Oxford Nanopore Technologies ASHG satellite event

Date: Wednesday 28th October 2020
Time: 9:00 am (EDT)
Location: online

Hear about the latest tech updates for Oxford Nanopore Technologies as well as talks from researchers using nanopore technology in the field of human genomics. 

There is no delegate fee for this event. Your place at this event will be confirmed via email from events@nanoporetech.com. Completion of this form does not constitute confirmation. 

The agenda below is subject to change

9:00 - 9:05 am Welcome and Introduction James Brayer
Oxford Nanopore Technologies Ltd
9:05 - 9:25 am Into the Unknown: The Epigenetics of Repetitive DNA Ariel Gershman
Johns Hopkins University
9:25 - 9:45 am Long-read sequencing of human tissues to study allelic effects on transcriptome structure Tuuli Lappalainen
New York Genome Centre
9:45 - 10:05 pm ACME: An Affinity-based Cas9-Mediated Enrichment method using nanopore sequencing Shruti Iyer
Cold Spring Harbor Laboratory
10:05- 10:25 am All in one Rosemary Dokos
Oxford Nanopore Technologies Ltd
10:25 - 10:30 am Closing remarks James Brayer
Oxford Nanopore Technologies Ltd

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Oxford Nanopore Technologies ASHG satellite event.

Speaker details:

Ariel Gershman, Johns Hopkins University

Ariel Gershman is a Ph.D. student in the Biochemistry, Cellular and Molecular Biology program in the Timp lab at Johns Hopkins University, where she focuses on using long-read sequencing for genome and transcriptome assembly. She has worked on generating reference genomes for the Ruby throated hummingbird (Archilochus colubris) and Tobacco Hornworm moth (Manduca sexta). Ariel is also interested in exploring the epigenome using nanopore sequencing in hard to assemble areas, contributing to methylation analysis in the Telomere-to-Telomere consortium.


Into the Unknown: The Epigenetics of Repetitive DNA

Improvements in sequencing technology and computational assembly methods have led to remarkable milestones in human genome assembly. Recently, the telomere to telomere (T2T) consortium generated the first telomere to telomere assembly of a complete human genome, due in part to the use of ultralong nanopore sequencing reads to stretch across these difficult regions. For the first time, we have a complete human reference spanning multi-megabase satellite arrays and rDNA arrays in the peri/centromeric regions and acrocentric short arms, as well as regions enriched in segmental duplications. While these large repetitive regions of the genome remain largely unexplored, there is evidence that epigenetic control of repeats contributes strongly to genome stability and disease.
Previous attempts to study epigenetics in centromeric, pericentromeric, telomeric, and macrosatellite regions have been precluded by the difficulty in mapping conventional NGS data to large repetitive arrays. Ultra long (>100kb) reads allow us to accurately map nanopore reads to these regions and investigate the epigenome of previously unassembled and unannotated sequences. We investigated the methylome of the centromeric higher order repeat (HOR) arrays, and observed a distinctive pattern of hyper and hypomethylation. Furthermore, we can use allele-specific methylation alone to phase microsatellite repeats, which we have demonstrated on the DXZ4 region of the X chromosome. There we found two clusters of reads which we attribute to either the active or inactive X allele. Our demonstrated ability to probe the epigenome of these repetitive areas will allow us to gain a greater understanding of their regulation and significance.


Tuuli Lappalainen, New York Genome Centre

Tuuli Lappalainen is an Associate Professor at the Department of Systems Biology at Columbia University, and a Core Faculty Member at the New York Genome Center. Her research focuses on functional genetic variation in human populations and its contribution to human traits and diseases. She has contributed to many major research consortia in human genetics, including the 1000 Genomes Project, Geuvadis Consortium, GTEx Project, and TOPMed.


Long-read sequencing of human tissues provides novel insights into transcriptome variation

In this study, we created a large long-read transcriptome sequencing data set using Oxford Nanopore technology from 88 tissue samples of the GTEx project that had Illumina RNA-seq and WGS data. We identified almost 100,000 novel transcripts with a high validation rate in mass spectrometry proteome data. We developed a novel pipeline, LORALS, to analyze allele specific expression and transcript structure from Oxford Nanopore data, which provided additional resolution to diverse genetic effects on the transcriptome. Our work demonstrates the additional insights into human transcriptome variation obtained from long-read data.

Shruti Iyer, Cold Spring Harbor Laboratory

Shruti Iyer is a Ph.D. candidate at Stony Brook University, working on her dissertation research in Dr. W. Richard McCombie's lab at Cold Spring Harbor Laboratory. Her current focus is on developing long-read sequencing strategies to resolve complex genomic regions associated with cancer. Shruti received a Bachelors degree in Genetic Engineering and a Masters in Molecular Biology and Human Genetics – as part of her master's studies, she worked at Emory University on understanding the genetic basis of post-traumatic stress disorder, or PTSD. 


An affinity-based Cas9-mediated enrichment method using nanopore sequencing

Affinity-based Cas9-Mediated Enrichment (ACME) is a modification of the Oxford Nanopore Cas9-based enrichment method, and uses HisTag Dynabeads to reduce the abundance of Cas9 bound non-target DNA in the sequencing pool. ACME was tested on a panel of 10 prominent cancer genes, ranging from 10kb–150kb in size, in two widely studied breast cell lines: MCF 10A (normal breast) and SK-BR-3 (HER2-amplified breast cancer). When compared with the traditional Cas9 approach, ACME helps boost coverage from 4x to 70x for targets as large as 90kb, consistently achieving 100-200x for 50-60kb targets, performing on par with whole genome long-read sequencing for variant detection.

Rosemary Dokos, Oxford Nanopore Technologies

Rosemary Dokos is the VP of Product & Programme Management at Oxford Nanopore Technologies. The Product Management team at Oxford Nanopore Technologies enable the release of novel products and improvements into the field. The team is led by Rosemary who has over 10 years of experience in the Life Science market covering Genomics, Proteomics and Cell Biology.