ArticleAmerican journal of human genetics2005
Accounting for decay of linkage disequilibrium in haplotype inference and missing-data imputation.
Article in American journal of human genetics, 2005. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 591 papers, 3 of them syntheses that pooled it.
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
591 citing papers in PubMed, 3 syntheses or guidelines pooled it, 1,359 citations in OpenAlex.
- Association of polymorphisms in the erythropoietin gene with diabetic retinopathy: a case-control study and systematic review with meta-analysis.BMC ophthalmology · 2022Pooled it
- Improved high-throughput MHC typing for non-model species using long-read sequencing.Molecular ecology resources · 2022Pooled it
- Integrative genomic analysis implicates ERCC6 and its interaction with ERCC8 in susceptibility to breast cancer.Scientific reports · 2020Pooled it
- Genetic variants of TLR4, including the novel variant, rs5030719, and related genes are associated with susceptibility to clinical malaria in African children.Malaria journal · 2023Trial
- Haplotypes of FOXP3 genetic variants are associated with susceptibility, autoantibodies, and TGF-β1 in patients with systemic lupus erythematosus.Scientific reports · 2021Trial
- Metformin Pharmacogenetics in Heart Failure Patients with Reduced Ejection Fraction: Impact on Metformin and Growth Differentiation Factor-15 Plasma Levels.Clinical pharmacokinetics · 2026Article
- Pharmacogenetic Risk Factors for Thiopurine-Induced Leukopenia in Patients with Inflammatory Bowel Disease.Yonsei medical journal · 2026Article
- Development and Evaluation of a Novel Microhaplotype Panel for DNA Mixture and Kinship Analysis.Electrophoresis · 2026Article
- Interplay between CDH1 polymorphisms, haplotypes, and genomic repetitive elements in urothelial bladder cancer prognosis.Molecular biology reports · 2026Article
- Article
- Advances in haplotype phasing and genotype imputation.Nature reviews. Genetics · 2026Review
- HaploExplore, a software specifically designed for the detection of minor allele (MiA-) haploblocks.NAR genomics and bioinformatics · 2025Article
- Boost or Bust? The Impact of Supplementation on Functional Genetic Diversity and Selective Processes in Tasmanian Devils.Molecular ecology · 2025Article
- Identification of new major histocompatibility complex-B haplotypes in chinese broilers.Poultry science · 2025Article
- TheInternational journal of molecular sciences · 2025Article
- Evaluation of imputation performance based on the single nucleotide polymorphism panel density and the reference population size in Korean native chicken.Animal bioscience · 2025Article
- Participation bias in the estimation of heritability and genetic correlation.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- HPTAS: An Alignment-Free Haplotype Phasing Algorithm Focused on Allele-Specific Studies Using Transcriptome Data.International journal of molecular sciences · 2025Article
- A cohort of GFPT1 related congenital myasthenic syndrome in China: high frequency of c.331 c > t variant.Orphanet journal of rare diseases · 2025Article
- Genome-wide diversity and MHC characterisation in a critically endangered freshwater turtle susceptible to disease.Immunogenetics · 2025Article
531 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
2 authors at 1 institution in 1 country.
Funding
Abstract
Although many algorithms exist for estimating haplotypes from genotype data, none of them take full account of both the decay of linkage disequilibrium (LD) with distance and the order and spacing of genotyped markers. Here, we describe an algorithm that does take these factors into account, using a flexible model for the decay of LD with distance that can handle both "blocklike" and "nonblocklike" patterns of LD. We compare the accuracy of this approach with a range of other available algorithms in three ways: for reconstruction of randomly paired, molecularly determined male X chromosome haplotypes; for reconstruction of haplotypes obtained from trios in an autosomal region; and for estimation of missing genotypes in 50 autosomal genes that have been completely resequenced in 24 African Americans and 23 individuals of European descent. For the autosomal data sets, our new approach clearly outperforms the best available methods, whereas its accuracy in inferring the X chromosome haplotypes is only slightly superior. For estimation of missing genotypes, our method performed slightly better when the two subsamples were combined than when they were analyzed separately, which illustrates its robustness to population stratification. Our method is implemented in the software package PHASE (v2.1.1), available from the Stephens Lab Web site.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.