SAIGE-GENE+ improves the efficiency and accuracy of set-based rare variant association tests.
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ABSTRACT:
SUBMITTER: Zhou W
PROVIDER: S-EPMC9534766 | biostudies-literature | 2022 Oct
REPOSITORIES: biostudies-literature
Publications
SAIGE-GENE+ improves the efficiency and accuracy of set-based rare variant association tests.
Zhou Wei W Bi Wenjian W Zhao Zhangchen Z Dey Kushal K KK Jagadeesh Karthik A KA Karczewski Konrad J KJ Daly Mark J MJ Neale Benjamin M BM Lee Seunggeun S
Nature genetics 20220922 10
Several biobanks, including UK Biobank (UKBB), are generating large-scale sequencing data. An existing method, SAIGE-GENE, performs well when testing variants with minor allele frequency (MAF) ≤ 1%, but inflation is observed in variance component set-based tests when restricting to variants with MAF ≤ 0.1% or 0.01%. Here, we propose SAIGE-GENE+ with greatly improved type I error control and computational efficiency to facilitate rare variant tests in large-scale data. We further show that incorp ...[more]
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