Investigation of germline variants in Bahraini women with breast cancer using next-generation sequencing based-multigene panel

Abstract

Germline variants in BRCA1 and BRCA2 (BRCA1/2) genes are the most common cause of hereditary breast cancer. However, a significant number of cases are not linked to these two genes and additional high-, moderate- and low-penetrance genes have been identified in breast cancer. The advent of next-generation sequencing (NGS) allowed simultaneous sequencing of multiple cancer-susceptibility genes and prompted research in this field. So far, cancer-predisposition genes other than BRCA1/2 have not been studied in the population of Bahrain. We performed a targeted NGS using a multi-panel covering 180 genes associated with cancer predisposition to investigate the spectrum and frequency of germline variants in 54 women with a positive personal and/or family history of breast cancer. Sequencing analysis revealed germline variants in 29 (53.7%) patients. Five pathogenic/likely pathogenic variants in four DNA repair pathway-related genes were identified in five unrelated patients (9.3%). Two BRCA1 variants, namely the missense variant c.287A>G (p.Asp96Gly) and the truncating variant c.1066C>T (p.Gln356Ter), were detected in two patients (3.7%). Three variants in non-BRCA1/2 genes were detected in three patients (1.85% each) with a strong family history of breast cancer. These included a monoallelic missense variant c.1187G>A (p.Gly396Asp) in MUTYH gene, and two truncating variants namely c.3343C>T (p.Arg1115Ter) in MLH3 gene and c.1826G>A (p.Trp609Ter) in PMS1 gene. Other variants of uncertain significance (VUS) were also detected, and some of them were found together with the deleterious variants. In this first application of NGS-based multigene testing in Bahraini women with breast cancer, we show that multigene testing can yield additional genomic information on low-penetrance genes, although the clinical significance of these genes has not been fully appreciated yet. Our findings also provide valuable epidemiological information for future studies and highlight the importance of genetic testing, and an NGS-based multigene analysis may be applied supplementary to traditional genetic counseling.

Fig 1. Summary of the data analysis pipeline in this study.

Fig 2. Gene-panel testing for 54 breast cancer patients.

A) Cases where pathogenic/likely pathogenic variants were identified. B) Percentage of pathogenic/likely pathogenic variants identified in each gene.

Fig 3. Pedigree of patient P-7 carrying the missense variant c.287A>G (p.Asp96Gly) in BRCA1 gene.

The patient was diagnosed with unilateral breast cancer at age 35 years, with her maternal aunt affected by breast cancer and thyroid cancer at age 28 years old, as well as other family members affected with breast cancer. The symbols used are proband (arrow), male (box), female (circle), affected female (black fill).

Fig 4. Pedigree of patient P-44 carrying the nonsense variant c.1066C>T (p.Gln356Ter) in BRCA1 gene.

The patient who descended from consanguineous parents was diagnosed with bilateral breast cancer at age 46 years and her maternal cousin was affected by bone cancer. The symbols used are proband (arrow), male (box), female (circle), affected male and female (black fill), consanguinity (double lining).

Fig 5. Pedigree of patient P-24 carrying the missense variant c.1187G>A (p.Gly396Asp) in MUTYH gene.

The patient was diagnosed with unilateral breast cancer at age 52 years with a strong family history of her mother died due to breast cancer at age 50 years, two other family members died due to breast cancer, and a family member died due to prostate cancer (all from the maternal branches) as well as three other family members died due to breast cancer. The symbols used are proband (arrow), male (box), female (circle), affected male and female (black fill), deceased (line through), consanguinity (double lining).

Fig 6. Pedigree of patient P-13 carrying the nonsense variant c.3343C>T (p.Arg1115Ter) in MLH3 gene.

The patient was diagnosed with unilateral breast cancer at age 32 years with her two paternal aunts affected by breast cancer and other family members affected by breast cancer and/or leukaemia. The symbols used are proband (arrow), male (box), female (circle), affected male and female (black fill).

Fig 7. Pedigree of patient P-52 carrying the nonsense variant c.1826G>A (p.Trp609Ter) in PMS1 gene.

The patient was diagnosed with unilateral breast cancer at age 43 years with a strong family history of her two sisters affected by breast cancer, as well as a family member who died due to leukaemia. The symbols used are proband (arrow), male (box), female (circle), affected male and female (black fill).