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Publication Details
AFRICAN RESEARCH NEXUS
SHINING A SPOTLIGHT ON AFRICAN RESEARCH
biochemistry, genetics and molecular biology
Linkage disequilibrium and haplotype homozygosity in population samples genotyped at a high marker density
Human Heredity, Volume 62, No. 4, Year 2006
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Description
Objective: Analyze the information contained in homozygous haplotypes detected with high density genotyping. Methods: We analyze the genotypes of ∼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 R2, 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. Copyright © 2006 S. Karger AG.
Authors & Co-Authors
Wang, Hui
Unknown Affiliation
Lin, Chia Ho
Unknown Affiliation
Service, Susan K.
Unknown Affiliation
Chen, Yuguo
Unknown Affiliation
Luben, Robert N.
Unknown Affiliation
Sabatti, Chiara
Unknown Affiliation
Karayiorgou, Maria
Unknown Affiliation
Roos, J. L.
Unknown Affiliation
Pretorious, Herman
Unknown Affiliation
Bedoya, Gabriel De Jesús
Unknown Affiliation
Ospina-Duque, Jorge
Unknown Affiliation
Ruiz-Linarès, Andrés D.Sign©s
Unknown Affiliation
Macedo, Antonio Ferreira
Unknown Affiliation
Palha, Joana A.
Unknown Affiliation
Heutink, Peter
Unknown Affiliation
Aulchenko, Yurii S.
Unknown Affiliation
Oostra, Ben A.
Unknown Affiliation
van Duijn, Cornelia M.
Unknown Affiliation
J̈arvelin, Märjo Riitta R.
Unknown Affiliation
Varilo, Teppo
Unknown Affiliation
Peddle, Lynette J.
Unknown Affiliation
Rahman, Proton
Unknown Affiliation
Piras, Giovanna
Unknown Affiliation
Monne, Maria
Unknown Affiliation
Peltonen-Palotie, Leena Johanna
Unknown Affiliation
Statistics
Citations: 27
Authors: 25
Affiliations: 21
Identifiers
Doi:
10.1159/000096599
ISSN:
00015652
Research Areas
Genetics And Genomics
Study Design
Cross Sectional Study