Prospect and challenge of detecting dynamic gene copy number increases in stem cells by whole genome sequencing. Ulrike Fischer, C. B., Tobias Fehlmann, V. G., & Andreas Keller, E. M. Journal of Molecular Medicine, 97:1099–1111, Springer Berlin Heidelberg, May, 2019.
doi  abstract   bibtex   
Gene amplification is an evolutionarily well-conserved and highly efficient mechanism to increase the amount of specific proteins. In humans, gene amplification is a hallmark of cancer and has recently been found during stem cell differentiation. Amplifications in stem cells are restricted to specific tissue areas and time windows, rendering their detection difficult. Here, we report on the performance of deep WGS sequencing (average 82-fold depth of coverage) on the BGISEQ with nanoball technology to detect amplifications in human mesenchymal and neural stem cells. As reference technology, we applied array-based comparative genomic hybridization (aCGH), fluorescence in situ hybridization (FISH), and qPCR. Using different in silico strategies for amplification detection, we analyzed the potential of WGS for amplification detection. Our results provide evidence that WGS accurately identifies changes of the copy number profiles in human stem cell differentiation. However, the identified changes are not in all cases consistent between WGS and aCGH. The results between WGS and the validation by qPCR were concordant in 83.3% of all tested 36 cases. In sum, both genome-wide techniques, aCGH and WGS, have unique advantages and specific challenges, calling for locus-specific confirmation by the low-throughput approaches qPCR or FISH.
@Article{Fischer2019,
  author       = {Ulrike Fischer, Christina Backes, Tobias Fehlmann, Valentina Galata, Andreas Keller, Eckart Meese},
  title        = {Prospect and challenge of detecting dynamic gene copy number increases in stem cells by whole genome sequencing},
  journal      = {Journal of Molecular Medicine},
  publisher    = {Springer Berlin Heidelberg},
  year         = {2019},
  volume       = {97},
  issue        = {8},
  pages        = {1099–1111},
  issn         = {1432-1440},
  issn-linking = {1099–1111},
  month        = may,
  abstract     = {Gene amplification is an evolutionarily well-conserved and highly efficient mechanism to increase the amount of specific proteins. In humans, gene amplification is a hallmark of cancer and has recently been found during stem cell differentiation. Amplifications in stem cells are restricted to specific tissue areas and time windows, rendering their detection difficult. Here, we report on the performance of deep WGS sequencing (average 82-fold depth of coverage) on the BGISEQ with nanoball technology to detect amplifications in human mesenchymal and neural stem cells. As reference technology, we applied array-based comparative genomic hybridization (aCGH), fluorescence in situ hybridization (FISH), and qPCR. Using different in silico strategies for amplification detection, we analyzed the potential of WGS for amplification detection. Our results provide evidence that WGS accurately identifies changes of the copy number profiles in human stem cell differentiation. However, the identified changes are not in all cases consistent between WGS and aCGH. The results between WGS and the validation by qPCR were concordant in 83.3% of all tested 36 cases. In sum, both genome-wide techniques, aCGH and WGS, have unique advantages and specific challenges, calling for locus-specific confirmation by the low-throughput approaches qPCR or FISH.},
  doi          = {10.1007/s00109-019-01792-y},
  pii          = {10.1007/s00109-019-01792-y},
}
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