Linkage disequilibrium and haplotype homozygosity in population samples genotyped at a high marker density.
OBJECTIVE
Analyze the information contained in homozygous haplotypes detected with high density genotyping.


METHODS
We analyze the genotypes of approximately 2,500 markers on chr 22 in 12 population samples, each including 200 individuals. We develop a measure of disequilibrium based on haplotype homozygosity and an algorithm to identify genomic segments characterized by non-random homozygosity (NRH), taking into account allele frequencies, missing data, genotyping error, and linkage disequilibrium.


RESULTS
We show how our measure of linkage disequilibrium based on homozygosity leads to results comparable to those of R(2), as well as the importance of correcting for small sample variation when evaluating D'. We observe that the regions that harbor NRH segments tend to be consistent across populations, are gene rich, and are characterized by lower recombination.


CONCLUSIONS
It is crucial to take into account LD patterns when interpreting long stretches of homozygous markers.
Wang
Hui
H
Department of Statistics, UCLA, Los Angeles, CA 90095, USA.
Lin
Chia-Ho
CH
Service
Susan
S
Chen
Yuguo
Y
Freimer
Nelson
N
Sabatti
Chiara
C
D002892:Chromosomes, Human, Pair 22; D005787:Gene Frequency; D005819:Genetic Markers; D005828:Genetics, Population / Q000379:methods; D005838:Genotype; D006239:Haplotypes; D006720:Homozygote; D006801:Humans; D015810:Linkage Disequilibrium / Q000502:physiology*; D008390:Markov Chains; D008957:Models, Genetic; D011153:Population / Q000235:genetics; D018401:Sample Size
D005819:Genetic Markers