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Reduced representation optical methylation mapping (R2OM2)

Assaf Grunwald, Hila Sharim, Tslil Gabrieli, Yael Michaeli, Dmitry Torchinsky, Matyas Juhasz, Kathryn R Wagner, Jonathan Pevsner, Jeff Reifenberger, Alex R Hastie, Han Cao, Elmar Weinhold, Yuval Ebenstein
doi: https://doi.org/10.1101/108084
Assaf Grunwald
1School of Chemistry, Center for Nanoscience and Nanotechnology, Center for Light-Matter Interaction, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv, Israel,
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Hila Sharim
1School of Chemistry, Center for Nanoscience and Nanotechnology, Center for Light-Matter Interaction, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv, Israel,
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Tslil Gabrieli
1School of Chemistry, Center for Nanoscience and Nanotechnology, Center for Light-Matter Interaction, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv, Israel,
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Yael Michaeli
1School of Chemistry, Center for Nanoscience and Nanotechnology, Center for Light-Matter Interaction, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv, Israel,
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Dmitry Torchinsky
1School of Chemistry, Center for Nanoscience and Nanotechnology, Center for Light-Matter Interaction, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv, Israel,
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Matyas Juhasz
2Institute of Organic Chemistry RWTH Aachen University D-52056 Aachen Germany
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Kathryn R Wagner
3Kennedy Krieger Institute and Departments of Neurology and Neuroscience, The Johns Hopkins School of Medicine
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Jonathan Pevsner
3Kennedy Krieger Institute and Departments of Neurology and Neuroscience, The Johns Hopkins School of Medicine
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Jeff Reifenberger
4Bionano Genomics, Inc., San Diego, California, USA.
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Alex R Hastie
4Bionano Genomics, Inc., San Diego, California, USA.
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Han Cao
4Bionano Genomics, Inc., San Diego, California, USA.
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Elmar Weinhold
2Institute of Organic Chemistry RWTH Aachen University D-52056 Aachen Germany
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Yuval Ebenstein
1School of Chemistry, Center for Nanoscience and Nanotechnology, Center for Light-Matter Interaction, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv, Israel,
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ABSTRACT

Reduced representation methylation profiling is a method of analysis in which a subset of CpGs is used to report the overall methylation status of the probed genomic regions. This approach has been widely adopted for genome-scale bisulfite sequencing since it requires fewer sequencing reads and uses significantly less starting material than whole-genome analysis. Consequently, this method is suitable for profiling medical samples and single cells at high throughput and reduced costs. Here, we use this concept in order to create a pattern of fluorescent optical methylation profiles along individual DNA molecules. Reduced representation optical methylation mapping (R2OM2) in combination with Bionano Genomics next generation genome mapping (NGM) technology provides a hybrid genetic/epigenetic genome map of individual chromosome segments spanning hundreds of kilobase pairs (kbp). These long reads, along with the single-molecule resolution, allow for epigenetic variation calling and methylation analysis of large structural aberrations such as pathogenic macrosatellite arrays not accessible to single-cell next generation sequencing (NGS). We apply this method to facioscapulohumeral dystrophy (FSHD) showing both structural variation and hypomethylation status of a disease-associated, highly repetitive locus on chromosome 4q.

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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 4.0 International license.
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Posted March 06, 2017.
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Reduced representation optical methylation mapping (R2OM2)
Assaf Grunwald, Hila Sharim, Tslil Gabrieli, Yael Michaeli, Dmitry Torchinsky, Matyas Juhasz, Kathryn R Wagner, Jonathan Pevsner, Jeff Reifenberger, Alex R Hastie, Han Cao, Elmar Weinhold, Yuval Ebenstein
bioRxiv 108084; doi: https://doi.org/10.1101/108084
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Reduced representation optical methylation mapping (R2OM2)
Assaf Grunwald, Hila Sharim, Tslil Gabrieli, Yael Michaeli, Dmitry Torchinsky, Matyas Juhasz, Kathryn R Wagner, Jonathan Pevsner, Jeff Reifenberger, Alex R Hastie, Han Cao, Elmar Weinhold, Yuval Ebenstein
bioRxiv 108084; doi: https://doi.org/10.1101/108084

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