ArticleBMC genetics2008
A systematic search for SNPs/haplotypes associated with disease phenotypes using a haplotype-based stepwise procedure.
Article in BMC genetics, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
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Who cites it
11 citing papers in PubMed, 18 citations in OpenAlex.
- Superior haplotypes for transforming crop breeding.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2026Review
- Research on multi-trait genome association study method based on Shannon information entropy.BMC bioinformatics · 2026Article
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- Article
- Sister haplotypes and recombination disequilibrium: a new approach to identify associations of haplotypes with complex diseases.Frontiers in genetics · 2023Article
- Selecting Closely-Linked SNPs Based on Local Epistatic Effects for Haplotype Construction Improves Power of Association Mapping.G3 (Bethesda, Md.) · 2019Article
- The acid phosphatase-encoding gene GmACP1 contributes to soybean tolerance to low-phosphorus stress.PLoS genetics · 2014Article
- Multi-locus stepwise regression: a haplotype-based algorithm for finding genetic associations applied to atopic dermatitis.BMC medical genetics · 2012Article
- Genetic diversity in cytokines associated with immune variation and resistance to multiple pathogens in a natural rodent population.PLoS genetics · 2011Article
- Exploring multilocus associations of inflammation genes and colorectal cancer risk using hapConstructor.BMC medical genetics · 2010Article
- Genetic variation in CXCL12 and risk of cervical carcinoma: a population-based case-control study.International journal of immunogenetics · 2009Article
Corrections and comments
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Authors and funding
5 authors at 1 institution in 1 country.
Funding
Abstract
backgroundGenotyping technologies enable us to genotype multiple Single Nucleotide Polymorphisms (SNPs) within selected genes/regions, providing data for haplotype association analysis. While haplotype-based association analysis is powerful for detecting untyped causal alleles in linkage-disequilibrium (LD) with neighboring SNPs/haplotypes, the inclusion of extraneous SNPs could reduce its power by increasing the number of haplotypes with each additional SNP.
methodsHere, we propose a haplotype-based stepwise procedure (HBSP) to eliminate extraneous SNPs. To evaluate its properties, we applied HBSP to both simulated and real data, generated from a study of genetic associations of the bactericidal/permeability-increasing (BPI) gene with pulmonary function in a cohort of patients following bone marrow transplantation.
resultsUnder the null hypothesis, use of the HBSP gave results that retained the desired false positive error rates when multiple comparisons were considered. Under various alternative hypotheses, HBSP had adequate power to detect modest genetic associations in case-control studies with 500, 1,000 or 2,000 subjects. In the current application, HBSP led to the identification of two specific SNPs with a positive validation.
conclusionThese results demonstrate that HBSP retains the essence of haplotype-based association analysis while improving analytic power by excluding extraneous SNPs. Minimizing the number of SNPs also enables simpler interpretation and more cost-effective applications.
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