Cited by 94Pluripotent Stem Cells ResearchSingle-cell and spatial transcriptomicsAnimal testing and alternatives

Taming Human Genetic Variability: Transcriptomic Meta-Analysis Guides the Experimental Design and Interpretation of iPSC-Based Disease Modeling

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Germain, Pierre-Luc, Testa, Giuseppe·2017·Stem Cell Reports

Abstract

Both the promises and pitfalls of the cell reprogramming research platform rest on human genetic variation, making the measurement of its impact one of the most urgent issues in the field. Harnessing large transcriptomics datasets of induced pluripotent stem cells (iPSC), we investigate the implications of this variability for iPSC-based disease modeling. In particular, we show that the widespread use of more than one clone per individual in combination with current analytical practices is detrimental to the robustness of the findings. We then proceed to identify methods to address this challenge and leverage multiple clones per individual. Finally, we evaluate the specificity and sensitivity of different sample sizes and experimental designs, presenting computational tools for power analysis. These findings and tools reframe the nature of replicates used in disease modeling and provide important resources for the design, analysis, and interpretation of iPSC-based studies.

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Authors
Germain, P.-L., & Testa, G.
Affiliations
  • European Institute of Oncology (IT)
  • University of Milan (IT)
Corresponding author
  • Germain, Pierre-Luc
  • Testa, Giuseppe
Venue
Stem Cell Reports
Publisher
Elsevier BV
Published
2017-06
Volume
8
Issue
6
Pages
1784-1796
ISSN
2213-6711 (ISSN-L)
OpenAlex
W2623260545
Cited by
94
References
34
Citations by year
2026: 5 · 2025: 9 · 2024: 8 · 2023: 6 · 2022: 13 · 2021: 14 · 2020: 17 · 2019: 12 · 2018: 6 · 2017: 3
FWCI
4.24
Type
journal article
Language
en
Open access
Locations
  • Stem Cell Reports (publishedVersion, cc-by-nc-nd)
  • Europe PMC (PubMed Central) (publishedVersion, cc-by-nc-nd)
  • PubMed Central (publishedVersion, cc-by-nc-nd)
  • PubMed (publishedVersion)
  • Archivio Istituzionale della Ricerca (Universita Degli Studi Di Milano) (submittedVersion, other-oa)
  • DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
Funders
  • European Research Council (DISEASEAVATARS 616441)
  • Telethon Foundation (GGP14265)
  • Italian Association for Cancer Research
  • Umberto Veronesi Foundation
  • Italian Ministry of Health
  • Regione Lombardia
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Pluripotent Stem Cells Research
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Single-cell and spatial transcriptomics
  • Health Sciences › Veterinary › Small Animals › Animal testing and alternatives
Keywords
induced pluripotent stem cells, experimental design, sample size, statistical power analysis, replicates, cellular reprogramming
MeSH terms
Humans, Models, Biological, Research Design, Genetic Variation, Gene Expression Profiling, Induced Pluripotent Stem Cells

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