A Simple Scalable Association Hypothesis Test Combining Gene-wide Evidence From Multiple Polymorphisms.

ABSTRACT:

Aims

In single-nucleotide polymorphism (SNP) scans, SNP-phenotype association hypotheses are tested, however there is biological interpretation only for genes that span multiple SNPs. We demonstrate and validate a method of combining gene-wide evidence using data for high-density lipoprotein cholesterol (HDLC).

Methodology

In a family based study (N=1782 from 482 families), we used 1000 phenotype-permuted datasets to determine the correlation of z-test statistics for 592 SNP-HDLC association tests comprising 14 genes previously reported to be associated with HDLC. We generated gene-wide p-values using the distribution of the sum of correlated z-statistics.

Results

Of the 14 genes, CETP was significant (p=4.0×10^-5 <0.05/14), while PLTP was sign

SUBMITTER: Vaidya D 

PROVIDER: S-EPMC3969754 | biostudies-literature | 2014 Mar

REPOSITORIES: biostudies-literature