Skat

SKAT

Record added by Jurg Ott (the original Rockefeller list)

Full Name

SNP-set (Sequence) Kernel Association Test

Description

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.

Author

Xihong Lin
Seunggeun Lee (Harvard Univ)

URL

http://www.hsph.harvard.edu/research/skat/index.html

Reference

Wu, Lee, Cai, Li, Boehnke, Lin (2011), “Rare variant association testing for sequencing data using the sequence kernel association test (SKAT)”, American Journal of Human Genetics, 89:82-93.
Wu, Kraft, Epstein, Taylor, Chanock, Hunter, Lin (2010), “Powerful SNP set analysis for case-control genomeWide association studies”, American Journal of Human Genetics , 86:929-942.