Faster Haplotype Frequency Estimation Using Unrelated Subjects

Linkage disequilibrium (LD) between tightly linked loci provides fine mapping information of disease-predisposing allelic variants. The most common method of LD analysis involves unrelated cases and controls. We have previously proposed model-free and permutation tests for diseases with unknown mode...

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Bibliographic Details
Published inHuman heredity Vol. 53; no. 1; pp. 36 - 41
Main Authors Zhao, Jing Hua, Sham, Pak Chung
Format Journal Article
LanguageEnglish
Published Basel, Switzerland S. Karger AG 01.01.2002
Subjects
Alcoholism - genetics
Aldehyde Dehydrogenase
Aldehyde Dehydrogenase, Mitochondrial
Gene Frequency
Genetic Markers
Haplotypes - genetics
HLA Antigens
Humans
Linkage Disequilibrium
Original Paper
Schizophrenia - genetics
Statistics as Topic - methods
Gene counting
Permutation tests
Case-control association analysis
EM algorithm
Linkage disequilibrium
Contingency table analysis
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Summary:Linkage disequilibrium (LD) between tightly linked loci provides fine mapping information of disease-predisposing allelic variants. The most common method of LD analysis involves unrelated cases and controls. We have previously proposed model-free and permutation tests for diseases with unknown mode of inheritance that can be applied to several highly polymorphic loci. However, performing such analyses remained computer intensive. In this report we propose a speed-up of both the genecounting procedure and the permutation procedure. We demonstrate the improved method with an analysis of schizophrenia and human leucocyte antigen markers, and an analysis of alcoholism and mitochondrial aldehyde dehydrogenase markers. Our implementation also allows the rapid calculation of permutation-based LD measures and related statistics.
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ISSN:0001-5652
1423-0062
DOI:10.1159/000048602