ArticleScientific reports2016
Beyond Rare-Variant Association Testing: Pinpointing Rare Causal Variants in Case-Control Sequencing Study.
Article in Scientific reports, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
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Who cites it
12 citing papers in PubMed, 23 citations in OpenAlex.
- 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
- Next-Generation Sequencing Data-Based Association Testing of a Group of Genetic Markers for Complex Responses Using a Generalized Linear Model Framework.Mathematics (Basel, Switzerland) · 2023Article
- Genetic Analysis of Functional Rare Germline Variants across Nine Cancer Types from an Electronic Health Record Linked Biobank.Cancer epidemiology, biomarkers & prevention : a publication of the American Association for Cancer Research, cosponsored by the American Society of Preventive Oncology · 2021Article
- The role of genomics and genetics in pulmonary arterial hypertension.Global cardiology science & practice · 2020Review
- Germline DNA Repair Gene Mutations in Young-onset Prostate Cancer Cases in the UK: Evidence for a More Extensive Genetic Panel.European urology · 2019Article
- Identifying individual risk rare variants using protein structure guided local tests (POINT).PLoS computational biology · 2019Article
- Multiple rare and common variants in APOB gene locus associated with oxidatively modified low-density lipoprotein levels.PloS one · 2019Article
- Exome-wide rare variant analyses of two bone mineral density phenotypes: the challenges of analyzing rare genetic variation.Scientific reports · 2018Article
- Testing an optimally weighted combination of common and/or rare variants with multiple traits.PloS one · 2018Article
- Adaptive combination of Bayes factors as a powerful method for the joint analysis of rare and common variants.Scientific reports · 2017Article
- A Fast Association Test for Identifying Pathogenic Variants Involved in Rare Diseases.American journal of human genetics · 2017Article
- Conditioning adaptive combination of P-values method to analyze case-parent trios with or without population controls.Scientific reports · 2016Article
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1 author at 1 institution in 1 country.
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Abstract
Rare-variant association testing usually requires some method of aggregation. The next important step is to pinpoint individual rare causal variants among a large number of variants within a genetic region. Recently Ionita-Laza et al. propose a backward elimination (BE) procedure that can identify individual causal variants among the many variants in a gene. The BE procedure removes a variant if excluding this variant can lead to a smaller P-value for the BURDEN test (referred to as "BE-BURDEN") or the SKAT test (referred to as "BE-SKAT"). We here use the adaptive combination of P-values (ADA) method to pinpoint causal variants. Unlike most gene-based association tests, the ADA statistic is built upon per-site P-values of individual variants. It is straightforward to select important variants given the optimal P-value truncation threshold found by ADA. We performed comprehensive simulations to compare ADA with BE-SKAT and BE-BURDEN. Ranking these three approaches according to positive predictive values (PPVs), the percentage of truly causal variants among the total selected variants, we found ADA > BE-SKAT > BE-BURDEN across all simulation scenarios. We therefore recommend using ADA to pinpoint plausible rare causal variants in a gene.
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