All DNA samples genotyped using the Illumina BeadChip are part of an ongoing genome-wide association study in neuroblastoma and satisfied stringent quality control as described elsewhere (8). Genotyping was performed using the Illumina Infinium ™ II HumanHap550 BeadChip (Illumina, San Diego, CA, USA) according to methods detailed elsewhere (9,10). All DNA samples were surveyed for quality both by optical density spectrophotometry and the pico-green assay, and samples judged to be of sufficient quality for genotyping were assayed at the Center for Applied Genomics, the Children's Hospital of Philadelphia. The genotyping signal intensity data for Illumina HumanHap1M arrays and Affymetrix Mapping 500K arrays were generated on HapMap individuals, and were acquired from Illumina Inc. and Affymetrix Inc., respectively. The genotyping signal intensity data for Affymetrix genome-wide 6.0 arrays were generated from an internal control collection recruited at Children's Hospital of Philadelphia. For the serial dilution experiment, varying quantities of DNA (187.5, 375, 750, 1500 and 2250 ng) from an anonymous individual were used for genotyping by the Illumina HumanHap550 array.
