Jackson as part of an ongoing genome-wide association study to identify genetic components of hip fracture in the Women's Health Initiative); InCHIANTI (data provided by InCHIANTI study of aging; http://www.inchiantistudy.net15,57); and WTCCC2 (NBS)58. Control CNV arrays were analyzed as described previously16. Briefly, a Hidden Markov Model (HMM) based on both allele frequencies and total intensity values was used to identify putative alterations, followed by manual inspection of large CNVs (>100 probes and >1 Mbp) in conjunction with user guided merging of nearby (<1 Mbp between for arrays with <1 million probes and <200 kbp for arrays with >1 million probes) calls, which represent a single region broken up by the HMM, or gaps. All samples on arrays with densities <1M probes were filtered by a maximal genome-wide LogR standard deviation of 0.25, while the high density 1.2 million probe WTCCC2 data was filtered using an increased standard deviation cut-off of 0.37. Large alterations with noncanonical allele frequencies indicative of mosaics were excluded due to the high likelihood of these resulting from cell culture immortalization. For the two datasets where the Illumina array mapping corresponded to build35 (NHGRI), we utilized the autosomal calls generated previously16 and mapped the coordinates to build36
