All samples were uniformly genotyped at the Center for Applied Genomics at the Children's Hospital of Philadelphia. DNA samples were surveyed for quality both by optical density spectrophotometry and the PicoGreen assay (Molecular Probes, Eugene, OR, USA).26 Samples judged to be of sufficient quality for genotyping were assayed on the Illumina Infinium II HumanHap550 BeadChip (Illumina, San Diego, CA, USA) as previously described.27 As BeadChip images were collected, intensity values were determined for all instances of each bead type, and data files were created that summarized intensity values for each bead type. A bead pool manifest was loaded into BeadStudio along with intensity data for the samples. BeadStudio uses a normalization algorithm to minimize BeadChip to BeadChip variability. Once the normalization was complete, a clustering algorithm was used to evaluate cluster positions for each locus and assign individual genotypes. logR ratios (LRRs) and B allele frequencies were calculated for every single nucleotide polymorphism (SNP) based on these clusters and the genotype of each SNP.
