User-friendly predictive molecular diagnostic assays for quality control of stem cell derivatives for transplantation and drug discovery

There is a critical need for better quality control analysis of stem cell-based therapeutic products and stem cell-derived cells used for other purposes, such as drug development and disease testing. Currently, PluriTest is the most popular method for assessing the pluripotency of human ES and iPSCs. We designed this application to be user-friendly and require no special expertise, which has encouraged researchers worldwide to substitute PluriTest for the teratoma assay, which requires laboratory mice and special skills. As of the fall of 2016, more than 14,500 datasets have been uploaded to our PluriTest website by 782 registered users in 29 countries. Our customers have requested a version of the assay that uses RNA sequencing data instead of the Illumina microarrays that have been used since we launched the application. Over the last year, we have collected a considerable amount of RNAseq data from our customers and colleagues, and have completed a beta version of PluriTest2 for RNAseq. We plan to release this application to beta users by the end of 2016. In addition, we have collected a large number of abnormal iPSC lines, which we will use to test the abilities of our new algorithm to detect abnormalities in genomic structure, an additional feature of PluriTest2 that we plan to implement during this grant award. Our long term goal is to make quality control assays available to all researchers and clinicians developing applications for pluripotent stem cells and their derivatives. To this end, we have collected multiple samples of iPSC and hESC-derived dopamine neurons from our lab and from others developing cell replacement therapies for Parkinson's disease. We are using these samples to develop DA-NeuroTest, the first of a family of user-friendly assays that will enable investigators to assure the safety of cell therapies. Other assays in this family will be used for quality control of neural derivatives used for high throughput screening and disease modeling, and for development of treatments for multiple sclerosis. We want every stem cell scientist to have access to tools that will assure that their cells are the correct type and are safe.