ArticlePloS one2014
Rare variant association testing by adaptive combination of P-values.
Article in PloS one, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers, 2 of them syntheses that pooled it.
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
23 citing papers in PubMed, 2 syntheses or guidelines pooled it, 30 citations in OpenAlex.
- A unified method for rare variant analysis of gene-environment interactions.Statistics in medicine · 2020Pooled it
- Convergent Genetic and Expression Datasets Highlight TREM2 in Parkinson's Disease Susceptibility.Molecular neurobiology · 2016Pooled it
- Excalibur: A new ensemble method based on an optimal combination of aggregation tests for rare-variant association testing for sequencing data.PLoS computational biology · 2023Article
- Targeted next-generation sequencing for genetic variants of left ventricular mass status among community-based adults in Taiwan.Frontiers in genetics · 2022Article
- A two-stage testing strategy for detecting genes×environment interactions in association studies.G3 (Bethesda, Md.) · 2021Article
- Germline DNA Repair Gene Mutations in Young-onset Prostate Cancer Cases in the UK: Evidence for a More Extensive Genetic Panel.European urology · 2019Article
- An integrative association method for omics data based on a modified Fisher's method with application to childhood asthma.PLoS genetics · 2019Article
- OPATs: Omnibus P-value association tests.Briefings in bioinformatics · 2019Review
- Association analysis of multiple traits by an approach of combining P values.Journal of genetics · 2018Article
- Article
- Association detection between ordinal trait and rare variants based on adaptive combination of P values.Journal of human genetics · 2018Article
- Adaptive combination of Bayes factors as a powerful method for the joint analysis of rare and common variants.Scientific reports · 2017Article
- DoEstRare: A statistical test to identify local enrichments in rare genomic variants associated with disease.PloS one · 2017Article
- Conditioning adaptive combination of P-values method to analyze case-parent trios with or without population controls.Scientific reports · 2016Article
- Beyond Rare-Variant Association Testing: Pinpointing Rare Causal Variants in Case-Control Sequencing Study.Scientific reports · 2016Article
- Article
- Associating Multivariate Quantitative Phenotypes with Genetic Variants in Family Samples with a Novel Kernel Machine Regression Method.Genetics · 2015Article
- Detecting association of rare and common variants by adaptive combination of P-values.Genetics research · 2015Article
- A Sequence Kernel Association Test for Dichotomous Traits in Family Samples under a Generalized Linear Mixed Model.Human heredity · 2015Article
- Rare-Variant Kernel Machine Test for Longitudinal Data from Population and Family Samples.Human heredity · 2015Article
Corrections and comments
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Authors and funding
4 authors at 3 institutions in 2 countries.
Funding
Abstract
With the development of next-generation sequencing technology, there is a great demand for powerful statistical methods to detect rare variants (minor allele frequencies (MAFs)<1%) associated with diseases. Testing for each variant site individually is known to be underpowered, and therefore many methods have been proposed to test for the association of a group of variants with phenotypes, by pooling signals of the variants in a chromosomal region. However, this pooling strategy inevitably leads to the inclusion of a large proportion of neutral variants, which may compromise the power of association tests. To address this issue, we extend the [Formula: see text]-MidP method (Cheung et al., 2012, Genet Epidemiol 36: 675-685) and propose an approach (named 'adaptive combination of P-values for rare variant association testing', abbreviated as 'ADA') that adaptively combines per-site P-values with the weights based on MAFs. Before combining P-values, we first imposed a truncation threshold upon the per-site P-values, to guard against the noise caused by the inclusion of neutral variants. This ADA method is shown to outperform popular burden tests and non-burden tests under many scenarios. ADA is recommended for next-generation sequencing data analysis where many neutral variants may be included in a functional region.
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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.