BRCA1andBRCA2Unclassified Variants and Missense Polymorphisms in Algerian Breast/Ovarian Cancer Families

Abstract

Background: BRCA1andBRCA2germline mutations predispose heterozygous carriers to hereditary breast/ovarian cancer. However, unclassified variants (UVs) (variants with unknown clinical significance) and missense polymorphisms inBRCA1andBRCA2genes pose a problem in genetic counseling, as their impact on risk of breast and ovarian cancer is still unclear. The objective of our study was to identify UVs and missense polymorphisms in Algerian breast/ovarian cancer patients and relatives tested previously forBRCA1andBRCA2genes germline mutations analysis.Methods: We analyzed 101 DNA samples from 79 breast/ovarian cancer families. The approach used is based onBRCA1andBRCA2sequence variants screening by SSCP or High-Resolution Melting (HRM) curve analysis followed by direct sequencing. In silico analyses have been performed using different bioinformatics programs to individualize genetics variations that can disrupt theBRCA1andBRCA2genes function.Results: Among 80 UVs and polymorphisms detected inBRCA1/2genes (33BRCA2and 47BRCA2), 31 were new UVs (10BRCA2and 21BRCA2), 7 were rare UVs (4BRCA2and 3BRCA2) and 42 were polymorphic variants (19BRCA2and 23BRCA2). Moreover, 8 new missense UVs identified in this study: twoBRCA1(c.4066C>A/p.Gln1356Lys, c.4901G>T/p.Arg1634Met) located respectively in exons 11 and 16, and sixBRCA2(c.1099G>A/p.Asp367Asn, c.2636C>A/p.Ser879Tyr, c.3868T>A/p.Cys1290Ser, c.5428G>T/p.Val1810Phe, c.6346C>G/p.His2116Asp and c.9256G>A/p.Gly3086Arg) located respectively in exons 10, 11 and 24, show a damaging PSIC score yielded by PolyPhen2 program and could be pathogenic. In addition, 5 newBRCA2missense UVs out of six that were found to be damaging by PolyPhen2 program, also were deleterious according to SIFT program. The rareBRCA2UV c.5332G>A/p.Asp1778Asn was found here for the first time in co-occurrence in trans with the deleteriousBRCA1mutation c.798_799delTT/p.Ser267LysfsX19 in young breast cancer patient. Moreover, 10 new identified intronic variants with unknown clinical significance (3BRCA1and 7BRCA2) in the present study, could be considered as benign, because GeneSplicer, SpliceSiteFinder and MaxEntScan prediction programs show no splice site alteration for these variants. Several missense polymorphisms ofBRCA1c.2612C>T/p.Pro871Leu, c.3548A>G/p.Lys1183Arg, c.4837A>G/p.Ser1613Gly andBRCA2c.865A>C/p.Asn289His, c.1114A>C/p.Asn372His, c.2971A>G/p.Asn991Asp, c.7150C>A/p.Gly2384Lys have been identified with high frequency in patients who were tested negative forBRCA1andBRCA2mutations. These missense polymorphisms could have a role as susceptibility breast cancer markers in Algerian breast/ovarian cancer families where pathologicalBRCA1andBRCA2mutations were not present.Conclusions: For the first time, UVs and missense polymorphisms inBRCA1andBRCA2genes have been identified in Algerian breast/ovarian cancer families. Evaluation of breast/ovarian cancer risk induced by the eight new missense UVs and common polymorphisms detected in our present work is on going in a larger study.