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UK Biobank Whole-Exome Sequence Binary Phenome Analysis with Robust Region-Based Rare-Variant Test
| Content Provider | Scilit |
|---|---|
| Author | Zhao, Zhang Chen Bi, Wenjian Zhou, Wei Haar, Peter Vande Fritsche, Lars G. Lee, Seunggeun |
| Copyright Year | 2019 |
| Description | Journal: American Journal of Human Genetics In biobank data analysis, most binary phenotypes have unbalanced case-control ratios, and this can cause inflation of type I error rates. Recently, a saddle point approximation (SPA) based single-variant test has been developed to provide an accurate and scalable method to test for associations of such phenotypes. For gene- or region-based multiple-variant tests, a few methods exist that can adjust for unbalanced case-control ratios; however, these methods are either less accurate when case-control ratios are extremely unbalanced or not scalable for large data analyses. To address these problems, we propose SKAT- and SKAT-O- type region-based tests; in these tests, the single-variant score statistic is calibrated based on SPA and efficient resampling (ER). Through simulation studies, we show that the proposed method provides well-calibrated p values. In contrast, when the case-control ratio is 1:99, the unadjusted approach has greatly inflated type I error rates (90 times that of exome-wide sequencing |
| Related Links | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7042481/pdf http://www.cell.com/article/S0002929719304331/pdf |
| ISSN | 00029297 |
| e-ISSN | 15376605 |
| DOI | 10.1016/j.ajhg.2019.11.012 |
| Journal | American Journal of Human Genetics |
| Issue Number | 1 |
| Volume Number | 106 |
| Language | English |
| Publisher | Elsevier BV |
| Publisher Date | 2019-12-19 |
| Access Restriction | Open |
| Subject Keyword | Journal: American Journal of Human Genetics Statistics and Probability Rare Variant Test Saddlepoint Approximation Efficient Resampling Unbalanced Case-control Whole Exome Sequence |
| Content Type | Text |
| Resource Type | Article |
| Subject | Genetics Genetics (clinical) |
