ArticleBioData mining2009
LD-spline: mapping SNPs on genotyping platforms to genomic regions using patterns of linkage disequilibrium.
Article in BioData mining, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 papers, 1 of them a synthesis that pooled it.
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Who cites it
9 citing papers in PubMed, 1 synthesis or guideline pooled it, 12 citations in OpenAlex.
- A comprehensive analysis of shared loci between systemic lupus erythematosus (SLE) and sixteen autoimmune diseases reveals limited genetic overlap.PLoS genetics · 2011Pooled it
- Genetic dissection of the root system architecture QTLome and its relationship with early shoot development, breeding and adaptation in durum wheat.The plant genome · 2025Article
- Genome-wide association study of Nelore and Angus heifers with low and high ovarian follicle counts.Animal reproduction · 2024Article
- Study of whole genome linkage disequilibrium patterns of Iranian water buffalo breeds using the Axiom Buffalo Genotyping 90K Array.PloS one · 2019Article
- Association of the GRM4 gene variants with juvenile myoclonic epilepsy in an Indian population.Journal of genetics · 2014Article
- Epistasis network centrality analysis yields pathway replication across two GWAS cohorts for bipolar disorder.Translational psychiatry · 2012Article
- Gene set analysis of genome-wide association studies: methodological issues and perspectives.Genomics · 2011Review
- Using biological knowledge to uncover the mystery in the search for epistasis in genome-wide association studies.Annals of human genetics · 2011Review
- Characteristics of linkage disequilibrium in North American Holsteins.BMC genomics · 2010Article
Corrections and comments
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Authors and funding
4 authors at 3 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundGene-centric analysis tools for genome-wide association study data are being developed both to annotate single locus statistics and to prioritize or group single nucleotide polymorphisms (SNPs) prior to analysis. These approaches require knowledge about the relationships between SNPs on a genotyping platform and genes in the human genome. SNPs in the genome can represent broader genomic regions via linkage disequilibrium (LD), and population-specific patterns of LD can be exploited to generate a data-driven map of SNPs to genes.
methodsIn this study, we implemented LD-Spline, a database routine that defines the genomic boundaries a particular SNP represents using linkage disequilibrium statistics from the International HapMap Project. We compared the LD-Spline haplotype block partitioning approach to that of the four gamete rule and the Gabriel et al. approach using simulated data; in addition, we processed two commonly used genome-wide association study platforms.
resultsWe illustrate that LD-Spline performs comparably to the four-gamete rule and the Gabriel et al. approach; however as a SNP-centric approach LD-Spline has the added benefit of systematically identifying a genomic boundary for each SNP, where the global block partitioning approaches may falter due to sampling variation in LD statistics.
conclusionLD-Spline is an integrated database routine that quickly and effectively defines the genomic region marked by a SNP using linkage disequilibrium, with a SNP-centric block definition algorithm.
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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.