ArticleGenetic epidemiology2011
Identification of genetic association of multiple rare variants using collapsing methods.
Article in Genetic epidemiology, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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Who cites it
14 citing papers in PubMed.
- Exome-wide screening identifies novel rare risk variants for bone mineral density.Osteoporosis international : a journal established as result of cooperation between the European Foundation for Osteoporosis and the National Osteoporosis Foundation of the USA · 2023Article
- Whole Exome Sequencing Study Identifies Novel Rare Risk Variants for Habitual Coffee Consumption Involved in Olfactory Receptor and Hyperphagia.Nutrients · 2022Article
- Exome-wide screening identifies novel rare risk variants for major depression disorder.Molecular psychiatry · 2022Article
- A gene-based test of association through an orthogonal decomposition of genotype scores.Human genetics · 2017Article
- Multiancestry Study of Gene-Lifestyle Interactions for Cardiovascular Traits in 610 475 Individuals From 124 Cohorts: Design and Rationale.Circulation. Cardiovascular genetics · 2017Article
- Gene-based segregation method for identifying rare variants in family-based sequencing studies.Genetic epidemiology · 2017Article
- A geometric framework for evaluating rare variant tests of association.Genetic epidemiology · 2013Article
- Assessing the impact of differential genotyping errors on rare variant tests of association.PloS one · 2013Article
- Integration of biological networks and pathways with genetic association studies.Human genetics · 2012Review
- Statistical tests for detecting rare variants using variance-stabilising transformations.Annals of human genetics · 2012Article
- Exome sequencing followed by large-scale genotyping suggests a limited role for moderately rare risk factors of strong effect in schizophrenia.American journal of human genetics · 2012Article
- Incorporating biological information into association studies of sequencing data.Genetic epidemiology · 2011Article
- Statistical analysis of rare sequence variants: an overview of collapsing methods.Genetic epidemiology · 2011Review
- Lessons learned from Genetic Analysis Workshop 17: transitioning from genome-wide association studies to whole-genome statistical genetic analysis.Genetic epidemiology · 2011Article
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Authors and funding
4 authors.
Funding
Abstract
Next-generation sequencing technology allows investigation of both common and rare variants in humans. Exomes are sequenced on the population level or in families to further study the genetics of human diseases. Genetic Analysis Workshop 17 (GAW17) provided exomic data from the 1000 Genomes Project and simulated phenotypes. These data enabled evaluations of existing and newly developed statistical methods for rare variant sequence analysis for which standard statistical methods fail because of the rareness of the alleles. Various alternative approaches have been proposed that overcome the rareness problem by combining multiple rare variants within a gene. These approaches are termed collapsing methods, and our GAW17 group focused on studying the performance of existing and novel collapsing methods using rare variants. All tested methods performed similarly, as measured by type I error and power. Inflated type I error fractions were consistently observed and might be caused by gametic phase disequilibrium between causal and noncausal rare variants in this relatively small sample as well as by population stratification. Incorporating prior knowledge, such as appropriate covariates and information on functionality of SNPs, increased the power of detecting associated genes. Overall, collapsing rare variants can increase the power of identifying disease-associated genes. However, studying genetic associations of rare variants remains a challenging task that requires further development and improvement in data collection, management, analysis, and computation.
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