ArticleGenetics2003
Modeling linkage disequilibrium and identifying recombination hotspots using single-nucleotide polymorphism data.
Article in Genetics, 2003. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 558 papers, 2 of them syntheses that pooled it.
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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
558 citing papers in PubMed, 2 syntheses or guidelines pooled it.
- Meta-imputation: An efficient method to combine genotype data after imputation with multiple reference panels.American journal of human genetics · 2022Pooled it
- Data Integration, Imputation, and Meta-analysis for Genome-Wide Association Studies.Methods in molecular biology (Clifton, N.J.) · 2022Pooled it
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- Faster inference of complex demographic models from large allele frequency spectra.Bioinformatics (Oxford, England) · 2026Article
- The rights and wrongs of rescaling in population genetics simulations.PLoS genetics · 2026Review
- The life history of recessive deleterious alleles as seen through the eyes of a honey bee (Apis mellifera).Molecular biology and evolution · 2026Article
- Local ancestry inference with poorly-matched reference panels.PLoS genetics · 2026Article
- Selphi, a tool for improving genotype imputation accuracy.Scientific reports · 2026Article
- Genome-wide associations of structural variants with human traits through imputation from long-read assemblies.Nature genetics · 2026Article
- Shifting Balancing Selection Underlies an Inversion Cline in Eurasian Blackcap.Ecology and evolution · 2026Article
- Diversification in ANME-1 archaea is associated with the presence of highly variable genomic hotspots.Nature communications · 2026Article
- ALGI: Sparse Convolutional Denoising Autoencoder Utilizing Local Genomic Information for Genotype Imputation.Animals : an open access journal from MDPI · 2026Article
- GS-Impute: A neural network framework for accurate imputation of low-density markers in across-population genomic selection.Plant communications · 2026Article
- Establishing standards for genome wide association studies in eusocial insects through a case study in honey bees.Scientific reports · 2026Article
- Graph transformer for ancient ancestry inference.bioRxiv : the preprint server for biology · 2026Article
- Benchmarking imputation accuracy in the presence or absence of a reference panel.Molecular biology and evolution · 2026Article
- Eye can see clearly now: Identifying the locus associated with a white-eye mutation in honey bees (Apis mellifera).Insect molecular biology · 2026Article
498 more citing papers are in PubMed but not listed here.
Corrections and comments
- Erratum issued
Authors and funding
2 authors.
Funding
Abstract
We introduce a new statistical model for patterns of linkage disequilibrium (LD) among multiple SNPs in a population sample. The model overcomes limitations of existing approaches to understanding, summarizing, and interpreting LD by (i) relating patterns of LD directly to the underlying recombination process; (ii) considering all loci simultaneously, rather than pairwise; (iii) avoiding the assumption that LD necessarily has a "block-like" structure; and (iv) being computationally tractable for huge genomic regions (up to complete chromosomes). We examine in detail one natural application of the model: estimation of underlying recombination rates from population data. Using simulation, we show that in the case where recombination is assumed constant across the region of interest, recombination rate estimates based on our model are competitive with the very best of current available methods. More importantly, we demonstrate, on real and simulated data, the potential of the model to help identify and quantify fine-scale variation in recombination rate from population data. We also outline how the model could be useful in other contexts, such as in the development of more efficient haplotype-based methods for LD mapping.
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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.