Fig 1: Effects of SAMD9 mutations on the derivation of fibroblasts into iPSCs and further differentiation into intermediate mesoderm.(A) PluriTest analysis of the array data. Undifferentiated patient-derived iPSCs fall within the empirically set thresholds for pluripotent cells. The plot shows that the 2 patient lines (patients 6 and 8) and the normal control iPSC line cluster with pluripotent stem cells (red cloud) in contrast to the fibroblasts they originated from that cluster with partly reprogrammed or differentiated cells (blue clouds). Each circle represents 1 iPSC or fibroblast line. (B) iPSCs of both patients stained positive for the pluripotency markers NANOG, tumor rejection antigen 1-60 (TRA-1-60) (cell surface), stage-specific embryonic antigen 4 (SSEA4) (cell surface), and OCT3/4 (nuclear). Nuclei were counterstained with Hoechst 33342. Scale bars: 50 µm. (C) Hierarchical clustering of patient and control samples showing clustering by cell type (fibroblasts, iPSCs, intermediate mesoderm). Within each cell group, patient samples containing SAMD9 mutations grouped together. Functional enrichment analysis using DAVID showed potential changes in biologically relevant pathways in the 2 patient samples compared with control samples in the different cell lines (Supplemental Table 3).