Skip to main content
  • AACR Publications
    • Cancer Discovery
    • Cancer Epidemiology, Biomarkers & Prevention
    • Cancer Immunology Research
    • Cancer Prevention Research
    • Cancer Research
    • Clinical Cancer Research
    • Molecular Cancer Research
    • Molecular Cancer Therapeutics

  • Register
  • Log in
Advertisement

Main menu

  • Home
  • About
    • The Journal
    • AACR Journals
    • Subscriptions
    • Permissions and Reprints
    • Reviewing
  • Articles
    • OnlineFirst
    • Current Issue
    • Past Issues
    • Focus on Computer Resources
    • 75th Anniversary
    • Meeting Abstracts
  • For Authors
    • Information for Authors
    • Author Services
    • Best of: Author Profiles
    • Submit
  • Alerts
    • Table of Contents
    • OnlineFirst
    • Editors' Picks
    • Citations
    • Author/Keyword
  • News
    • Cancer Discovery News
  • AACR Publications
    • Cancer Discovery
    • Cancer Epidemiology, Biomarkers & Prevention
    • Cancer Immunology Research
    • Cancer Prevention Research
    • Cancer Research
    • Clinical Cancer Research
    • Molecular Cancer Research
    • Molecular Cancer Therapeutics

User menu

  • Register
  • Log in

Search

  • Advanced search
Cancer Research
Cancer Research

Advanced Search

  • Home
  • About
    • The Journal
    • AACR Journals
    • Subscriptions
    • Permissions and Reprints
    • Reviewing
  • Articles
    • OnlineFirst
    • Current Issue
    • Past Issues
    • Focus on Computer Resources
    • 75th Anniversary
    • Meeting Abstracts
  • For Authors
    • Information for Authors
    • Author Services
    • Best of: Author Profiles
    • Submit
  • Alerts
    • Table of Contents
    • OnlineFirst
    • Editors' Picks
    • Citations
    • Author/Keyword
  • News
    • Cancer Discovery News
Molecular and Cellular Biology, Genetics

Abstract 3608: Detection of somatic structural variants using nanopore sequencing

Alexis L. Norris, Rachael E. Workman, Yunfan Fan, James R. Eshleman and Winston Timp
Alexis L. Norris
Johns Hopkins University, Baltimore, MD.
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Rachael E. Workman
Johns Hopkins University, Baltimore, MD.
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Yunfan Fan
Johns Hopkins University, Baltimore, MD.
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
James R. Eshleman
Johns Hopkins University, Baltimore, MD.
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Winston Timp
Johns Hopkins University, Baltimore, MD.
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
DOI: 10.1158/1538-7445.AM2016-3608 Published July 2016
  • Article
  • Info & Metrics
Loading
Proceedings: AACR 107th Annual Meeting 2016; April 16-20, 2016; New Orleans, LA

Abstract

Structural variants (SVs) are a hallmark of human cancer, but remain difficult to reliably and accurately detect with next generation sequencing (NGS). This is in part due to the difficult in mapping NGS's short reads (<300bp) to repetitive elements, which often flank the genomic rearrangements of SVs. Nanopore sequencing, a 3rd generation sequencing technology, offers long sequencing reads (up to 20kb), that should allow for more reliable mapping of SVs. Nanopore sequencing relies on a similar concept to a Coulter counter, reading the DNA sequence from the change in electrical current resulting from a DNA strand being forced through a nanometer-sized pore embedded in a membrane. Here, we have tested the ability of nanopore sequencing to detect a series of well-characterized SVs (including large deletions, inversions, and translocations), that inactivate the CDKN2A/p16 and SMAD4/DPC4 tumor suppressor genes in pancreatic cancer. Using PCR amplicon mixes, we show that nanopore sequencing on the MinION platform can detect large deletions, translocations, and inversions at dilutions as low as 1:100. Given the speed, small footprint (USB size), and low capital cost, nanopore sequencing could become the ideal tool for the low-level detection of somatic SVs, with clinical applications of molecular relapse, early detection, or therapeutic monitoring.

Citation Format: Alexis L. Norris, Rachael E. Workman, Yunfan Fan, James R. Eshleman, Winston Timp. Detection of somatic structural variants using nanopore sequencing. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 3608.

  • ©2016 American Association for Cancer Research.
Previous
Back to top
Cancer Research: 76 (14 Supplement)
July 2016
Volume 76, Issue 14 Supplement
  • Table of Contents
  • Index by Author

Sign up for alerts

Article Alerts
Sign In to Email Alerts with your Email Address
Email Article

Thank you for sharing this Cancer Research article.

NOTE: We request your email address only to inform the recipient that it was you who recommended this article, and that it is not junk mail. We do not retain these email addresses.

Enter multiple addresses on separate lines or separate them with commas.
Abstract 3608: Detection of somatic structural variants using nanopore sequencing
(Your Name) has forwarded a page to you from Cancer Research
(Your Name) thought you would be interested in this article in Cancer Research.
Citation Tools
Abstract 3608: Detection of somatic structural variants using nanopore sequencing
Alexis L. Norris, Rachael E. Workman, Yunfan Fan, James R. Eshleman and Winston Timp
Cancer Res July 15 2016 (76) (14 Supplement) 3608; DOI: 10.1158/1538-7445.AM2016-3608

Citation Manager Formats

  • BibTeX
  • Bookends
  • EasyBib
  • EndNote (tagged)
  • EndNote 8 (xml)
  • Medlars
  • Mendeley
  • Papers
  • RefWorks Tagged
  • Ref Manager
  • RIS
  • Zotero
Share
Abstract 3608: Detection of somatic structural variants using nanopore sequencing
Alexis L. Norris, Rachael E. Workman, Yunfan Fan, James R. Eshleman and Winston Timp
Cancer Res July 15 2016 (76) (14 Supplement) 3608; DOI: 10.1158/1538-7445.AM2016-3608
del.icio.us logo Digg logo Reddit logo Twitter logo CiteULike logo Facebook logo Google logo Mendeley logo
  • Tweet Widget
  • Facebook Like
  • Google Plus One

Jump to section

  • Article
  • Info & Metrics
Advertisement

Related Articles

Cited By...

More in this TOC Section

Molecular and Cellular Biology, Genetics

  • Abstract LB-323: Comparative miRNA microarray profiling indicates miR-363 promotes chemoresistance in ovarian cancer cells by targeting the Hippo member, LATS2
  • Abstract LB-268: Rate of temporal citrate efflux from malignant mitochondria predicts clinical aggressiveness in breast tumors
  • Abstract LB-324: Methylation-associated silencing of miR-193a-3p promotes ovarian cancer aggressiveness via targeting GRB7
Show more 3

Poster Presentations - Proffered Abstracts

  • Abstract LB-328: Mir-520b as a novel molecular target for suppressing stemness phenotype of head-neck cancer by inhibiting CD44
  • Abstract LB-331: Advanced DNA-gold nanoprobe-based direct and sensitive quantification of novel microRNAs in prostate cancer
  • Abstract LB-336: Specific serine phosphorylation of IRE-1 controls enhanced splicing of XBP-1 and regulated IRE-1-dependent decay (RIDD)
Show more 3

Poster Presentations - Genomic Technologies

  • Abstract 3621: High efficiency detection of low frequency alleles in cell-free DNA
  • Abstract 3605: ICGC in the cloud
  • Abstract 3619: Copy number estimation of cancer samples with genome, exome and targeted panel next generation sequencing
Show more 3
  • Home
  • Alerts
  • Feedback
Facebook  Twitter  LinkedIn  YouTube  RSS

Articles

  • Online First
  • Current Issue
  • Past Issues
  • Meeting Abstracts

Info for

  • Authors
  • Subscribers
  • Advertisers
  • Librarians
  • Reviewers

About Cancer Research

  • About the Journal
  • Editorial Board
  • Permissions
  • Submit a Manuscript
AACR logo

Copyright © 2018 by the American Association for Cancer Research.

Cancer Research Online ISSN: 1538-7445
Cancer Research Print ISSN: 0008-5472
Journal of Cancer Research ISSN: 0099-7013
American Journal of Cancer ISSN: 0099-7374

Advertisement