Data from genome-wide association studies now provide an opportunity to detect chromosomal variation in tens of thousands of people of all ages and to investigate the association of mosaicism with disease. Single nucleotide polymorphism (SNP) microarray data are used routinely to detect chromosomal anomalies (copy number variants (CNV) and uniparental disomy (UPD)) in clinical cytogenetic laboratories11,12 and to detect small CNVs in population studies13–15. However, the analytical methods used in population studies are not optimized for detecting large anomalies or mosaicism. Therefore, we developed an efficient method to identify and localize large (50 kb to whole-chromosome) anomalies and mosaicism within a single DNA sample. This method requires a relatively high frequency of cells (>5–10%) with the same abnormal karyotype (presumably of clonal origin) in the presence of normal cells. Therefore, we use the term ‘detectable clonal mosaicism’, rather than simply ‘chromosomal mosaicism’, to emphasize the observation of clones of cells with abnormal karyotype that occur at a frequency sufficient for detection using SNP microarray data.
