Previous analysis of RNA sequencing (RNA-seq) data from human naive pluripotent stem cells reported multiple point "mutations" in cancer-related genes and implicated selective culture conditions. We observed, however, that those mutations were only present in co-cultures with mouse feeder cells. Inspection of reads containing the polymorphisms revealed complete identity to the mouse reference genome. After we filtered reads to remove sequences of mouse origin, the actual incidence of oncogenic polymorphisms arising in naive pluripotent stem cells is close to zero.We are grateful to James Clarke for cell culture support and to Vicki Murry and Maike Paramor for generating sequencing libraries. This research was funded by the Medical Research Council (MRC) of the United Kingdom. The Wellcome-MRC Cambridge Stem Cell Institute receives core support from Wellcome and MRC. AS is a Medical Research Council Professor
