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SNP analysis of human induced pluripotent stem cells

ABSTRACT: Human induced pluripotent stem cells (hIPSCs) represent a unique opportunity for regenerative medicine since they offer the prospect of generating unlimited quantities of cells for autologous transplantation as a novel treatment for a broad range of disorders. However, the use of hIPSCs in the context of genetically inherited human disease will require correction of disease-causing mutations in a manner that is fully compatible with clinical applications. We analyzed hiPSC line and genetically modified derivatives using high-density SNP array to investigate genomic instability associated reprogramming and genetic modification. Primary iPSC lines derived from patients with alpha-1 antitrypsin deficiency were generated. This genetic disorder is caused by homozygous mutation (Glu342Lys) in the SERPINA1 gene. We carried out mutation correction by 2 steps: zinc-finger nuclease-stimuated gene targeting and piggyBac trasnsposon-mediated selection cassette elimination. Parental fibroblast lines, primary iPSC lines and homozygously targeted iPSC lines were subjected to SNP genotyping using Illumina CytoSNP-12 BeadChiP.

ORGANISM(S): Homo sapiens

SUBMITTER: Kosuke Yusa

PROVIDER: E-GEOD-31035 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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SNP analysis of human induced pluripotent stem cells

Project description:Human induced pluripotent stem cells (hIPSCs) represent a unique opportunity for regenerative medicine since they offer the prospect of generating unlimited quantities of cells for autologous transplantation as a novel treatment for a broad range of disorders. However, the use of hIPSCs in the context of genetically inherited human disease will require correction of disease-causing mutations in a manner that is fully compatible with clinical applications. We analyzed hiPSC line and genetically modified derivatives using high-density SNP array to investigate genomic instability associated reprogramming and genetic modification.

2011-09-01 | GSE31035 | GEO

CGH analyses of human induced pluripotent stem cells

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2011-09-01 | E-MEXP-3316 | biostudies-arrayexpress

Chromothripsis in AML

Project description:This dataset contains data from two acute myeloid leukaemia (AML) specimens processed with the Illumina CytoSNP-12 SNP array platform. SNP array data showed evidence of chromothripsis in these two specimens. Each deletion in the mosaic specimen was present in the same proportion of cells, which supports the view that the many breaks occur as a single event. Complementary FISH studies highlighted the inclusion of centromeres from different chromosomes during the formation of the new chromosomes. Residual bone marrow specimens were chosen from patients who were determined to have a complex karyotype which included abnormalities of chromosomes 5 and 17, by routine cytogenetic examination.

2013-08-04 | E-GEOD-43522 | biostudies-arrayexpress

Protein Profiling of human iPSC-derived cardiomyocytes with a recessive LZTR1 variant in comparison to wild type cells

Project description:Genetic variants in LZTR1 are associated with the development of Noonan syndrome. Here, we analyzed the proteome of cultured cardiomyocytes derived from hiPSCs with a pathological homozygous LZTR1 variant L580P in comparison to two wild type iPSC lines.

2024-07-02 | PXD038425 | Pride

Protein Profiling of human iPSC-derived cardiomyocytes with a recessive LZTR1 variant in comparison to CRISPR/Cas9-corrected cells

2024-07-02 | PXD038417 | Pride

SNP data from induced Pluripotent Stem cells from Parkinson's Disease patients harbouring G2019S mutations in the LRRK2 gene

Project description:We have generated human induced Pluripotent Stem cells (hiPSc) using Retroviral virus-mediated delivery of reprogramming factors. hiPSc lines have been screened using SNP array to assess chromosomal stability (alongside the fibroblast lines from which they derived), and validation of the pluripotency of the hiPSc lines is provided by Pluritest assessment of transcriptome datasets, prior to differentiation and downstream assays. Gene expression profiling in patient-derived dopamine neurons identifies candidate therapeutic molecules in Parkinsonâs disease. human iPSc lines were derived from human dermal fibroblasts from 3 PD LRRK2 G2019S patients and 3 control donors. SNP and gene expression datasets were generated from patient and control lines. Note that iPS OX1-19 and iPS-NHDF-1, also used in the current study, have been published previously so datasets are not given here [GSE45472 PMID:23951090 ; GSE43904 PMID:24586273]

2016-02-09 | E-GEOD-77662 | biostudies-arrayexpress

SNP data from human fibroblasts and induced Pluripotent Stem cells

Project description:Human induced Pluripotent Stem cells (hiPSc) and their differentiated progeny have great potential for modelling disease. To realise this potential, robust protocols need to be developed for deriving authentic differentiated cell lineages and these lineages need to be rigorously characterised. We have generated hiPSc using retrovirus-mediated delivery of reprogramming factors, and have used them for characterising mid-brain dopaminergic neurons. hiPSc lines have been screened using SNP array to assess chromosomal stability, and validation of the pluripotency of the hiPSc lines is provided by Pluritest assessment of transcriptome datasets. A mature physiological cellular model of human dopaminergic neurons. human iPSc lines were derived from normal human dermal fibroblasts.

2013-01-31 | E-GEOD-43902 | biostudies-arrayexpress

An Automated, High Platform for Induced Pluripotent Stem Cell Derivation, Characterization and Differentiation

Project description:Induced pluripotent stem cells (iPSCs) have become an essential tool for both modeling how causal genetic variants impact cellular function in disease, as well as being an emerging source of tissue for transplantation medicine. Unfortunately the preparation of somatic cells, their reprogramming and the subsequent verification of iPSC pluripotency are laborious, manual processes that limit the scale and level of reproducibility of this technology. Here we describe a modular, robotic platform for iPSC reprogramming that enables automated, high-throughput conversion of skin biopsies into iPSCs and differentiated cells with minimal manual intervention. Using this platform, we demonstrate that automated reprogramming and the pooled selection of pluripotent cells results in high quality, stable, iPSCs. These lines display less line-to-line variation than either manually produced lines or lines produced through automation followed by single colony-subcloning. The robotic platform we describe will enable the application of iPSCs to population-scale biomedical problems including the study of complex genetic diseases and the development of personalized medicines. Two independent human fibroblast lines were reprogrammed, using modified mRNA, into induced pluripotent stem cells (iPSCs). The genomic stability of several cell lines was evaluated using SNP arrays. Three iPSCs originating from one fibroblast line were tested at passages 8 and 20, with two of these derived as picked (clonal) lines and the third being a pooled population. Five iPSCs originating from a second fibroblast line were tested at passages 8 and 20, with three of these derives derived as picked (clonal) lines and two derived as pooled populations. The iPSCs were compared against the original parental fibroblasts.

2015-08-03 | E-GEOD-69868 | biostudies-arrayexpress

Chromothripsis in AML

2013-08-04 | GSE43522 | GEO

Comparison of the molecular profiles of human embryonic and isogenic induced pluripotent stem cells. [Agilent]

Project description:Many studies have compared the genetic and epigenetic profiles of human induced pluripotent stem cells (hiPSCs) to human embryonic stem cells (hESCs) and yet the picture remains unclear. To address this, we derived a population of neural precursor cells (NPCs) from the H1 (WA01) hESC line and generated isogenic iPSC lines by reprogramming. The gene expression and methylation profile of three lines were compared to the parental line and intermediate NPC population. We found no gene probe with expression that differed significantly between hESC and iPSC samples under undifferentiated or differentiated conditions. Analysis of the global methylation pattern also showed no significant difference between the two PSC populations. Both undifferentiated populations were distinctly different from the intermediate NPC population in both gene expression and methylation profiles. One point to note is that H1 is a male line and so extrapolation to female lines should be cautioned. However, these data confirm our previous findings that there are no significant differences between hESCs and hiPSCs at the gene expression or methylation level. 22 samples: 1 human NPC, 2 human ESC (UNDIFF), 5 human iPSC (UNDIFF), 2 human ESC (EB_ecto), 5 human iPSC (EB_ecto), 2 human ESC (EB_mesend), 5 human iPSC (EB_mesend)

2014-01-01 | E-GEOD-51561 | biostudies-arrayexpress

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