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 2: Informatics in Genetic and Expression Analysis

Systematic analyses of the functional impacts of trinucleotide repeats in the coding regions of cancer-related genes.

Hamdi Jarjanazi, Noel Pabalan, Keith Wong and Hilmi Ozcelik
Hamdi Jarjanazi
Fred A. Litwin Center for Cancer Genetics, Samuel Lunenfeld Research Institute; Mount Sinai Hospital, Toronto, ON, Canada
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Noel Pabalan
Fred A. Litwin Center for Cancer Genetics, Samuel Lunenfeld Research Institute; Mount Sinai Hospital, Toronto, ON, Canada
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Keith Wong
Fred A. Litwin Center for Cancer Genetics, Samuel Lunenfeld Research Institute; Mount Sinai Hospital, Toronto, ON, Canada
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Hilmi Ozcelik
Fred A. Litwin Center for Cancer Genetics, Samuel Lunenfeld Research Institute; Mount Sinai Hospital, Toronto, ON, Canada
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
DOI:  Published May 2005
  • Article
  • Info & Metrics
Loading
Proc Amer Assoc Cancer Res, Volume 46, 2005

Abstract

33

Microsatellites or simple sequence repeats (SSRs) are widely present in the human genome. About 3% of the human genome is composed of such repeats in the form of mono, di, tri, or up to six nucleotide repeats. Repeat sequences occurring in the coding regions of the DNA are likely to influence the function of the proteins. Trinucleotide repeats have been associated with the inheritance of several genetic disorders. To date, at least 30 diseases are linked to trinucleotide repeat expansions (TRE). The purpose of this study is to systematically identify trinucleotide repeats in the coding region of all cancer related genes and to study their potential influence on the protein structure and function using bioinformatics and computational approaches. The coding sequences of 2245 cancer related genes involved in 18 different pathways listed at CGAP web site (cgap.nci.nih.gov) were retrieved from ensemble database (www.ensembl.org) by using EnSamrt Batch data/ sequence retrieval system (www.ensembl.org/EnsMart). Trinucleotide repeat sequences were mapped using the UNIX version of Perfect Tandem Repeat Finding Program (PTRF) (ncisgi.ncifcrf.gov/∼collinsj/Tandem_Repeats/downloads). For further systematic analyses of the repeats, a local relational database, which contains repeats, genes, protein domains and pathway data, was created. Since larger repeats are more likely to be unstable in the genome, in this study we have only focused on repeats that have repeat length of 6 units and more (n=95) for further analysis. For these repeats, the exact exonic location of the repeat and the coded amino acid sequence was determined and recorded using the transcript structure data from Ensembl database. Using the peptide structure data in the same database, the functional domains where the repeated sequence occurs were determined for each repeat and added to the summary table. In this study we have shown that the majority (59%) of the repast are located in the first exon of the cancer genes. Alanine (24%) and glutamine (16%) were shown to be the most abundant amino acid repeats in cancer genes. Interestingly 47% of the repeats were found to occur within a known functional protein domain. Comprehensive Pubmed literature search for each repeat revealed that 20% of these repeats have been studied and found be polymorphic, indicating that they are likely to interfere with the function of the protein domains in the polymorphic state. We believe that screening of the potentially functional repeats in cancer patients and comparing them to their frequencies in normal population is necessary and might have a great impact on elucidating the molecular bases of cancer related to trinucleotide repeats. This strategy provides candidate cancer genes, functions of which may be influenced by the polymorphism of trinucleotide tracts, and more likely to contribute to development of cancer.

  • American Association for Cancer Research
Previous
Back to top
Cancer Research: 65 (9 Supplement)
May 2005
Volume 65, 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.
Systematic analyses of the functional impacts of trinucleotide repeats in the coding regions of cancer-related genes.
(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
Systematic analyses of the functional impacts of trinucleotide repeats in the coding regions of cancer-related genes.
Hamdi Jarjanazi, Noel Pabalan, Keith Wong and Hilmi Ozcelik
Cancer Res May 1 2005 (65) (9 Supplement) 8;

Citation Manager Formats

  • BibTeX
  • Bookends
  • EasyBib
  • EndNote (tagged)
  • EndNote 8 (xml)
  • Medlars
  • Mendeley
  • Papers
  • RefWorks Tagged
  • Ref Manager
  • RIS
  • Zotero
Share
Systematic analyses of the functional impacts of trinucleotide repeats in the coding regions of cancer-related genes.
Hamdi Jarjanazi, Noel Pabalan, Keith Wong and Hilmi Ozcelik
Cancer Res May 1 2005 (65) (9 Supplement) 8;
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

  • Potential biomarkers of human proliferative breast disease identified through secretome analysis of gene expression data.
  • Integration of expression profiling and chromosome aberration data in human hepatocellular carcinoma.
  • Correlation of protein and mRNA expression levels in the NCI-60 cell panel.
Show more Cellular and Molecular Biology 2: Informatics in Genetic and Expression Analysis
  • 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