Identifying Functional Genetic Variants in DNA Repair Pathway Using Protein Conservation Analysis

Identifying Functional Genetic Variants in DNA Repair Pathway Using Protein Conservation Analysis

¹Fred A. Litwin Centre for Cancer Genetics, Samuel Lunenfeld Research Institute, ²Department of Pathology and Laboratory Medicine, Mount Sinai Hospital, Ontario, Canada and
³Department of Laboratory Medicine and Pathobiology, University of Toronto, Ontario, Canada

Requests for reprints:
Hilmi Ozcelik, Mount Sinai Hospital Samuel Lunenfeld Research Institute, 600 University Avenue Room 992A, Toronto, ON M5G 1X5, Canada. Phone: (416) 586-4996; Fax: (416) 586-8869. E-mail: ozcelik{at}mshri.on.ca

Abstract

The role of DNA repair in initiation, promotion, and progression of malignancy suggests that variations in DNA repair genes confer altered cancer risk. Accordingly, DNA repair gene variants have been studied extensively in the context of cancer predisposition. Single nucleotide polymorphisms (SNPs) are the most common genetic variations in the human genome. A fraction of SNPs are located within the genes, which are likely to alter the gene expression and function. SNPs that change the encoded amino acid sequence of the proteins (non-synonymous; nsSNPs) are potentially genetic disease determinant variations. However, as not all amino acid substitutions are supposed to lead to a change in protein function, it will be necessary to have a priori prediction and determination of the functional consequences of amino acid substitutions per se, and then together with other genetic and environmental factors to study their possible association with a trait. Here we report the analysis of nsSNPs in 88 DNA repair genes and their functional evaluation based on the conservation of amino acids among the protein family members. Our analysis demonstrated that >30% of variants of DNA repair proteins are highly likely to affect the function of the proteins drastically. In this study, we have shown that three nsSNPs, which were predicted to have functional consequences (XRCC1-R399Q, XRCC3-T241M, XRCC1-R280H), were already found to be associated with cancer risk. The strategy developed and applied in this study has the potential to identify functional protein variants of DNA repair pathway that may be associated with cancer predisposition.

Footnotes

↵2 Internet address: http://lpgws.nci.nih.gov/html-cgap/cgl/DNA_damage.html).
↵3 Internet address: http://www.ncbi.nlm.nih.gov/SNP/.
↵4 Internet address: http://hgvbase.cgb.ki.se/.
↵5 Internet address: http://lpgws.nci.nih.gov/.
↵6 Internet address: http://snp500cancer.nci.nih.gov/home.cfm.
↵7 Internet address: http://www.genome.utah.edu/genesnps/.
↵8 M. Edmenson, K. Buetow. The BLAST against gene transcripts tool (unpublished). Internet address: http://lpgws.nci.nih.gov:80/perl/blast2.
↵9 Internet address: http://www.ncbi.nlm.nih.gov/BLAST/.
↵10 Internet address: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=unigene.
↵11 Internet address: http://us.expasy.org/sprot/.
↵12 Internet address: http://blocks.fhcrc.org/sift/SIFT_seq_submit2.html.
↵13 A few number of nsSNPs were screened in population(s) but could not be detected: we still report them as there was a chance that these nsSNPs could not be validated because they may represent either ethnic group specific or rare nsSNPs.
↵14 J. C. Figueiredo, J. A. Knight, L. Briollais, I. L. Andrulis, H. Ozcelik. Polymorphisms XRCC1-R399Q and XRCC3-T241M and the risk of breast cancer at the Ontario site of the breast cancer family registry, in press.
↵15 J. C. Figueiredo, N. Diaz-Granados, J. A. Knight, S. Savas, L. Briollais, H. Ozcelik. XRCC1-R399Q and XRCC3-T241M: a systematic review of biological importance and role in cancer, in preparation.
Grant support: Grant (BCTR0100627) from Susan Komen Breast Cancer Foundation, USA and “CIHR Strategic Training Program Grant—The Samuel Lunenfeld Research Institute Training Program: Applying Genomics to Human Health” fellowship (S. Savas).
The costs of publication of this article were defrayed in part by the payment of page charges. This article must therefore be hereby marked advertisement in accordance with 18 U.S.C. Section 1734 solely to indicate this fact.
- Accepted December 24, 2003.
- Received September 24, 2003.
- Revision received December 4, 2003.