Development of genetic quality tests for good manufacturing practice-compliant induced pluripotent stem cells and their derivatives.

Scientific Reports
Hye-Yeong JoJung-Hyun Kim

Abstract

Although human induced pluripotent stem cell (hiPSC) lines are karyotypically normal, they retain the potential for mutation in the genome. Accordingly, intensive and relevant quality controls for clinical-grade hiPSCs remain imperative. As a conceptual approach, we performed RNA-seq-based broad-range genetic quality tests on GMP-compliant human leucocyte antigen (HLA)-homozygous hiPSCs and their derivatives under postdistribution conditions to investigate whether sequencing data could provide a basis for future quality control. We found differences in the degree of single-nucleotide polymorphism (SNP) occurring in cells cultured at three collaborating institutes. However, the cells cultured at each centre showed similar trends, in which more SNPs occurred in late-passage hiPSCs than in early-passage hiPSCs after differentiation. In eSNP karyotyping analysis, none of the predicted copy number variations (CNVs) were identified, which confirmed the results of SNP chip-based CNV analysis. HLA genotyping analysis revealed that each cell line was homozygous for HLA-A, HLA-B, and DRB1 and heterozygous for HLA-DPB type. Gene expression profiling showed a similar differentiation ability of early- and late-passage hiPSCs into cardiomyoc...Continue Reading

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Citations

Mar 15, 2021·Stem Cell Research·Jung-Hyun KimYong-Ou Kim

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Datasets Mentioned

BETA
R001856

Methods Mentioned

BETA
RNA-seq
chromosomal aberrations
chromosomal aberration
RNAseq
chip
chromosomal
genotyping
PCR

Software Mentioned

BiomaRt
MySQL
DESeq2
eSNP karyotyping package
STEMdiff
HLAProfiler
TopHat2
BWA
htseq
Ensembl

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