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Series GSE164389 Query DataSets for GSE164389
Status Public on Feb 14, 2021
Title Quantitative evaluation of chromosomal rearrangements in primary gene-edited human stem cells by preclinical CAST-Seq
Organism Homo sapiens
Experiment type Other
Summary Genome editing with programmable nucleases has shown great promise for clinical translation but also revealed the risk of genotoxicity caused by chromosomal translocations or the insertion of mutations at off-target sites. Here, we describe CAST-Seq, an innovative assay to identify and quantify chromosomal aberrations derived from on- and off-target activities of CRISPR-Cas nucleases or TALENs. CAST-Seq also detected novel types of chromosomal rearrangements, including homology-mediated translocations that are mediated by homologous recombination. Depending on the employed designer nuclease, translocations occurred in 0–0.5% of gene-edited human stem cells and some 20% of target loci harbored gross aberrations. In conclusion, CAST-Seq analyses are particularly relevant for therapeutic editing of stem cells to enable a thorough risk assessment before clinical application of gene editing products.
 
Overall design CD34 positive HSPC were treated with CRISPR/CAS9 or TALEN nucleases. In total 30 samples treated with nulceases were analysed together with their respective untreated controls (one control per sample). The same non-treated sample was used whenever we analysed the Wild-Type or the High Fidelity (HiFi) nuclease. Several days post treatment were considered: 1, 4 and 14.
 
Contributor(s) Turchiano G, Andrieux G, Klermund J, Boerries M, Cathomen T
Citation(s) 33626327
Submission date Jan 07, 2021
Last update date May 17, 2021
Contact name Geoffroy Andrieux
Organization name University clinics Freiburg
Street address Breisacherstr 153
City Freiburg
ZIP/Postal code 79110
Country Germany
 
Platforms (1)
GPL15520 Illumina MiSeq (Homo sapiens)
Samples (52)
GSM5008881 CAST-seq telomeric CCR5#1 CRISPR/Cas9 treated CD34+ cells, Day1 post treatment.
GSM5008882 CAST-seq telomeric CCR5#1 CRISPR/Cas9 treated CD34+ cells, Day4 post treatment
GSM5008883 CAST-seq telomeric CCR5#1 CRISPR/Cas9 treated CD34+ cells, duplicate Day4 post treatment
Relations
BioProject PRJNA690516
SRA SRP300758

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE164389_RAW.tar 5.0 Mb (http)(custom) TAR (of XLSX)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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