Targeted sequencing with Oxford Nanopore Technologies - Nanopore seminars: an online series
Speaker details:
Frederieke Koller, Strategic Relationship Manager - Benelux, Oxford Nanopore Technologies
Frederieke joined Oxford Nanopore Technologies in May 2019 as a Strategic Relationship Manager for the Benelux. She has a background in microbiology and molecular biology. She has been working in the field of Human Genetics in different research labs in UMCUtrecht and RadboudUMC for almost 10 years, this is where she made her first steps in NGS world. After her academic career she joined PerkinElmer in 2014 where she had different sales roles within the life science working with different accounts in Academia, Biotech and Pharma. In her last role at PerkinElmer she was responsible for in cellular and tissue imaging covering the Benelux.
Anupama Chandramouli, Technical Services Specialist, Oxford Nanopore Technologies
Anupama joined Oxford Nanopore Technologies in July 2018 as a Technical Support Specialist. After graduating from Delhi University with a B.Sc. in Microbiology and M.Sc. in Plant Molecular Biology, she pursued her doctoral research in Cancer Biology at The University of Arizona. She then moved to New York to conduct postdoctoral work at New York Langone Medical Center. She has worked in the fields of skin, pancreatic, colon and breast cancers and immunology .
Thidathip Wongsurawat, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok
Thidathip Wongsurawat (Tip) research interest focuses on utilizing the sequencing technology in cancer research and diagnosis with the primary goal of translating genomic data and novel ideas into clinical reality. Currently, she works closely with multi-disciplinary team of scientists and clinicians on a nanopore-based project to develop a cutting-edge method for cancer diagnosis and treatment decisions.
Abstract
GLIoma Molecular Marker Enrichment & long-Read Sequencing (GLIMMERS)
Nanopore technology allows mutation and methylation detection directly from native DNA, without the need for the bisulfite treatment and PCR. Combining a CRISPR-Cas9 system to nanopore technology, here, we simultaneously assessed the mutations and methylation status of the major glioma molecular markers, IDH1, IDH2, and MGMT promoter. We applied this method on 2 well-characterized DNA standards, 4 cell lines and 8 brain tumor samples. In this presentation, we will show the results of mutation and methylation status assessment from both nanopore and conventional methods. These efforts are in line with improving precision medicine and can be applied to other cancer types.
Alexander Payne, University of Nottingham, School of Life Sciences
Alex is a BBSRC iCASE PhD student at the University of Nottingham, funded by BBSRC and Oxford Nanopore Technologies. After studying Biology for his undergraduate degree Alex became interested in genomics and bioinformatics. During his PhD, his focus has been on developing methods and applications for “Read Until”, a selective sequencing approach for nanopore devices that analyses molecules as they are being sequenced and either accepting or rejecting the in-progress read. In addition to real-time analysis Alex is the author of BulkVis - a tool for finding ultra-long reads in nanopore datasets.
Abstract
Nanopore sequencers enable selective sequencing in real-time by allowing individual DNA molecules to be rejected and replaced to enrich or deplete reads to address a biological question. Using “Read Until” and GPU accelerated base calling we are able to enrich for specific genomic targets such as 717 genes implicated in cancer, achieving mean 40X coverage in 72 hours. This method can be used to efficiently screen any target panel without specialised sample preparation using a single computer. I will discuss optimisations and practical uses for our toolkit: https://github.com/LooseLab/readfish