METHODS article
Front. Cell Dev. Biol.
Sec. Stem Cell Research
Volume 13 - 2025 | doi: 10.3389/fcell.2025.1599923
Chromosomal Quality Control in hPSCs: A Practical Guide to SNP Array analysis with GenomeStudio
Provisionally accepted
Josephine Haake
Laura Steenpass*- German Collection of Microorganisms and Cell Cultures GmbH (DSMZ), Braunschweig, Germany
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Human pluriptotent stem cells (hPSCs) are important tools in pre-clinical research and disease modelling. Valid results can only be obtained with the use of thoroughly quality-controlled hPSCs, which includes ensuring chromosomal stability. Chromosomal aberrations, which frequently arise during reprogramming, gene editing or maintenance cultivation, can compromise the utility of these cells in research and therapeutic applications. While traditional G-banding remains a valuable genome-wide analysis method, its limited resolution necessitates complementary approaches. SNP array analysis offers a high-resolution alternative, providing a more detailed genomic overview. In this manuscript, we present a practical and user-friendly guide for detecting chromosomal aberrations using Illumina’s GenomeStudio, offering an easy-to-follow protocol to simplify quality control workflows for researchers with minimal bioinformatics expertise. While SNP array analysis for hPSC quality control is not novel, this step-by-step guide highlights critical quality control metrics, thresholds, and values, streamlining the process to make it more accessible and efficient for broader adoption. In 32 hPSCs, we identified chromosomal aberrations in 9 of them, including the frequently reported gain of 20q11.21 — a common anomaly in hPSC cultures. Examples from our routine practices underscore the importance of monitoring chromosomal integrity. This guide serves as a practical resource for standardizing and enhancing quality control processes, ensuring the genomic stability of hPSCs for research and clinical applications.
Keywords: SNP array analysis, GenomeStudio, chromosomal stability in hPSCs, quality control of hPSCs, B allele frequency, Log R ratio
Received: 25 Mar 2025; Accepted: 03 Jun 2025.
Copyright: © 2025 Haake and Steenpass. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
* Correspondence: Laura Steenpass, German Collection of Microorganisms and Cell Cultures GmbH (DSMZ), Braunschweig, Germany
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