PROBLEM: Stem cell genetic, epigenetic and expression profiling are important tools for understanding of stem cell reprogramming, and perhaps for quality control of therapeutic stem cells. Classical tools for preparing DNA for microarrays and next-generation sequencing are sufficient for studying mixtures of thousands of cells but are inadequate for studying heterogeneities within stem cell cultures or for identifying rare events, such as infrequent mutations that could lead to unstable behavior or cancer. Molecular studies of single stem cells using PCR, microarrays or NGS could elucidate the roles of DNA sequence, copy number changes, DNA methylation, and expression in stem cell reprogramming, as well as the timing and stochastic nature of those processes. BACKGROUND: Methods for amplification of total DNA, total RNA, and total methylated DNA in single cells have been very useful for discovering cancer biomarkers in small amounts of tissue and plasma. One of these single-cell methods, PicoPlex™ whole genome amplification (WGA), has been used to test for mutations and aneuploidies in tens of thousands of single human blastomeres and oocytes every year in order to select embryos for implantation. HYPOTHESIS: PicoPlex WGA should be adaptable to facilitate genetic, epigenetic, and expression profiling of single stem cells using either microarrays or high-throughput sequencing. RESEARCH: PicoPlex and a related technology called MethylPlex have been adapted for next-generation sequencing of single cells. PicoPlex was tested on multiple single cancer cells in order to characterize the representation and reproducibility of testing single cells using PCR and microarrays. PicoPlex-NGS, is starting to be evaluated for sequencing single cells on the illumina Genome Analyzer. MethylPlex has been tested using small numbers of cells and shows very good performance for identifying candidate biomarkers and detecting rare methylation events in cancer tissue and plasma using either microarrays or NGS. Data will be shown. OBSERVATIONS AND CONCLUSIONS: Reproducible single cell genetic screening using microarrays and PCR is now routine using PicoPlex. PicoPlex-NGS will start providing NGS information about mutations and copy number variations in the near future. MethylPlex-NGS currently provides reliable profiling of CpG island methylation from nanogram amounts of DNA using single lanes of the Illumina GA, and will soon be tested for detecting methylation in single cancer cells and blastomeres. STEM CELL OBSERVATIONS AND CONCLUSIONS: PicoPlex-NGS and MethylPlex-NGS have not yet been tested on single stem cells or on stem cell cultures, however we are seeking stem cell laboratories that want to begin genetic and epigenetic studies of stem cell reprogramming in the near future.