ArticleGenetics2018
Linkage Disequilibrium Estimation in Low Coverage High-Throughput Sequencing Data.
Article in Genetics, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
What it found
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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.
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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
18 citing papers in PubMed.
- Unveiling the genetic determinants of germination efficiency in common bermudagrass: A genome-wide association study.The plant genome · 2026Article
- Article
- SimGBS: a rapid method for simulating large-scale genotyping-by-sequencing data.BMC bioinformatics · 2025Article
- Assessing population allele frequency differences using low-depth sequencing data.Journal of the Royal Society of New Zealand · 2025Article
- MhGeneS: An Analytical Pipeline to Allow for Robust Microhaplotype Genotyping.Molecular ecology resources · 2025Article
- Construction of relatedness matrices in autopolyploid populations using low-depth high-throughput sequencing data.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2024Article
- Population genomics and geographic dispersal in Chagas disease vectors: Landscape drivers and evidence of possible adaptation to the domestic setting.PLoS genetics · 2022Article
- Genotyping Strategies Using ddRAD Sequencing in Farmed Arctic Charr (Animals : an open access journal from MDPI · 2021Article
- Can the genomics of ecological speciation be predicted across the divergence continuum from host races to species? A case study inPhilosophical transactions of the Royal Society of London. Series B, Biological sciences · 2020Article
- Consequences of Single-Locus and Tightly Linked Genomic Architectures for Evolutionary Responses to Environmental Change.The Journal of heredity · 2020Article
- Application of Low Coverage Genotyping by Sequencing in Selectively Bred Arctic Charr (G3 (Bethesda, Md.) · 2020Article
- Parallel and nonparallel genomic responses contribute to herbicide resistance in Ipomoea purpurea, a common agricultural weed.PLoS genetics · 2020Article
- Estimating effective population size using RADseq: Effects of SNP selection and sample size.Ecology and evolution · 2020Article
- Exclusion and Genomic Relatedness Methods for Assignment of Parentage Using Genotyping-by-Sequencing Data.G3 (Bethesda, Md.) · 2019Article
- Breaking Free: The Genomics of Allopolyploidy-Facilitated Niche Expansion in White Clover.The Plant cell · 2019Article
- Accurate sequence variant genotyping in cattle using variation-aware genome graphs.Genetics, selection, evolution : GSE · 2019Article
- Developing Successful Breeding Programs for New Zealand Aquaculture: A Perspective on Progress and Future Genomic Opportunities.Frontiers in genetics · 2019Article
- Predictive ability of genomic selection models in a multi-population perennial ryegrass training set using genotyping-by-sequencing.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2018Article
Corrections and comments
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Authors and funding
7 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
High-throughput sequencing methods that multiplex a large number of individuals have provided a cost-effective approach for discovering genome-wide genetic variation in large populations. These sequencing methods are increasingly being utilized in population genetic studies across a diverse range of species. Two side-effects of these methods, however, are (1) sequencing errors and (2) heterozygous genotypes called as homozygous due to only one allele at a particular locus being sequenced, which occurs when the sequencing depth is insufficient. Both of these errors have a profound effect on the estimation of linkage disequilibrium (LD) and, if not taken into account, lead to inaccurate estimates. We developed a new likelihood method, GUS-LD, to estimate pairwise linkage disequilibrium using low coverage sequencing data that accounts for undercalled heterozygous genotypes and sequencing errors. Our findings show that accurate estimates were obtained using GUS-LD, whereas underestimation of LD results if no adjustment is made for the errors.
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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.