Reprogramming human somatic cells into induced pluripotent stem cells (iPSCs) has been suspected of causing de novo copy number variations (CNVs)1-4. To explore this issue, we performed a whole-genome and transcriptome analysis of 20 human iPSC lines derived from primary skin fibroblasts of 7 individuals using next-generation sequencing. We find that, on average, an iPSC line manifests two CNVs not apparent in the fibroblasts from which the iPSC was derived. Using qPCR, PCR, and digital droplet PCR (ddPCR), we show that at least 50% of those CNVs are present as low frequency somatic genomic variants in parental fibroblasts (i.e. the fibroblasts from which each corresponding hiPSC line is derived) and are manifested in iPSC colonies due to the colonies’ clonal origin. Hence, reprogramming does not necessarily lead to de novo CNVs in iPSC, since most of line-manifested CNVs reflect somatic mosaicism in the human skin. Moreover, our findings demonstrate that clonal expansion, and iPSC lines in particular, can be used as a discovery tool to reliably detect low frequency CNVs in the tissue of origin. Overall, we estimate that approximately 30% of the fibroblast cells have somatic CNVs in their genomes, suggesting widespread somatic mosaicism in the human body. Our study paves the way to understanding the fundamental question of the extent to which cells of the human body normally acquire structural alterations in their DNA post-zygotically.

Objective The objective of this study was to evaluate the effects of mechanical loading on knee articular cartilage T1ρ and T2 relaxation times in patients with and without OA. Design MR images were acquired from 137 subjects with and without knee OA under two conditions: unloaded and loaded at 50% body weight. Three sequences were acquired: a high-resolution 3D-CUBE, a T1ρ relaxation time, and a T2 relaxation time sequences. Cartilage regions of interest included: medial and lateral femur (MF, LF); medial and lateral tibia (MT, LT), laminar analysis (superficial and deep layers), and subcompartments. Changes in relaxation times in response to loading were evaluated using generalized estimating equations adjusting for age, gender, and BMI. Results In response to loading, we observed significant reductions in T1ρ relaxation times in the MT and LT. In both the MF and LF, loading resulted in significant decreases in the superficial layer and significant increases in the deep layer of the cartilage for T1ρ and T2. All subcompartment of MT and LT showed significant reduction in T1ρ relaxation times. Reductions were larger for subjects with OA (range: 13–19% change) when compared to healthy controls (range: 3–13% change). Conclusions Loading of the cartilage resulted in significant changes in relaxation times in the femur and tibia, with novel findings regarding laminar and subcompartmental variations. In general, changes in relaxation times with loading were larger in the OA group suggesting that the collagen-proteoglycan matrix of subjects with OA is less capable of retaining water, and may reflect a reduced ability to dissipate loads.

Purpose To develop and compare with classical ROI-based approach, a fully-automatic, local and unbiased way of studying the knee T1ρ relaxation time by creating an atlas and using Voxel Based Relaxometry (VBR) in OA and ACL subjects Materials and Methods In this study 110 subjects from 2 cohorts: (i) Mild OA 40 patients with mild-OA KL ≤ 2 and 15 controls KL ≤ 1; (ii) ACL cohort (a model for early OA): 40 ACL-injured patients imaged prior to ACL reconstruction and 1-year post-surgery and 15 controls are analyzed. All the subjects were acquired at 3T with a protocol that includes: 3D-FSE (CUBE) and 3D-T1ρ. A Non-rigid registration technique was applied to align all the images on a single template. This allows for performing VBR to assess local statistical differences of T1ρ values using z-score analysis. VBR results are compared with those obtained with classical ROI-based technique Results ROI-based results from atlas-based segmentation were consistent with classical ROI-based method (CV = 3.83%). Voxel-based group analysis revealed local patterns that were overlooked by ROI-based approach; e.g. VBR showed posterior lateral femur and posterior lateral tibia significant T1ρ elevations in ACL injured patients (sample mean z-score=9.7 and 10.3). Those elevations were overlooked by the classical ROI-based approach (sample mean z-score =1.87, and −1.73) Conclusion VBR is a feasible and accurate tool for the local evaluation of the biochemical composition of knee articular cartilage. VBR is capable of detecting specific local patterns on T1ρ maps in OA and ACL subjects

4. Laryngoscope, 127:1976-1982, 2017.