Measuring mutation accumulation in single human adult stem cells by whole-genome sequencing of organoid cultures

2017 ◽  
Vol 13 (1) ◽  
pp. 59-78 ◽  
Author(s):  
Myrthe Jager ◽  
Francis Blokzijl ◽  
Valentina Sasselli ◽  
Sander Boymans ◽  
Roel Janssen ◽  
...  
Keyword(s):  
Stem Cells ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Adult Stem Cells ◽  
Mutation Accumulation ◽  
Whole Genome ◽  
Human Adult ◽  
Organoid Cultures

EYE ON CHINA

2013 ◽  
Vol 17 (08) ◽  
pp. 18-23
Keyword(s):  
Stem Cells ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Health Research ◽  
Whole Genome ◽  
Wine Grapes ◽  
Chronic Mountain Sickness ◽  
Research Cooperation ◽  
Cultivation Technique ◽  
Mountain Sickness

Unique wine-grapes cultivation technique invented. Whole-genome sequencing unravels the puzzle of chronic mountain sickness. China eyes health research cooperation with Africa. Diamonds are for finding stem cells. Chi-huey Wong's team make advances in quest to develop carbohydrate-based vaccines. ScinoPharm Changshu teams up with Sundia MediTech.

scholarly journals Whole Genome Sequencing of Mutation Accumulation Lines Reveals a Low Mutation Rate in the Social Amoeba Dictyostelium discoideum

PLoS ONE ◽  
2012 ◽  
Vol 7 (10) ◽  
pp. e46759 ◽  
Author(s):  
Gerda Saxer ◽  
Paul Havlak ◽  
Sara A. Fox ◽  
Michael A. Quance ◽  
Sharu Gupta ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Dictyostelium Discoideum ◽  
Genome Sequencing ◽  
Mutation Rate ◽  
Mutation Accumulation ◽  
Whole Genome ◽  
Social Amoeba ◽  
The Social

scholarly journals Targeted and genome-wide sequencing reveal single nucleotide variations impacting specificity of Cas9 in human stem cells

2014 ◽  
Vol 5 (1) ◽  
Author(s):  
Luhan Yang ◽  
Dennis Grishin ◽  
Gang Wang ◽  
John Aach ◽  
Cheng-Zhong Zhang ◽  
...  
Keyword(s):  
Stem Cells ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
In Silico ◽  
High Efficiency ◽  
Specific Gene ◽  
Whole Genome ◽  
Single Nucleotide ◽  
Target Sites ◽  
Target Effects

Abstract CRISPR/Cas9 has demonstrated a high-efficiency in site-specific gene targeting. However, potential off-target effects of the Cas9 nuclease represent a major safety concern for any therapeutic application. Here, we knock out the Tafazzin gene by CRISPR/Cas9 in human-induced pluripotent stem cells with 54% efficiency. We combine whole-genome sequencing and deep-targeted sequencing to characterise the off-target effects of Cas9 editing. Whole-genome sequencing of Cas9-modified hiPSC clones detects neither gross genomic alterations nor elevated mutation rates. Deep sequencing of in silico predicted off-target sites in a population of Cas9-treated cells further confirms high specificity of Cas9. However, we identify a single high-efficiency off-target site that is generated by a common germline single-nucleotide variant (SNV) in our experiment. Based on in silico analysis, we estimate a likelihood of SNVs creating off-target sites in a human genome to be ~1.5–8.5%, depending on the genome and site-selection method, but also note that mutations might be generated at these sites only at low rates and may not have functional consequences. Our study demonstrates the feasibility of highly specific clonal ex vivo gene editing using CRISPR/Cas9 and highlights the value of whole-genome sequencing before personalised CRISPR design.

scholarly journals Targeting specificity of APOBEC-based cytosine base editor in human iPSCs determined by whole genome sequencing

2019 ◽  
Vol 10 (1) ◽  
Author(s):  
Erica McGrath ◽  
Hyunsu Shin ◽  
Linyi Zhang ◽  
Je-Nie Phue ◽  
Wells W. Wu ◽  
...  
Keyword(s):  
Stem Cells ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Cytidine Deaminase ◽  
Point Mutations ◽  
Whole Genome ◽  
Human Stem Cells ◽  
Dna Double Strand Breaks ◽  
Base Editing ◽  
Human Ipscs

AbstractDNA base editors have enabled genome editing without generating DNA double strand breaks. The applications of this technology have been reported in a variety of animal and plant systems, however, their editing specificity in human stem cells has not been studied by unbiased genome-wide analysis. Here we investigate the fidelity of cytidine deaminase-mediated base editing in human induced pluripotent stem cells (iPSCs) by whole genome sequencing after sustained or transient base editor expression. While base-edited iPSC clones without significant off-target modifications are identified, this study also reveals the potential of APOBEC-based base editors in inducing unintended point mutations outside of likely in silico-predicted CRISPR-Cas9 off-targets. The majority of the off-target mutations are C:G->T:A transitions or C:G->G:C transversions enriched for the APOBEC mutagenesis signature. These results demonstrate that cytosine base editor-mediated editing may result in unintended genetic modifications with distinct patterns from that of the conventional CRISPR-Cas nucleases.

scholarly journals Tissue-specific mutation accumulation in human adult stem cells during life

Nature ◽  
2016 ◽  
Vol 538 (7624) ◽  
pp. 260-264 ◽  
Author(s):  
Francis Blokzijl ◽  
Joep de Ligt ◽  
Myrthe Jager ◽  
Valentina Sasselli ◽  
Sophie Roerink ◽  
...  
Keyword(s):  
Stem Cells ◽  
Adult Stem Cells ◽  
Mutation Accumulation ◽  
Tissue Specific ◽  
Specific Mutation ◽  
Human Adult
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