The Agilent 105K CNV genotyping array was designed by the WTCCC in collaboration with the other co-authors of this paper. After pilot experiments, each locus was targeted with at least 10 probes. Agilent array data were generated by Oxford Gene Technologies at their UK service facility as part of the pipeline developed for the large WTCCC association experiment (pipeline to be described elsewhere). We assessed the quality of the experiments on the 450 HapMap samples and repeated 90 poorer quality experiments to improve data consistency. The Illumina 660W array data were generated by Illumina Inc.
