Abstract: The present invention provides methods and assays for screening cells, such as stem cells, for chromosomal aberrations. In particular, the present invention provides a rapid, sensitive assay platform for detecting high and low levels of chromosomal aberrations present in a cell population. This includes, but is not limited to, detection of extra chromosomes (trisomies) as well as insertions of small segments that are undetectable using standard cytogenetic studies, wherein the abnormal cells comprise a low percentage of the total cell population.