ArticleAnnals of human genetics2016
On Efficient and Accurate Calculation of Significance P-Values for Sequence Kernel Association Testing of Variant Set.
Article in Annals of human genetics, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers, 1 of them a synthesis that pooled it.
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Who cites it
15 citing papers in PubMed, 1 synthesis or guideline pooled it, 32 citations in OpenAlex.
- A gene based combination test using GWAS summary data.BMC bioinformatics · 2023Pooled it
- Gene variants associated with pediatric-onset erythromelalgia: Mendelian and rare-variant association analyses.Pain reports · 2026Article
- Multi-omics identifies oxidative stress, prothrombotic pathways, and lactoperoxidase variants as key factors in COVID-19 severity.EBioMedicine · 2026Article
- A New Method for Conditional Gene-Based Analysis Effectively Accounts for the Regional Polygenic Background.Genes · 2024Article
- An adaptive and robust method for multi-trait analysis of genome-wide association studies using summary statistics.European journal of human genetics : EJHG · 2024Article
- A comprehensive comparison of multilocus association methods with summary statistics in genome-wide association studies.BMC bioinformatics · 2022Article
- Overlapping group screening for detection of gene-environment interactions with application to TCGA high-dimensional survival genomic data.BMC bioinformatics · 2022Article
- TS: a powerful truncated test to detect novel disease associated genes using publicly available gWAS summary data.BMC bioinformatics · 2020Article
- Pleiotropy informed adaptive association test of multiple traits using genome-wide association study summary data.Biometrics · 2019Article
- A review of kernel methods for genetic association studies.Genetic epidemiology · 2019Review
- Overlapping group screening for detection of gene-gene interactions: application to gene expression profiles with survival trait.BMC bioinformatics · 2018Article
- Statistical methods to detect novel genetic variants using publicly available GWAS summary data.Computational biology and chemistry · 2018Article
- Article
- Article
- AP-SKAT: highly-efficient genome-wide rare variant association test.BMC genomics · 2016Article
Corrections and comments
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
Abstract
The objective of this paper is to discuss and develop alternative computational methods to accurately and efficiently calculate significance P-values for the commonly used sequence kernel association test (SKAT) and adaptive sum of SKAT and burden test (SKAT-O) for variant set association. We show that the existing software can lead to either conservative or inflated type I errors. We develop alternative and efficient computational algorithms that quickly compute the SKAT P-value and have well-controlled type I errors. In addition, we derive an alternative and simplified formula for calculating the significance P-value of SKAT-O, which sheds light on the development of efficient and accurate numerical algorithms. We implement the proposed methods in the publicly available R package that can be readily used or adapted to large-scale sequencing studies. Given that more and more large-scale exome and whole genome sequencing or re-sequencing studies are being conducted, the proposed methods are practically very important. We conduct extensive numerical studies to investigate the performance of the proposed methods. We further illustrate their usefulness with application to associations between rare exonic variants and fasting glucose levels in the Atherosclerosis Risk in Communities (ARIC) study.
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