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Nat Protoc. 2016 Nov;11(11):2154-2169. doi: 10.1038/nprot.2016.129. Epub 2016 Oct 6.

Modeling and correction of structural variations in patient-derived iPSCs using CRISPR/Cas9.

Park CY1,2,3, Sung JJ1,2, Choi SH1,2, Lee DR1,2, Park IH3, Kim DW1,2.

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Department of Physiology, Yonsei University College of Medicine, Seoul, Korea.
Brain Korea 21 Plus Project for Medical Science, Yonsei University College of Medicine, Seoul, Korea.
Department of Genetics, Yale Stem Cell Center, Yale School of Medicine, New Haven, Connecticut, USA.


Genome engineering technology using engineered nucleases has been rapidly developing, enabling the efficient correction of simple mutations. However, the precise correction of structural variations (SVs) such as large inversions remains limited. Here we describe a detailed procedure for the modeling or correction of large chromosomal rearrangements and short nucleotide repeat expansions using engineered nucleases in human induced pluripotent stem cells (hiPSCs) from a healthy donor and patients with SVs. This protocol includes the delivery of engineered nucleases with no donor template to hiPSCs, and genotyping and derivation/characterization of gene-manipulated hiPSC clones. With engineered nucleases, genomic inversions, reversions, and deletions of short nucleotide expansions can be identified in 2 weeks, and desired clones can be generated in as little as 3-4 weeks. This protocol enables the correction of large inverted segments and short nucleotide repeat expansions in diseases such as hemophilia A, fragile X syndrome, Hunter syndrome, and Friedreich's ataxia.

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