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| Status |
Public on Oct 31, 2012 |
| Title |
Somatic copy-number mosaicism in human skin revealed by induced pluripotent stem cells (sequencing) |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
Reprogramming human somatic cells into induced pluripotent stem cells (iPSC) has been suspected of causing de novo copy number variations (CNVs). 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) to amplify across the CNVs' breakpoints, we show that at least 50% of those CNVs are present as low frequency somatic genomic variants in parental fibroblasts and are manifested in iPSC colonies due to their 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, 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.
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| Overall design |
We have generated and characterized hiPSC lines derived from skin fibroblasts collected from seven members of two families, which were competent to be differentiated into neuronal progenitors and neurons
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| Contributor(s) |
Abyzov A, Mariani J, Palejev D, Zhang Y, Haney MS, Tomasini L, Ferrandino A, Belmaker LR, Szekely A, Wilson MP, Kocabas A, Calixto NE, Grigorenko EL, Huttner A, Chawarska K, Weissman S, Urban AE, Gerstein MB, Vaccarino F |
| Citation(s) |
23160490 |
| Submission date |
Oct 19, 2012 |
| Last update date |
Mar 26, 2021 |
| Contact name |
Flora Vaccarino |
| Organization name |
Yale University
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| Department |
Child Study Center
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| Lab |
Vaccarino
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| Street address |
230 South Frontage Road
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| City |
New Haven |
| State/province |
CT |
| ZIP/Postal code |
06520 |
| Country |
USA |
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| Platforms (1) |
| GPL11154 |
Illumina HiSeq 2000 (Homo sapiens) |
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| Samples (29)
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| GSM1023062 |
RNA 03-01, i9 |
| GSM1023063 |
RNA 03-02, F |
| GSM1023064 |
RNA 03-02, i5 |
| GSM1023065 |
RNA 03-02, i8 |
| GSM1023066 |
RNA 03-02, i9 |
| GSM1023067 |
RNA 03-03, F |
| GSM1023068 |
RNA 03-03, i2 |
| GSM1023069 |
RNA 03-03, i3 |
| GSM1023070 |
RNA 03-03, i4 |
| GSM1023071 |
RNA 03-04, F |
| GSM1023072 |
RNA 03-04, i1 |
| GSM1023073 |
RNA 03-04, i5 |
| GSM1023074 |
RNA 03-04, i6 |
| GSM1023075 |
RNA S1123-01, F |
| GSM1023076 |
RNA S1123-01, i1 |
| GSM1023077 |
RNA S1123-01, i3 |
| GSM1023078 |
RNA S1123-01, i4 |
| GSM1023079 |
RNA S1123-02, F |
| GSM1023080 |
RNA S1123-02, i11 |
| GSM1023081 |
RNA S1123-02, i17 |
| GSM1023082 |
RNA S1123-02, i2 |
| GSM1023083 |
RNA S1123-03, F |
| GSM1023084 |
RNA S1123-03, i1 |
| GSM1023085 |
RNA S1123-03, i8 |
| GSM1023086 |
RNA S1123-03, i9 |
| GSM1023087 |
RNA H1, i |
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| Relations |
| BioProject |
PRJNA178020 |
| SRA |
SRP016568 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE41716_RAW.tar |
7.3 Mb |
(http)(custom) |
TAR (of RPKM) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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