Genome-wide association (GWA) studies for complex human diseases are now feasible. Many GWA studies rely on commercial SNP chips, for which a common evaluation criterion is global coverage of the genome. Although providing an overall evaluation of an SNP chip, the global coverage does not tell us how the coverage varies across the genome, an important feature that should be taken into consideration, as coverage variation often results in power variation and potentially biased search in subsequent association analysis. To achieve a fuller understanding of SNP chip coverage, we conducted detailed evaluation of coverage, including (1) a map of local coverage - calculated over small consecutive genomic regions and (2) gene coverage - calculated for each known gene in the genome. These evaluations can reveal the degree of variation of each SNP chip in covering the genome and can facilitate SNP chip comparisons at a finer scale.
Bibliographical noteFunding Information:
We thank Drs Goncalo Abecasis, Michael Boehnke, Vivian Cheung, and Richard Spielman for discussion and critical reading of an earlier version of the paper, and Dr Kai Wang for providing the KEGG and BioCarta pathway information. This work was supported by an internal grant from the Center for Human Genetics Research at Vanderbilt University (to CL), and by the University Research Foundation grant and the McCabe Pilot Award from the University of Pennsylvania (to ML).