ArticleGenetics2014
Detecting local haplotype sharing and haplotype association.
Article in Genetics, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 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
20 citing papers in PubMed, 1 synthesis or guideline pooled it, 38 citations in OpenAlex.
- Genetic association of BIN1 and GAB2 in Alzheimer's disease: A meta-analysis and systematic review.Geriatrics & gerontology international · 2021Pooled it
- The male and female genomes of golden pompano (Trachinotus ovatus) provide insights into the sex chromosome evolution and rapid growth.Journal of advanced research · 2024Article
- SNP-based and haplotype-based genome-wide association on drug dependence in Han Chinese.BMC genomics · 2024Article
- Limitations of principal components in quantitative genetic association models for human studies.eLife · 2023Article
- Dissecting the loci underlying maturation timing in Atlantic salmon using haplotype and multi-SNP based association methods.Heredity · 2022Article
- Genome properties of key oil palm (Elaeis guineensis Jacq.) breeding populations.Journal of applied genetics · 2022Article
- Demographic history differences between Hispanics and Brazilians imprint haplotype features.G3 (Bethesda, Md.) · 2022Article
- Whole genome sequencing identified a 16 kilobase deletion on ECA13 associated with distichiasis in Friesian horses.BMC genomics · 2020Article
- Fine-Scale Inference of Ancestry Segments Without Prior Knowledge of Admixing Groups.Genetics · 2019Article
- Fast Model-Fitting of Bayesian Variable Selection Regression Using the Iterative Complex Factorization Algorithm.Bayesian analysis · 2019Article
- Evaluation of an HMGA2 variant for pleiotropic effects on height and metabolic traits in ponies.Journal of veterinary internal medicine · 2019Article
- A graph-based algorithm for estimating clonal haplotypes of tumor sample from sequencing data.BMC medical genomics · 2019Article
- A locus on chromosome 5 shows African ancestry-limited association with alloimmunization in sickle cell disease.Blood advances · 2018Article
- Genome-Wide Signatures of Selection Reveal Genes Associated With Performance in American Quarter Horse Subpopulations.Frontiers in genetics · 2018Article
- On the Null Distribution of Bayes Factors in Linear Regression.Journal of the American Statistical Association · 2018Article
- Genomic history of the origin and domestication of common bean unveils its closest sister species.Genome biology · 2017Article
- Genome-Wide Association Mapping of Flowering and Ripening Periods in Apple.Frontiers in plant science · 2017Article
- Regional Association Analysis of MetaQTLs Delineates Candidate Grain Size Genes in Rice.Frontiers in plant science · 2017Article
- Strong Selection at MHC in Mexicans since Admixture.PLoS genetics · 2016Article
- Multiscale parcellation of dynamic causal models of the brain.Imaging neuroscience (Cambridge, Mass.)Article
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 2 institutions in 2 countries.
Funding
Abstract
A novel haplotype association method is presented, and its power is demonstrated. Relying on a statistical model for linkage disequilibrium (LD), the method first infers ancestral haplotypes and their loadings at each marker for each individual. The loadings are then used to quantify local haplotype sharing between individuals at each marker. A statistical model was developed to link the local haplotype sharing and phenotypes to test for association. We devised a novel method to fit the LD model, reducing the complexity from putatively quadratic to linear (in the number of ancestral haplotypes). Therefore, the LD model can be fitted to all study samples simultaneously, and, consequently, our method is applicable to big data sets. Compared to existing haplotype association methods, our method integrated out phase uncertainty, avoided arbitrariness in specifying haplotypes, and had the same number of tests as the single-SNP analysis. We applied our method to data from the Wellcome Trust Case Control Consortium and discovered eight novel associations between seven gene regions and five disease phenotypes. Among these, GRIK4, which encodes a protein that belongs to the glutamate-gated ionic channel family, is strongly associated with both coronary artery disease and rheumatoid arthritis. A software package implementing methods described in this article is freely available at http://www.haplotype.org.
Indexed as
Identifiers
What OpenQuestion 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 OpenQuestion graph.