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Cas9-Assisted Targeting of CHromosome segments (CATCH) for targeted nanopore sequencing and optical genome mapping

Tslil Gabrieli, Hila Sharim, Yael Michaeli, Yuval Ebenstein
doi: https://doi.org/10.1101/110163
Tslil Gabrieli
School of Chemistry, Center of Nanoscience and Nanotechnology, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv, Israel.
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Hila Sharim
School of Chemistry, Center of Nanoscience and Nanotechnology, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv, Israel.
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Yael Michaeli
School of Chemistry, Center of Nanoscience and Nanotechnology, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv, Israel.
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  • For correspondence: uv@post.tau.ac.il
Yuval Ebenstein
School of Chemistry, Center of Nanoscience and Nanotechnology, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv, Israel.
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  • For correspondence: uv@post.tau.ac.il
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ABSTRACT

Variations in the genetic code, from single point mutations to large structural or copy number alterations, influence susceptibility, onset, and progression of genetic diseases and tumor transformation. Next-generation sequencing analyses are unable to reliably capture aberrations larger than the typical sequencing read length of several hundred bases. Long-read, single-molecule sequencing methods such as SMRT and nanopore sequencing can address larger variations, but require costly whole genome analysis. Here we describe a method for isolation and enrichment of a large genomic region of interest for targeted analysis based on Cas9 excision of two sites flanking the target region and isolation of the excised DNA segment by pulsed field gel electrophoresis. The isolated target remains intact and is ideally suited for optical genome mapping and long-read sequencing at high coverage. In addition, analysis is performed directly on native genomic DNA that retains genetic and epigenetic composition without amplification bias. This method enables detection of mutations and structural variants as well as detailed analysis by generation of hybrid scaffolds composed of optical maps and sequencing data at a fraction of the cost of whole genome sequencing.

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The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
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Posted February 20, 2017.
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Cas9-Assisted Targeting of CHromosome segments (CATCH) for targeted nanopore sequencing and optical genome mapping
Tslil Gabrieli, Hila Sharim, Yael Michaeli, Yuval Ebenstein
bioRxiv 110163; doi: https://doi.org/10.1101/110163
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Cas9-Assisted Targeting of CHromosome segments (CATCH) for targeted nanopore sequencing and optical genome mapping
Tslil Gabrieli, Hila Sharim, Yael Michaeli, Yuval Ebenstein
bioRxiv 110163; doi: https://doi.org/10.1101/110163

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