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
Cellular and Molecular Biology

Abstract #1449: Lung squamous cell carcinoma is composed of reproducible molecular subtypes

Matthew Wilkerson, Xiaoying Yin, C. Miller, William Funkhouser, Philip Bernard, Leigh Thorne, Mark Socinski, Alden Parsons, Charles Perou and D. Hayes
Matthew Wilkerson
Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC; University of Utah, Salt Lake City, UT
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Xiaoying Yin
Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC; University of Utah, Salt Lake City, UT
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
C. Miller
Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC; University of Utah, Salt Lake City, UT
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
William Funkhouser
Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC; University of Utah, Salt Lake City, UT
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Philip Bernard
Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC; University of Utah, Salt Lake City, UT
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Leigh Thorne
Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC; University of Utah, Salt Lake City, UT
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Mark Socinski
Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC; University of Utah, Salt Lake City, UT
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Alden Parsons
Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC; University of Utah, Salt Lake City, UT
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Charles Perou
Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC; University of Utah, Salt Lake City, UT
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
D. Hayes
Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC; University of Utah, Salt Lake City, UT
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
DOI:  Published May 2009
  • Article
  • Info & Metrics
Loading
AACR Annual Meeting-- Apr 18-22, 2009; Denver, CO

Abstract

Background: Over the coming year, the NIH Cancer Genome Atlas (TCGA) initiative will profile several hundred lung squamous cell carcinomas (LSCC) for gene expression, DNA copy number aberrations, and somatic mutation events as has already been dramatically reported for glioblastoma. In the recent TCGA glioblastoma subtype study, analysis of existing datasets was essential in validating molecular subtypes and copy number associations. In preparation for the forthcoming TCGA LSCC project, this abstract presents an analysis of public LSCC datasets to produce a consensus molecular subtype classification. No consensus classification has been attempted so far. Methods: Raw data was obtained from three of the largest published LSCC microarray datasets: Veridex (N = 129; Raponi, et al. 2006), Duke (N = 52; Bild, et al. 2006), Expo (N = 36; International Genomics Consortium, 2008). Microarray probes were mapped to the latest RefSeq gene build (GenBank release 161) by BLAT and ambiguously mapped probes were discarded. Using this mapping, gene expression values were calculated by the Robust Multichip Average method. Genes were then filtered for reliability and variability using Integrative Correlations and median absolute deviation. Consensus Clustering of the agglomerative hierarchical algorithm was independently completed by data source to determine a number of LSCC groups. To evaluate whether LSCC groups represent the same genetic profiles across datasets, centroids (median expression profiles) of each dataset's groups were clustered by the agglomerative hierarchical algorithm and validated by the SigClust method. Gene Set Enrichment Analysis was used to discern biological pathways, and genomic copy number by the proxy of cytoband gene differential expression. Survival outcome was modeled by the Kaplan-Meier method. Results: All datasets supported four LSCC groups. Each datasets' centroids unambiguously clustered with exactly one centroid from the other datasets, which demonstrates that the four groups\#8217; genetic profiles are consistent across cohorts. Using summaries of subtype-enriched pathways, the subtypes are named: immune-mediation, E2F-regulated, xenobiotic-predominant, and developmental. Subtypes were enriched with distinct cytobands: 3q:26-29 - xenobiotic, 18q:12 - xenobiotic & developmental, 8q24 - developmental. 3q26 contains the oncogene PIK3CA and is a known common amplification in LSCC. There are distinct 3-year survival outcomes among the subtypes, maximally 24%. In continuing to profile these subtypes, we are assaying a cohort of 77 patients at UNC by SNP arrays. Conclusions: These results demonstrate, for the first time, that LSCC subtypes are reproducible across multiple, independent cohorts and represent distinct biological processes, clinical outcomes and putative copy number events. These results constitute a molecular subtype classification reference for the TCGA LSCC project.

Citation Information: In: Proc Am Assoc Cancer Res; 2009 Apr 18-22; Denver, CO. Philadelphia (PA): AACR; 2009. Abstract nr 1449.

Footnotes

  • 100th AACR Annual Meeting-- Apr 18-22, 2009; Denver, CO

  • American Association for Cancer Research
Back to top
Cancer Research: 69 (9 Supplement)
May 2009
Volume 69, Issue 9 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 #1449: Lung squamous cell carcinoma is composed of reproducible molecular subtypes
(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 #1449: Lung squamous cell carcinoma is composed of reproducible molecular subtypes
Matthew Wilkerson, Xiaoying Yin, C. Miller, William Funkhouser, Philip Bernard, Leigh Thorne, Mark Socinski, Alden Parsons, Charles Perou and D. Hayes
Cancer Res May 1 2009 (69) (9 Supplement) 1449;

Citation Manager Formats

  • BibTeX
  • Bookends
  • EasyBib
  • EndNote (tagged)
  • EndNote 8 (xml)
  • Medlars
  • Mendeley
  • Papers
  • RefWorks Tagged
  • Ref Manager
  • RIS
  • Zotero
Share
Abstract #1449: Lung squamous cell carcinoma is composed of reproducible molecular subtypes
Matthew Wilkerson, Xiaoying Yin, C. Miller, William Funkhouser, Philip Bernard, Leigh Thorne, Mark Socinski, Alden Parsons, Charles Perou and D. Hayes
Cancer Res May 1 2009 (69) (9 Supplement) 1449;
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

Cellular and Molecular Biology

  • Abstract SY29-01: Functions of wild type and mutant p53
  • Abstract SY34-02: The impact of O2 availability on human cancer
  • Abstract SY19-01: Cell to cell variability in the responses of tumor cells to death ligands
Show more 3

Oncogenomics 2: Genome-wide mRNA Profiling of Cancer -- Poster Presentations - Proffered Abstracts

  • Abstract #1456: A genomic and transcriptional analysis of HPV-infected oropharyngeal head and neck squamous cell carcinoma.
  • Abstract #1453: Identification of interactive networks of gene expression associated with osteosarcoma oncogenesis by integrated molecular profiling of DNA methylation, copy number and gene expression
  • Abstract #1432: Genome-wide gene expression profiling in a novel "patient-like" rat model of intrahepatic cholangiocarcinoma progression closely mimicking the human disease
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