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BRCA1 and BRCA2 Mutations in an Asian Clinic-based Population Detected Using a Comprehensive Strategy

¹ Department of Medical Oncology and ² Laboratory of Molecular Oncology, Division of Medical Sciences, National Cancer Centre; ³ Singapore Biomedical Computing Resources, Bioinformatics Institute; ⁴ Department of Pathology, Singapore General Hospital; and ⁵ Department of Microbiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore

Requests for reprints: Ann S.G. Lee, Division of Medical Sciences, National Cancer Center, Singapore 169610, Singapore. Phone: 65-6436-8313; Fax: 65-6372-0161. E-mail: dmslsg{at}nccs.com.sg

Background and objective: Genetic testing for germ line mutations in the BRCA1 and BRCA2 genes for some families at high risk for breast and/or ovarian cancer may yield negative results due to unidentified mutations or mutations with unknown clinical significance. We aimed to accurately determine the prevalence of mutations in these genes in an Asian clinic-based population by using a comprehensive testing strategy.

Materials and Methods: Ninety-four subjects from 90 families were accrued from risk assessment clinics. In addition to conventional mutational screening of BRCA1 and BRCA2, multiplex ligation-dependent probe amplification for the detection of large genomic rearrangements, evaluation of splice site alterations using transcript analysis and SpliceSiteFinder prediction, and analysis of missense mutations of unknown significance by multiple sequence alignment, PolyPhen analysis, and comparison of Protein Data Bank structures were incorporated into our testing strategy.

Results: The prevalence rates for clearly deleterious BRCA1 and BRCA2 mutations were 6.7% (6 of 90) and 8.9% (8 of 90), respectively, or 7.8% (7 of 90) and 11.1% (10 of 90), respectively, by including missense mutations predicted to be deleterious by computational analysis. In contrast to observations from European and American populations, deleterious mutations in BRCA2 (10 families) were more common than for BRCA1 (7 families). Overall, the frequency of mutations was 12.2% (n = 11) by conventional screening. However, by including deleterious mutations detected using multiplex ligation-dependent probe amplification (n = 1), transcript analysis (n = 2), and computational evaluation of missense mutations (n = 3), the frequency increased substantially to 18.9%. This suggests that the comprehensive strategy used is effective for identifying deleterious mutations in Asian individuals at high risk for breast and/or ovarian cancer. (Cancer Epidemiol Biomarkers Prev 2007;16(11):2276–84)

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