ArticleGenetics2010
A hidden markov model combining linkage and linkage disequilibrium information for haplotype reconstruction and quantitative trait locus fine mapping.
Article in Genetics, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 100 papers, 1 of them a synthesis that pooled it.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
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.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
100 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Integrated analysis of genome-wide association studies and 3D epigenomic characteristics reveal the BMP2 gene regulating loin muscle depth in Yorkshire pigs.PLoS genetics · 2023Pooled it
- Genome-wide association and fine-mapping analyses identify novel candidate genes affecting serum cortisol levels using imputed whole-genome sequencing data in pigs.Journal of animal science and technology · 2025Article
- An overview of recent technological developments in bovine genomics.Veterinary and animal science · 2024Review
- Genetic and genomic analysis of Belgian Blue's susceptibility for psoroptic mange.Genetics, selection, evolution : GSE · 2024Article
- Genetic dissection and genomic prediction for pork cuts and carcass morphology traits in pig.Journal of animal science and biotechnology · 2023Article
- Mutations on a conserved distal enhancer in the porcine C-reactive protein gene impair its expression in liver.Frontiers in immunology · 2023Article
- Genomic prediction of carcass traits using different haplotype block partitioning methods in beef cattle.Evolutionary applications · 2022Article
- An imputed whole-genome sequence-based GWAS approach pinpoints causal mutations for complex traits in a specific swine population.Science China. Life sciences · 2022Article
- Benchmarking phasing software with a whole-genome sequenced cattle pedigree.BMC genomics · 2022Article
- High male specific contribution of the X-chromosome to individual global recombination rate in dairy cattle.BMC genomics · 2022Article
- A maximum-likelihood method to estimate haplotype frequencies and prevalence alongside multiplicity of infection from SNP data.Frontiers in epidemiology · 2022Article
- Evolutionary genetics of malaria.Frontiers in genetics · 2022Article
- Article
- Genome-wide association studies for production, respiratory disease, and immune-related traits in Landrace pigs.Scientific reports · 2021Article
- Inference of Ancestries and Heterozygosity Proportion and Genotype Imputation in West African Cattle Populations.Frontiers in genetics · 2021Article
- Genetic architecture of individual variation in recombination rate on the X chromosome in cattle.Heredity · 2020Article
- Haplotype-based genome-wide association studies for carcass and growth traits in chicken.Poultry science · 2020Article
- RAINBOW: Haplotype-based genome-wide association study using a novel SNP-set method.PLoS computational biology · 2020Article
- Genome-Wide Association Study Using Individual Single-Nucleotide Polymorphisms and Haplotypes for Erythrocyte Traits in Alpine Merino Sheep.Frontiers in genetics · 2020Article
- Genetic parameters and genomic breeding values for digital dermatitis in Holstein Friesian dairy cattle: host susceptibility, infectivity and the basic reproduction ratio.Genetics, selection, evolution : GSE · 2019Article
40 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.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Faithful reconstruction of haplotypes from diploid marker data (phasing) is important for many kinds of genetic analyses, including mapping of trait loci, prediction of genomic breeding values, and identification of signatures of selection. In human genetics, phasing most often exploits population information (linkage disequilibrium), while in animal genetics the primary source of information is familial (Mendelian segregation and linkage). We herein develop and evaluate a method that simultaneously exploits both sources of information. It builds on hidden Markov models that were initially developed to exploit population information only. We demonstrate that the approach improves the accuracy of allele phasing as well as imputation of missing genotypes. Reconstructed haplotypes are assigned to hidden states that are shown to correspond to clusters of genealogically related chromosomes. We show that these cluster states can directly be used to fine map QTL. The method is computationally effective at handling large data sets based on high-density SNP panels.
Indexed as
Identifiers
What Socratic holds
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 Socratic graph.