Previous studies have documented the use of measures of allelic imbalance (BAF) and relative intensity (LRR) for detecting chromosomal aberrations with SNP array data [Conlin, et al. 2010; Peiffer, et al. 2006]. Aneuploidy and large (multi-megabase) duplications and deletions have been detected in tumor cells and in lymphoblastoid cell lines [Simon-Sanchez, et al. 2007]. We also find such aberrations in blood and buccal cell samples. The frequencies and types of aberrations will be reported elsewhere, but some examples are given here from the Lung Cancer project. The upper panel of Figure 2 shows ‘sample 1’, a female with low X chromosome intensity and heterozygosity. Chromosome 8 in this sample has a normal pattern of three BAF bands, but on chromosome X the intermediate band (corresponding to heterozygous SNPs) is split into two, widely separated bands. These characteristics are expected for a mosaic population of disomic and monosomic cells in which monosomic cells predominate. The lower panel shows ‘sample 2’, which has a high intensity of chromosome 8 relative to its other chromosomes. In this case, the separation of the two
