As reprogramming methodologies have become more reliable and efficient, corresponding improvements were needed in the characterization workflow as well; specifically in terms of the speed, efficiency, specificity and sensitivity of the methods used.  Molecular analysis platforms offer a quantitative, accurate, and fast alternative to current methods and have recently been utilized to qualify pluripotent stem cells (PSC). When characterizing stem cells, it is important to confirm that a cell line a)  has not acquired any genomic abnormalities during derivation or genetic engineering, b) has or (maintains) the  capacity to differentiate into all three germ layers, and c) maintains expression of pluripotency associated markers. In addition to the characteristics described above, it is highly desirable to be able to uniquely ID every parental and subsequent derivative cell line; especially in core facilities, stem cell banks, or cell therapy development.
Here we describe three characterization methods: PluriTest, KaryoStat, and ScoreCard,. PluriTest and KaryoStat leverage microarray based platforms that provide a comprehensive gene expression profile to determine the state of pluripotency and whole genome coverage to detect chromosomal abnormalities via copy number variations, respectively. ScoreCard utilizes a focused panel of TaqMan qPCR based assays to assess expression of specifically selected genes that confirm pluripotency and differentiation potential.  These three methods provide a complete solution to fully characterize PSC lines for pluripotency, differentiation potential, genomic integrity and sample ID.