arthritis Consortium data was detected by every method, and additional analyses attempted to control for this strong result to allow detection of additional haplotype associations.
Hauser
Elizabeth
E
Center for Human Genetics, Duke University, Durham, North Carolina 27710, USA. Elizabeth.Hauser@duke.edu
Cremer
Nadine
N
Hein
Rebecca
R
Deshmukh
Harshal
H
D001172:Arthritis, Rheumatoid / Q000453:epidemiology / Q000235:genetics / Q000276:immunology; D002896:Chromosomes, Human, Pair 6 / Q000235:genetics; D055106:Genome-Wide Association Study / Q000379:methods*; D006680:HLA Antigens / Q000235:genetics; D006239:Haplotypes; D006801:Humans; D015810:Linkage Disequilibrium; D017720:Molecular Epidemiology; D020641:Polymorphism, Single Nucleotide
D006680:HLA Antigens