Time: 3:00 pm (UK time)/ 10:00 am (EST)
Please join us for the next seminar in this series in which you will first hear from Danielle Folkard, Strategic Account Manager - UK & Ireland, Oxford Nanopore Technologies Ltd., who will give an overview of the platform before we are joined by Chloe Goldsmith, Lyon Cancer Research Center, and Adrien Leger, EMBL-European Bioinformatics Institute, who will each present their latest research with nanopore sequencing.
Participants of this session will learn:
There will also be an opportunity to submit questions throughout the talks which will be answered in the live Q&A session following the presentations.
Please register below to attend this webinar. You will receive a confirmation of your place from events@nanoporetech.com.
Cancer epigenetics, and DNA methylation in particular are promising fields in cancer research. We aim to better understand and exploit the unique characteristics of the methylome during cell transformation and established malignancies. Our final goal is to develop DNA methylation protocols useful for clinical translation.
Abstract
Long read landscapes of 5mC in liver pathophysiology
Methylation of Hepatitis B Virus (HBV) DNA in a CpG context (5mCpG) can alter the expression patterns of viral genes related to infection and cellular transformation. Moreover, it may also provide clues to why certain infections are cleared, or persist with or without progression to cancer. The detection of 5mCpG often requires techniques that damage DNA or introduce bias through a myriad of limitations. Therefore, we developed a method for the detection of 5mCpG on the HBV genome that does not rely on bisulfite conversion or PCR. With cas9 guided RNPs to specifically target we enriched in HBV DNA from PHH infected with HBV Genotype A, E or D prior to sequencing with Nanopores MinION. In addition, we were also able to enrich and sequence HBV from patient liver tissue achieving coverage of ~2000x. Moreover, using the developed technique, we have provided the first de novo assembly of native HBV DNA, as well as the first landscape of 5mCpG from native HBV sequences. Furthermore, the developed tools are scalable to the Nanopore Flongle devise providing whole genome length HBV sequences in < 4h. This method is a novel approach that enables the enrichment of viral DNA in a mixture of nucleic acid material from different species and will serve as a valuable tool for infectious disease monitoring.
Adrien is a computational biologist working at the EMBL-EBI in Ewan Birney's Team. His PhD was at the bench in virology and epigenetics at the INSERM 1089. After his PhD, he was promoted to a junior team leader position and obtained an additional master's degree in bioinformatics. He then decided to move to the EMBL-EBI to expand his skills in data analysis and software development. At the EBI, he has been working on methods and algorithms for next generation sequencing data. In particular, he (co-)developed and maintains nanopore related software, including pycoQC, NanoCompore, pycoMeth and NanoCount.
Abstract
Differential DNA and RNA methylation analysis from nanopore sequencing data.
Nanopore sequencing has the unique ability to sense the presence of small chemical modifications on both DNA and RNA. Accurately detecting and quantifying the presence of such modifications is challenging, but not impossible. For DNA, there are now many options but downstream analyses are still complicated, in particular when trying to identify differently methylated regions. For RNA, the bar is even higher due to the sheer number of known modifications and the absence of robust modified nucleotide models. Together with collaborators, I have been developing and validating toolsets for DNA differential CpG analysis (pycoMeth) as well as for RNA modifications single molecule detection (NanoCompore).