ArticleAmerican journal of human genetics2000
The accuracy of statistical methods for estimation of haplotype frequencies: an example from the CD4 locus.
Article in American journal of human genetics, 2000. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 55 papers, 1 of them a synthesis that pooled it.
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55 citing papers in PubMed, 1 synthesis or guideline pooled it, 128 citations in OpenAlex.
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- Markov chain Monte Carlo Gibbs sampler approach for estimating haplotype frequencies among multiple malaria infected human blood samples.Malaria journal · 2021Article
- βJournal of clinical medicine · 2019Article
- Haplotype analysis ofThe Indian journal of medical research · 2019Article
- Markov chain Monte Carlo and expectation maximization approaches for estimation of haplotype frequencies for multiply infected human blood samples.Malaria journal · 2016Article
- Intraspecific evolution of human RCCX copy number variation traced by haplotypes of the CYP21A2 gene.Genome biology and evolution · 2013Article
- Analytical methods for immunogenetic population data.Methods in molecular biology (Clifton, N.J.) · 2012Article
- A SOCS-1 promoter variant is associated with total serum IgE levels.Journal of immunology (Baltimore, Md. : 1950) · 2011Article
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- Nuclear gene phylogeography using PHASE: dealing with unresolved genotypes, lost alleles, and systematic bias in parameter estimation.BMC evolutionary biology · 2010Article
- g you The direct determination of haplotypes from extended regions of genomic DNA.BMC genomics · 2010Article
- Association analysis of Rgs7 variants with panic disorder.Journal of neural transmission (Vienna, Austria : 1996) · 2009Article
- Vitamin D related genes, CYP24A1 and CYP27B1, and colon cancer risk.Cancer epidemiology, biomarkers & prevention : a publication of the American Association for Cancer Research, cosponsored by the American Society of Preventive Oncology · 2009Article
- IL1 gene cluster polymorphisms and its haplotypes may predict the risk to develop invasive pulmonary aspergillosis and modulate C-reactive protein level.Journal of clinical immunology · 2008Article
- Molecular evidence of founder effects of fatal familial insomnia through SNP haplotypes around the D178N mutation.Neurogenetics · 2008Article
- Mapping MHC-resident transplantation determinants.Biology of blood and marrow transplantation : journal of the American Society for Blood and Marrow Transplantation · 2007Article
- MHC haplotype matching for unrelated hematopoietic cell transplantation.PLoS medicine · 2007Article
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Abstract
Haplotype analysis has become increasingly important for the study of human disease as well as for reconstruction of human population histories. Computer programs have been developed to estimate haplotype frequencies statistically from marker phenotypes in unrelated individuals. However, there currently are few empirical reports on the accuracy of statistical estimates that must infer linkage phase. We have analyzed haplotypes at the CD4 locus on chromosome 12 that consist of a short tandem-repeat polymorphism and an Alu insertion/deletion polymorphism located 9.8 kb apart, in 398 individuals from 10 geographically diverse sub-Saharan African populations. Haplotype frequency estimates obtained using gene counting based on molecularly haplotyped (phase-known) data were compared with haplotype frequency estimates obtained using the expectation-maximization algorithm. We show that the estimated frequencies of common haplotypes do not differ significantly with the use of phase-known versus phase-unknown data. However, rare haplotypes are occasionally miscalled when their presence/absence must be inferred. Thus, for those research questions for which the common haplotypes are most important, frequency estimates based on the phase-unknown marker-typing results from unrelated individuals will be sufficient. However, in cases where knowledge of rare haplotypes is critical, molecular haplotyping will be necessary to determine linkage phase unambiguously.
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