ArticleGenetics2014
Genome-wide estimation of linkage disequilibrium from population-level high-throughput sequencing data.
Article in Genetics, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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Who cites it
15 citing papers in PubMed.
- Genome-wide association study of salicylic acid provides genetic insights for tea plant selective breeding.Horticulture research · 2025Article
- Evolutionary Insights from a Large-Scale Survey of Population-Genomic Variation.Molecular biology and evolution · 2023Article
- Evolutionary Insights from a Large-scale Survey of Population-genomic Variation.bioRxiv : the preprint server for biology · 2023Article
- Genome-wide association study of leaf-related traits in tea plant in Guizhou based on genotyping-by-sequencing.BMC plant biology · 2023Article
- The Linkage-Disequilibrium and Recombinational Landscape in Daphnia pulex.Genome biology and evolution · 2022Article
- Scalable bias-corrected linkage disequilibrium estimation under genotype uncertainty.Heredity · 2021Article
- Genetic control of male production inProceedings of the National Academy of Sciences of the United States of America · 2019Article
- Genetic diversity, linkage disequilibrium, and population structure analysis of the tea plant (Camellia sinensis) from an origin center, Guizhou plateau, using genome-wide SNPs developed by genotyping-by-sequencing.BMC plant biology · 2019Article
- On the Extent of Linkage Disequilibrium in the Genome of Farm Animals.Frontiers in genetics · 2019Review
- Article
- Genotype Calling from Population-Genomic Sequencing Data.G3 (Bethesda, Md.) · 2017Article
- Population Genomics ofGenetics · 2017Article
- Inferring Population Size History from Large Samples of Genome-Wide Molecular Data - An Approximate Bayesian Computation Approach.PLoS genetics · 2016Article
- Article
- Article
Corrections and comments
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Authors and funding
2 authors.
Funding
Abstract
Rapidly improving sequencing technologies provide unprecedented opportunities for analyzing genome-wide patterns of polymorphisms. In particular, they have great potential for linkage-disequilibrium analyses on both global and local genetic scales, which will substantially improve our ability to derive evolutionary inferences. However, there are some difficulties with analyzing high-throughput sequencing data, including high error rates associated with base reads and complications from the random sampling of sequenced chromosomes in diploid organisms. To overcome these difficulties, we developed a maximum-likelihood estimator of linkage disequilibrium for use with error-prone sampling data. Computer simulations indicate that the estimator is nearly unbiased with a sampling variance at high coverage asymptotically approaching the value expected when all relevant information is accurately estimated. The estimator does not require phasing of haplotypes and enables the estimation of linkage disequilibrium even when all individual reads cover just single polymorphic sites.
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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.