Decoding the epigenome with Oxford Nanopore real-time methylation detection
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Oxford Nanopore sequencing enables accurate real-time detection of modifications in DNA and RNA without the need for chemical or enzymatic alterations. Nanopore methylation detection seamlessly integrates with native DNA or RNA sequencing, eliminating the necessity for additional library preparation. Our advanced basecaller, Dorado, accurately calls bases and modifications simultaneously, simplifying the workflow. For interpretation, we offer modkit — a tool for processing modification BAM files and generating summary statistics. This streamlined analysis workflow answers key questions in epigenetics and broader biological inquiries.
In this Knowledge exchange, we focus on the relevance of modifications, particularly DNA methylation at the fifth position of cytosine (5mC), in studying disease mechanisms in humans. We present benchmarking results against other techniques and cover essential information for modification analysis, including modkit's new features. Lastly, we showcase the benefits of using native Oxford Nanopore sequencing for modification calling in real-world applications with high accuracy reads.
Please note, this Knowledge Exchange will be broadcast at 7am (GMT)/3pm (SGT) and 4pm (GMT)/11am(EST). You can select the one suitable for you below.
Meet the speakers
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Rocio Esteban, Applications Support Bioinformatician, Oxford NanoporeRocio completed a biotechnology degree in the University of Lleida and a Master’s degree in computational sciences in the University of Vigo. Prior to joining Oxford Nanopore, she worked as a Bioinformatics Specialist for a genomics company, helping to develop various bioinformatics pipelines including genotyping projects for population genomics studies, and genome assembly and annotation. She joined Oxford Nanopore 4 years ago, starting in the benchmarking team, where her work focused on methylation calling and germline and somatic SV calling general benchmarking. Rocio also worked on adaptive sampling, helping to develop the Reduced-Representation Methylation Sequencing (RRMS) method. Currently, she provides bioinformatic support in customer-facing projects covering a range of different topics such as trio sequencing or pharmacogenomics
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Arthur Rand, Research Scientist, Machine Learning, Oxford NanoporeArt was introduced to nanopore sequencing and Oxford Nanopore Technologies in graduate school where he was a member of Mark Akeson's lab (the UCSC nanopore group). He started as a wet-lab biochemist and transitioned to bioinformatics mid-way through the program. He started working on DNA methylation detection and classification with nanopores from the get-go. He lives in Santa Cruz, California and enjoys road cycling and backpacking in his free time
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7am (GMT) moderator: Cheng Yong Tham, Applications Bioinformatician, Oxford NanoporeCheng Yong is an applications bioinformatician at Oxford Nanopore, who leads and facilitates collaborative projects with APAC customers to provide comprehensive data analysis support and guidance that enables the successful implementation of existing and novel applications.
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4pm (GMT) moderator: Sayonika Mohanta, Strategic Marketing Manager – Methylation, Oxford NanoporeSayonika completed a Bioengineering degree at University of California Los Angeles and a Master’s degree in Chemical and Biomolecular Engineering at Johns Hopkins University. Prior to joining Oxford Nanopore, she has worked at a variety of biotechnology companies understanding the current challenges and needs of modern scientists and researchers. Her expertise extends to genomics, where she has adeptly translated complex genomic advancements into compelling and engaging content. In her current role, she employs her deep understanding of methylation and genomics to drive initiatives, working with cross-functional teams and establishing strategic partnerships for the ever-evolving biotech and genomics landscape. She hopes to foster connections and build a community of knowledge sharing between science and industry.
