ArticleGenetic epidemiology2012
Haplotype-based methods for detecting uncommon causal variants with common SNPs.
Article in Genetic epidemiology, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
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Who cites it
22 citing papers in PubMed.
- Effects of 'Candidatus Liberibacter solanacearum' haplotypes A and B on tomato gene expression and geotropism.BMC plant biology · 2022Article
- Genome-wide haplotype association study in imaging genetics using whole-brain sulcal openings of 16,304 UK Biobank subjects.European journal of human genetics : EJHG · 2021Article
- Impairments of Photoreceptor Outer Segments Renewal and Phototransduction Due to a Peripherin Rare Haplotype Variant: Insights from Molecular Modeling.International journal of molecular sciences · 2021Article
- Comparison of haplotype-based tests for detecting gene-environment interactions with rare variants.Briefings in bioinformatics · 2020Review
- An integrative association method for omics data based on a modified Fisher's method with application to childhood asthma.PLoS genetics · 2019Article
- A Family-Based Rare Haplotype Association Method for Quantitative Traits.Human heredity · 2018Article
- Comparison of haplotype-based statistical tests for disease association with rare and common variants.Briefings in bioinformatics · 2016Article
- Beyond Rare-Variant Association Testing: Pinpointing Rare Causal Variants in Case-Control Sequencing Study.Scientific reports · 2016Article
- Associating Multivariate Quantitative Phenotypes with Genetic Variants in Family Samples with a Novel Kernel Machine Regression Method.Genetics · 2015Article
- Kullback-Leibler divergence for detection of rare haplotype common disease association.European journal of human genetics : EJHG · 2015Article
- Detecting associations of rare variants with common diseases: collapsing or haplotyping?Briefings in bioinformatics · 2015Article
- Rare-Variant Kernel Machine Test for Longitudinal Data from Population and Family Samples.Human heredity · 2015Article
- A Sequence Kernel Association Test for Dichotomous Traits in Family Samples under a Generalized Linear Mixed Model.Human heredity · 2015Article
- FamLBL: detecting rare haplotype disease association based on common SNPs using case-parent triads.Bioinformatics (Oxford, England) · 2014Article
- The power comparison of the haplotype-based collapsing tests and the variant-based collapsing tests for detecting rare variants in pedigrees.BMC genomics · 2014Article
- Using haplotypes for the prediction of allelic identity to fine-map QTL: characterization and properties.Genetics, selection, evolution : GSE · 2014Article
- Kernel-machine testing coupled with a rank-truncation method for genetic pathway analysis.Genetic epidemiology · 2014Article
- Detecting rare haplotype-environment interaction with logistic Bayesian LASSO.Genetic epidemiology · 2014Article
- Article
- Adaptive combination of P-values for family-based association testing with sequence data.PloS one · 2014Article
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7 authors.
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Abstract
Detecting uncommon causal variants (minor allele frequency [MAF] < 5%) is difficult with commercial single-nucleotide polymorphism (SNP) arrays that are designed to capture common variants (MAF > 5%). Haplotypes can provide insights into underlying linkage disequilibrium (LD) structure and can tag uncommon variants that are not well tagged by common variants. In this work, we propose a wei-SIMc-matching test that inversely weights haplotype similarities with the estimated standard deviation of haplotype counts to boost the power of similarity-based approaches for detecting uncommon causal variants. We then compare the power of the wei-SIMc-matching test with that of several popular haplotype-based tests, including four other similarity-based tests, a global score test for haplotypes (global), a test based on the maximum score statistic over all haplotypes (max), and two newly proposed haplotype-based tests for rare variant detection. With systematic simulations under a wide range of LD patterns, the results show that wei-SIMc-matching and global are the two most powerful tests. Among these two tests, wei-SIMc-matching has reliable asymptotic P-values, whereas global needs permutations to obtain reliable P-values when the frequencies of some haplotype categories are low or when the trait is skewed. Therefore, we recommend wei-SIMc-matching for detecting uncommon causal variants with surrounding common SNPs, in light of its power and computational feasibility.
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