American Association of Cancer Research: Oxford Nanopore showcases breakthrough technology to generate most comprehensive insights into cancer genomes

Meet our team of nanopore experts in booth #801 and mark your calendars for our industry spotlight workshop on Tuesday, 18th April at 12:30PM (EST).

The genetic underpinnings of cancer are diverse and many types of genomic aberration — from SNVs to SVs, fusion transcripts, and epigenetic modifications (e.g. DNA/RNA methylation) — can fuel or signal disease. As a result, researchers have traditionally relied on multiple techniques to identify and analyse different forms of cancer. Nanopore sequencing is disrupting that model by delivering a streamlined and rapid solution for complete characterisation of cancer samples. For the first time, cancer researchers can accelerate scientific discovery by using nanopore sequencing to:

• Generate sequencing reads of any length, including ultra-long reads in excess of 4 Mb that can span complex genomic regions

• Detect integrated base modification

• Achieve real-time results.

Oxford Nanopore will be at the year’s American Association of Cancer Research (AACR) conference in Orlando, 16th – 19th April. Highlights include:

• Lunchtime spotlight theater presentation on Tuesday, 18th April (12:30 PM, Theater C) - see details and register below.

• ‘Data for Breakfast’ - join us daily on booth #801 for coffee and bioinformatics! View the agenda below to see our classes for Monday, Tuesday and Wednesday. Each 15-minute class kicks off at 9:30am in booth #801.

• Live demos on our booth - see daily schedule. Learn how to use adaptive sampling to enrich any cancer gene panel of interest, see a rapid BRCA1/2 nanopore sequencing assay and set up a time to consult with an expert from the Oxford Nanopore team.

• Broad poster presentations from a range of nanopore sequencing experts (full list below).

Follow us on twitter @nanopore for updates and news throughout the conference.

AACR 2023 Annual Meeting Spotlight Theater: Nanopore sequencing for the most comprehensive view of the cancer genome (12:30 PM, Theater C)

Native, PCR-free nanopore sequencing, with unrestricted read lengths, offers a unique view into the human genome, allowing the identification of single nucleotide variants, structural variants, and epigenetic modifications, plus phasing — from a single dataset. In this session, we’ll explore how these technical benefits open up a new window of understanding into cancer genomes, featuring projects ranging from cancer whole-genome sequencing to cell-free DNA with methylation, and single-cell sequencing.

Join us to hear the latest from scientists using nanopore sequencing to access new genomic and transcriptomic information, giving an unprecedented view of the mechanisms involved in cancer progression and evolution.

Presentations include:

• Nanopore sequencing of advanced cancers from the Personalized OncoGenomics Program - Laura Williamson, BC Cancer

• Simultaneous detection of same-cell genotypes and phenotypes from single cell nanopore RNA sequencing data with scNanoGPS - Ruli Gao, Northwestern University

Register here.

‘Data for breakfast’ agenda

Monday, 17th April 9:30am - 9:45am	Class 1: Introduction to nanopore sequencing data analysis	Learn how to use the Oxford Nanopore human variation workflow to simultaneously phase genomic and epigenomic variants from data-rich nanopore sequencing reads.
Tuesday, 18th April 9:30 - 9:45am	Class 2: New Oxford Nanopore cancer bioinformatics tools and workflows	Advanced cancer bioinformatic tools for nanopore sequencing data analysis: perform somatic variant calling of SNVs, SVs and differential methylation at the haplotype level from a single data set. Find out how to get full-length transcripts at the single level as well.
Wednesday, 19th April 9:30 - 9:45am	Class 3: Get started with nanopore data analysis for cancer research	If you missed the first two classes, join us for this summary. This session will cover the basics of nanopore data analysis, plus cancer bioinformatics tools and workflows for genomic, epigenomic, and transcriptomic analysis.

Live demonstrations on booth #801

Live demo: PCR-free, flexible enrichment of a comprehensive cancer gene	Learn how to use adaptive sampling to enrich any cancer gene panel of interest. This on-flow-cell targeted sequencing method enables simultaneous genomic and epigenomic variant detection without the need for PCR.	Sunday – 3:30pm Monday – 11:30am Tuesday – 3:00pm Wednesday – 11:30am
Live demo: Rapid BRCA1/2 nanopore sequencing assay	Discover how rapid nanopore sequencing can be used to accurately detect pathogenic variants in BRCA1/2.	Monday – 3:00pm Tuesday – 11:00am

In the poster hall

April 16, 2023, 1:30 PM - 5:00 PM

• 260/24, Section 9: Long RNA and DNA sequencing reveals HEK293 diversity between commercial sources
  Presenter: Bradley W. Langhorst, New England Biolabs, Inc.

• 315/17, Section 11: HPV-related genome rearrangements in head and neck cancer cell lines
  Presenter: Vera Mukhina, University of Maryland School of Medicine

• 786/28, Section 28: Single molecule methylation sequencing of circulating DNA identifies individuals with breast cancer
  Presenter: Hanlee P. Ji, Stanford University

April 17, 2023, 9:00 AM - 12:30 PM

• 2069/5, Section 33: ScNanoGPS: A robust tool for simultaneous calculation of same-cell genotypes and phenotypes from single cell long read transcriptomes
  Presenter: Cheng-Kai Shiau, Northwestern University Feinberg School of Medicine

• 2081/17, Section 33: Nano2NGS: A framework for converting nanopore sequencing data to NGS-liked sequencing data for data analysis
  Presenter: Jidong Lang, Bioinformatics, Qitan Technology (Beijing) Co., Ltd

• 2115/18, Section 38: Zero-waste molecular diagnostics from biopsy needle wash water
  Presenter: Jack Wadden, Pediatrics, University of Michigan Medical School

• LB080/23, Section 34: SAVANA: a computational method to characterize structural variation in human cancer genomes using nanopore sequencing
  Presenter: Hillary Elrick, European Molecular Biology Laboratory, European Bioinformatics Institute

• LB081/24, Section 34: Concurrent characterization of somatic nucleotide mutations, 5mC, and 5hmC methylation in clinical research samples using a single nanopore sequencing assay
  Presenter: Sergey Aganezov, Oxford Nanopore Technologies

April 17, 2023, 1:30 PM - 5:00 PM

• 2989/3, Section 25: Colorectal cancer displays three patterns of tumor-specific MHC-II inducibility and dynamics, with implications for combining epigenetic therapy with immunotherapy
  Presenter: Oliver J. Pickles, University of Birmingham

• April 18, 2023, 9:00 AM - 12:30 PM
  3814/22, Section 12: In CLL the U1 snRNA driver mutation alters splicing in multiple genes and pathways
  Presented by: Andrea Senff-Ribeiro, Ontario Institute for Cancer Research

• 4289/20, Section 32: Long-read, assembly-based characterization of rearranged cancer karyotypes
  Presented by: Mikhail Kolmogorov, Center for Cancer Research, National Cancer Institute, NCI.

For more information please see: Cancer applications page