ArticleBioinformatics (Oxford, England)2018
A new haplotype block detection method for dense genome sequencing data based on interval graph modeling of clusters of highly correlated SNPs.
Article in Bioinformatics (Oxford, England), 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 31 papers, 1 of them a synthesis that pooled it.
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Who cites it
31 citing papers in PubMed, 1 synthesis or guideline pooled it, 79 citations in OpenAlex.
- Fully exploiting SNP arrays: a systematic review on the tools to extract underlying genomic structure.Briefings in bioinformatics · 2022Pooled it
- A reference panel for linkage disequilibrium and genotype imputation using whole-genome sequencing data from 2,680 participants across India.HGG advances · 2026Article
- Enhancing genomic prediction ability of blast resistance using genome-wide association study-derived marker weights in two rice (Oryza sativa L.) populations.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2026Article
- Comparative genomic analysis of QTL for resistance to Aphanomyces euteiches between pea, lentil, faba bean, and the model species Medicago truncatula.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2025Article
- Admixed and single-continental genome segments of the same ancestry have distinct linkage disequilibrium patterns.Genome biology · 2025Article
- Determinant-based grouping of SNPs and its application for detecting disease-associated genomic loci.NAR genomics and bioinformatics · 2025Article
- RegionScan: a comprehensive R package for region-level genome-wide association testing with integration and visualization of multiple-variant and single-variant hypothesis testing.Bioinformatics advances · 2025Article
- Population dynamics of potentially harmful haplotypes: a pedigree analysis.BMC genomics · 2024Article
- A SIMPLE AND FLEXIBLE TEST OF SAMPLE EXCHANGEABILITY WITH APPLICATIONS TO STATISTICAL GENOMICS.The annals of applied statistics · 2024Article
- Article
- An in-depth association analysis of genetic variants within nicotine-related loci: Meeting in middle of GWAS and genetic fine-mapping.Molecular and cellular neurosciences · 2023Article
- Variants of IL6, IL10, FCN2, RNASE3, IL12B and IL17B loci are associated with Schistosoma mansoni worm burden in the Albert Nile region of Uganda.PLoS neglected tropical diseases · 2023Article
- Evaluation of Density-Based Spatial Clustering for Identifying Genomic Loci Associated with Ischemic Stroke in Genome-Wide Data.International journal of molecular sciences · 2023Article
- Expanding the application of haplotype-based genomic predictions to the wild: A case of antibody response against Teladorsagia circumcincta in Soay sheep.BMC genomics · 2023Article
- NOMe-HiC: joint profiling of genetic variant, DNA methylation, chromatin accessibility, and 3D genome in the same DNA molecule.Genome biology · 2023Article
- SNP- and haplotype-based single-step genomic predictions for body weight, wool, and reproductive traits in North American Rambouillet sheep.Journal of animal breeding and genetics = Zeitschrift fur Tierzuchtung und Zuchtungsbiologie · 2023Article
- Genome-Wide Analysis of Rare Haplotypes Associated with Breast Cancer Risk.Cancer research · 2023Article
- Prioritized candidate causal haplotype blocks in plant genome-wide association studies.PLoS genetics · 2022Article
- SCN1A overexpression, associated with a genomic region marked by a risk variant for a common epilepsy, raises seizure susceptibility.Acta neuropathologica · 2022Article
- A major-effect genetic locus, ApRVII, controlling resistance against both adapted and non-adapted aphid biotypes in pea.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2022Article
Corrections and comments
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Authors and funding
5 authors at 3 institutions in 2 countries.
Funding
Abstract
Motivation: Linkage disequilibrium (LD) block construction is required for research in population genetics and genetic epidemiology, including specification of sets of single nucleotide polymorphisms (SNPs) for analysis of multi-SNP based association and identification of haplotype blocks in high density sequencing data. Existing methods based on a narrow sense definition do not allow intermediate regions of low LD between strongly associated SNP pairs and tend to split high density SNP data into small blocks having high between-block correlation. Results: We present Big-LD, a block partition method based on interval graph modeling of LD bins which are clusters of strong pairwise LD SNPs, not necessarily physically consecutive. Big-LD uses an agglomerative approach that starts by identifying small communities of SNPs, i.e. the SNPs in each LD bin region, and proceeds by merging these communities. We determine the number of blocks using a method to find maximum-weight independent set. Big-LD produces larger LD blocks compared to existing methods such as MATILDE, Haploview, MIG ++, or S-MIG ++ and the LD blocks better agree with recombination hotspot locations determined by sperm-typing experiments. The observed average runtime of Big-LD for 13 288 240 non-monomorphic SNPs from 1000 Genomes Project autosome data (286 East Asians) is about 5.83 h, which is a significant improvement over the existing methods. Availability and implementation: Source code and documentation are available for download at http://github.com/sunnyeesl/BigLD. Contact: yyoo@snu.ac.kr. Supplementary information: Supplementary data are available at Bioinformatics online.
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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.