Test for association between a set of rare (and common) variants and continuous/dichotomous phenotypes using kernel machine methods
SKAT is a SNP-set (e.g., a gene or a region) level test for association between a set of rare (or common) variants and dichotomous or quantitative phenotypes, SKAT aggregates individual score test statistics of SNPs in a SNP set and efficiently computes SNP-set level p-values, e.g. a gene or a region level p-value, while adjusting for covariates, such as principal components to account for population stratification. SKAT also allows for power/sample size calculations for designing for sequence association studies.
User Group:
Please join in the SKAT/MetaSKAT Google Group to ask / discuss / comment about SKAT/MetaSKAT.
References:
- Ionita-Laza, I.*, Lee, S.*, Makarov, V., Buxbaum, J. Lin, X. (2013) Sequence kernel association tests for the combined effect of rare and common variants. American Journal of Human Genetics, 92, 841–853
* contributed equally. - Lee, S., Emond, M.J., Bamshad, M.J., Barnes, K.C., Rieder, M.J., Nickerson, D.A., NHLBI GO Exome Sequencing Project-ESP Lung Project Team, Christiani, D.C., Wurfel, M.M. and Lin, X. (2012) Optimal unified approach for rare variant association testing with application to small sample case-control whole-exome sequencing studies. American Journal of Human Genetics, 91, 224-237
- Lee, S., Wu, M. C., and Lin, X. (2012). Optimal tests for rare variant effects in sequencing association studies. Biostatistics, 13, 762-775.
- Wu, M. C.*, Lee, S.*, Cai, T., Li, Y., Boehnke, M., and Lin, X. (2011) Rare Variant Association Testing for Sequencing Data Using the Sequence Kernel Association Test (SKAT). American Journal of Human Genetics , 89, 82-93.
* contributed equally. - Wu, M. C., Kraft, P., Epstein, M. P.,Taylor, D., M., Chanock, S. J., Hunter, D., J., and Lin, X. (2010)Powerful SNP Set Analysis for Case-Control GenomeWide Association Studies. American Journal of Human Genetics , 86, 929-942.
