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 intermediate bands is smaller. The positions of these bands (at about 0.4 and 0.6) and the high intensity indicate a mosaic population of trisomic and disomic cells. (A purely trisomic cell population would have the intermediate bands at 0.33 and 0.66.) Samples with a chromosome aberration are included in the posting on dbGaP, but we flag the affected chromosome to be filtered out during association analysis, since it is likely to have a high rate of genotyping errors. In addition, we suggest filtering out any sample-chromosome combination with a missing call rate greater than 5%, since such chromosomes may contain undetected aberrations.
