ArticleEuropean journal of human genetics : EJHG2009
Gains in power for exhaustive analyses of haplotypes using variable-sized sliding window strategy: a comparison of association-mapping strategies.
Article in European journal of human genetics : EJHG, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 28 papers.
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Who cites it
28 citing papers in PubMed, 36 citations in OpenAlex.
- Exploring the genetic basis of essential hypertension: association with AGT gene variants in an Iranian population.BMC genomics · 2025Article
- Effect of genomic regions harboring putative lethal haplotypes on reproductive performance in closed experimental selection lines of Nellore cattle.Scientific reports · 2025Article
- Unraveling genomic regions with transmission ratio distortion harboring putative lethal alleles and their biological implications in Nellore cattle from experimental selection lines.Journal of animal science · 2025Article
- Analysis of dog breed diversity using a composite selection index.Scientific reports · 2023Article
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- Status and prospects of genome-wide association studies in plants.The plant genome · 2021Review
- A Genome-Wide Association Study for Calving Interval in Holstein Dairy Cows Using Weighted Single-Step Genomic BLUP Approach.Animals : an open access journal from MDPI · 2020Article
- A Genome-Wide Association Study on Feed Efficiency Related Traits in Landrace Pigs.Frontiers in genetics · 2020Article
- Exploring effective approaches for haplotype block phasing.BMC bioinformatics · 2019Article
- Sliding window haplotype approaches overcome single SNP analysis limitations in identifying genes for meat tenderness in Nelore cattle.BMC genetics · 2019Article
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- Comparison of haplotype-based statistical tests for disease association with rare and common variants.Briefings in bioinformatics · 2016Article
- Loci, genes, and mechanisms associated with tolerance to ferrous iron toxicity in rice (Oryza sativa L.).TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2015Article
- Genetic association between germline JAK2 polymorphisms and myeloproliferative neoplasms in Hong Kong Chinese population: a case-control study.BMC genetics · 2014Article
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- Single nucleotide polymorphisms and haplotypes associated with feed efficiency in beef cattle.BMC genetics · 2013Article
- Haplotype kernel association test as a powerful method to identify chromosomal regions harboring uncommon causal variants.Genetic epidemiology · 2013Article
- Insulin-like growth factor 1 is not associated with high myopia in a large Japanese cohort.Molecular vision · 2013Article
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Corrections and comments
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Authors and funding
5 authors at 2 institutions in 2 countries.
Funding
Abstract
Linkage disequilibrium (LD)-based association mapping is often performed by analyzing either individual SNPs or block-based multi-SNP haplotypes. Sliding windows of several fixed sizes (in terms of SNP numbers) were also applied to a few simulated or real data sets. In comparison, exhaustively testing based on variable-sized sliding windows (VSW) of all possible sizes of SNPs over a genomic region has the best chance to capture the optimum markers (single SNPs or haplotypes) that are most significantly associated with the traits under study. However, the cost is the increased number of multiple tests and computation. Here, a strategy of VSW of all possible sizes is proposed and its power is examined, in comparison with those using only haplotype blocks (BLK) or single SNP loci (SGL) tests. Critical values for statistical significance testing that account for multiple testing are simulated. We demonstrated that, over a wide range of parameters simulated, VSW increased power for the detection of disease variants by approximately 1-15% over the BLK and SGL approaches. The improved performance was more significant in regions with high recombination rates. In an empirical data set, VSW obtained the most significant signal and identified the LRP5 gene as strongly associated with osteoporosis. With the use of computational techniques such as parallel algorithms and clustering computing, it is feasible to apply VSW to large genomic regions or those regions preliminarily identified by traditional SGL/BLK methods.
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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.