were repeated. CEL (cell intensity) files were transferred to WTCCC for quantile normalization, and genotypes called using a new genotyping algorithm, CHIAMO, developed for this project. QC/QA measures included sample call rate, overall heterozygosity and evidence of non-European ancestry (809 samples excluded; 16,179 retained for analysis). SNPs were excluded from analysis because of missing data rates, departures from Hardy-Weinberg equilibrium and other metrics (31,011 excluded; 469,557 retained). Standard 1-d.f. and 2-d.f. tests of case-control association were supplemented with bayesian approaches, multilocus methods (data imputation) and analyses with combined data sets, either as additional cases (to detect variants influencing multiple phenotypes) or as an expanded reference group (to increase power). Results for each SNP for all analyses reported will be available from http://www.wtccc.org.uk, as will details allowing other researchers to apply for access to WTCCC genotype data. Software packages developed within the WTCCC are available on request (see Methods for details).
