A fast and flexible statistical model for large-scale population genotype data: applications to inferring missing genotypes and haplotypic phase.
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Summary
A statistical model based on the idea that, over short regions, haplotypes in a population tend to cluster into groups of similar haplotypes that allows cluster memberships to change continuously along the chromosome according to a hidden Markov model to capture the fact that recombination tends to be local in nature.
- Type
- article
- Published
- 2006-04-01
- Cited by
- 1,994
- References
- 29
- Access
- Open access
- OpenAlex
- https://openalex.org/W2115837368
- Semantic Scholar
- https://api.semanticscholar.org/CorpusID:13415760
Keywords
Linkage disequilibrium, International HapMap Project, Haplotype, Population, Missing data
References
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- Modeling linkage disequilibrium and identifying recombination hotspots using single-nucleotide polymorphism data.
- Detecting Disease Associations due to Linkage Disequilibrium Using Haplotype Tags: A Class of Tests and the Determinants of Statistical Power
- Model-Based Inference of Haplotype Block Variation
- A comparison of phasing algorithms for trios and unrelated individuals.
- The Combination of Forecasts
- Coalescent-Based Association Mapping and Fine Mapping of Complex Trait Loci
- A Genetic Mixture Analysis for use with Incomplete Source Population Data
- An MDL Method for Finding Haplotype Blocks and for Estimating the Strength of Haplotype Block Boundaries
- Accounting for decay of linkage disequilibrium in haplotype inference and missing-data imputation.
- Maximum likelihood from incomplete data via the EM - algorithm plus discussions on the paper
- A comparison of bayesian methods for haplotype reconstruction from population genotype data.
- A Block-Free Hidden Markov Model for Genotypes and Its Application to Disease Association
- Inference of population structure using multilocus genotype data.
- Haplotype reconstruction from genotype data using Imperfect Phylogeny
- A new statistical method for haplotype reconstruction from population data.
- Detecting immigration by using multilocus genotypes.
- A tutorial on hidden Markov models and selected applications in speech recognition
- A new look at the statistical model identification
- Estimating the Dimension of a Model
Cited by
- Testing Untyped Alleles (TUNA)—applications to genome‐wide association studies
- Inferring missing genotypes in large SNP panels using fast nearest-neighbor searches over sliding windows
- Prevalence of common disease-associated variants in Asian Indians
- Evaluation of Potential Power Gain with Imputed Genotypes in Genome-Wide Association Studies
- Detection of prion gene promoter and intron1 indel polymorphisms in Anatolian water buffalo (Bubalus bubalis).
- A genome-wide scan for signatures of recent selection in Holstein cattle.
- Comprehensive Analysis of HLA-G: Implications for Recurrent Spontaneous Abortion
- A validated genome-wide association study in 2 dairy cattle breeds for milk production and fertility traits using variable length haplotypes.
- Accuracy of direct genomic values derived from imputed single nucleotide polymorphism genotypes in Jersey cattle.
- Accelerating Haplotype-Based Genome-Wide Association Study Using Perfect Phylogeny and Phase-Known Reference Data
- No Evidence for Strong Recent Positive Selection Favoring the 7 Repeat Allele of VNTR in the DRD4 Gene
- A Targeted Association Study of Immunity Genes and Networks Suggests Novel Associations with Placental Malaria Infection
- Association of genetic variants of human telomerase with colorectal polyps and colorectal cancer risk
- Origins and Genetic Legacy of Neolithic Farmers and Hunter-Gatherers in Europe
- An ensemble-based approach to imputation of moderate-density genotypes for genomic selection with application to Angus cattle.
- Positive Selection on the Osteoarthritis-Risk and Decreased-Height Associated Variants at the GDF5 Gene in East Asians
- Phenotype prediction from genome-wide association studies: application to smoking behaviors
- The admixed population structure in Danish Jersey dairy cattle challenges accurate genomic predictions.
- Association of surfactant protein B gene polymorphisms (C/A-18, C/T1580, intron 4 and A/G9306) and haplotypes with bronchopulmonary dysplasia in chinese han population
- A Major Gene for Bovine Ovulation Rate
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