Organoids as Miniature Twins—Challenges for Comparability and Need for Data Standardization and Access
Open accessAbstract
Organoids derived from human stem cell lines represent genetically mostly identical models of their donors. Their use as personalized in vitro miniature twins of living individuals creates challenges of reproducibility, comparability and standardization. To fully exploit personalization, it is essential to assess individual variabilities in organoid function, morphology or maturity. There is a need to establish platforms to compare individual organoids and to link them to data elements related to the individual donor. Moreover, principal ethical issues arise because of their infinite repetition for an unlimited period of time and global dissemination. This infinite temporal and spatial space applies to the biological material but also to the data associated with it. It increases the possibility of uses that are unpredictable at the time of donation, and thus, beyond the donor’s consented choices. We propose an open data platform to address the issue of authenticity and persistent comparability of the biological organoid models, and of preserving the ethical provenance information. The platform would collect standardized donors, organoids and ethical information to create a system suitable for quality control of individual organoids. We discuss whether the human pluripotent stem cell registry (hPSCreg), a well-established resource for stem cell data, provides a suitable model platform.
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Gene Expression Omnibus is generally recommended for transcriptomics-related organoid data.
“For transcriptomics-related data, such as gene expression, non-coding RNA, ChIP, genome methylation, high-throughput RT-PCR, SNP arrays, SAGE, protein arrays, Gene Expression Omnibus (GEO) is generally recommended231,232.”
From Organoids (2022) · cites this paper as [231]
Section 2 discusses standardizing organoid data and depositing it in a transparent database; the Conclusions discuss hPSCreg as a possible platform. Neither passage recommends Gene Expression Omnibus for transcriptomics-related data. Searches for GEO, Gene Expression Omnibus, and the listed data types found no passage addressing that recommendation. (LLM, conf=0.74)
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- Authors
- Fuhr, A., Kurtz, A., Hiepen, C., & Müller, S.
- Affiliations
- Fraunhofer Institute for Biomedical Engineering (DE)
- Fraunhofer Institute for Biomedical Engineering (IBMT), Joseph-von-Fraunhofer-Weg 1, 66280 Sulzbach, Germany
- Venue
- Organoids
- Publisher
- MDPI AG
- Published
- 2022-04-09
- Volume
- 1
- Issue
- 1
- Pages
- 28-36
- ISSN
- 2674-1172 (ISSN-L)
- OpenAlex
- W4223594616
- Cited by
- 10
- References
- 39
- Citations by year
- 2026: 3 · 2025: 2 · 2024: 1 · 2023: 3 · 2022: 1
- FWCI
- 0.57
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- Locations
- Organoids (publishedVersion, cc-by)
- Fraunhofer-Publica (Fraunhofer-Gesellschaft) (submittedVersion)
- Funders
- European Union (726320)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Pluripotent Stem Cells Research
- Health Sciences › Medicine › Physiology › Biomedical Ethics and Regulation
- Physical Sciences › Computer Science › Information Systems › Research Data Management Practices
- Keywords
- human pluripotent stem cells, personalized medicine, reproducibility, comparability, data standardization, open data portals, donor consent, quality control
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