Use of unphased multilocus genotype data in indirect association studies.
It is usually assumed that detection of a disease susceptability gene via marker polymorphisms in linkage disequilibrium with it is facilitated by consideration of marker haplotypes. However, capture of the marker haplotype information requires resolution of gametic phase, and this must usually be inferred statistically. Recently, we questioned the value of the marker haplotype information, and suggested that certain analyses of multivariate marker data, not based on haplotypes explicitly and not requiring resolution of gametic phase, are often more powerful than analyses based on haplotypes. Here, we review this work and assess more carefully the situations in which our conclusions might apply. We also relate these analyses to alternative approaches to haplotype analysis, namely those based on haplotype similarity and those inspired by cladistics.
Clayton
David
D
Diabetes and Inflammation Laboratory, Cambridge Institute for Medical Research, University of Cambridge, Cambridge CB2 2XY, UK.
Chapman
Juliet
J
Cooper
Jason
J
D005819:Genetic Markers; D020022:Genetic Predisposition to Disease / Q000453:epidemiology*; D005828:Genetics, Population; D005838:Genotype; D006239:Haplotypes; D006801:Humans; D015810:Linkage Disequilibrium / Q000235:genetics*; D008957:Models, Genetic; D015233:Models, Statistical
D005819:Genetic Markers