Genotyping iPSC Clones with SNP Arrays

Genomic DNA from iPSC clones modified by gene editing were genotyped using an Infinium OmniExpress-24 v1.2 and v1.3 (Illumina) SNP array according to the manufacturer’s recommendations. Median probe spacing is around 2 kb. Array scanning was performed on an iScan Bead Array Scanner (Illumina). Scanned data were processed using Illumina GenomeStudio (2011.1 for v1.2 and 2.0.4 for v1.3) with human genome Build 37 and FinalReports were exported according to the manufacturer’s protocol. CNV call was done using a combination of PennCNV^{53 (link)} (1.0.3), GWASTools^{54 (link)} (v1.2.R), and MAD^{55 (link)} (1.0.1). Karyograms were prepared using GenomeJack (Mitsubishi Space Software).

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Grajcarek J., Monlong J., Nishinaka-Arai Y., Nakamura M., Nagai M., Matsuo S., Lougheed D., Sakurai H., Saito M.K., Bourque G, & Woltjen K. (2019). Genome-wide microhomologies enable precise template-free editing of biologically relevant deletion mutations. Nature Communications, 10, 4856.

Publication 2019

iScan Bead Array Scanner GenomeStudio

Clones Genomic Human genome Ipsc

Corresponding Organization : Kyoto University

Other organizations : McGill University, Ontario Genomics

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Variable analysis

independent variables

Genomic DNA from iPSC clones modified by gene editing

dependent variables

SNP genotypes from Infinium OmniExpress-24 v1.2 and v1.3 arrays
Copy number variations (CNVs) identified using PennCNV, GWASTools, and MAD

control variables

Median probe spacing of around 2 kb on the Infinium OmniExpress-24 arrays
Human genome Build 37 used for data processing
Illumina GenomeStudio (2011.1 for v1.2 and 2.0.4 for v1.3) used for data processing

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