Impact of High-to-Moderate Penetrance Genes on Genetic Testing: Looking over Breast Cancer

Abstract

Breast cancer (BC) is the most common cancer and the leading cause of cancer death in women worldwide. Since the discovery of the highly penetrant susceptibility genes BRCA1 and BRCA2, many other predisposition genes that confer a moderate risk of BC have been identified. Advances in multigene panel testing have allowed the simultaneous sequencing of BRCA1/2 with these genes in a cost-effective way. Germline DNA from 521 cases with BC fulfilling diagnostic criteria for hereditary BC were screened with multigene NGS testing. Pathogenic (PVs) and likely pathogenic (LPVs) variants in moderate penetrance genes were identified in 15 out of 521 patients (2.9%), including 2 missense, 7 non-sense, 1 indel, and 3 splice variants, as well as two different exon deletions, as follows: ATM (n = 4), CHEK2 (n = 5), PALB2 (n = 2), RAD51C (n = 1), and RAD51D (n = 3). Moreover, the segregation analysis of PVs and LPVs into first-degree relatives allowed the detection of CHEK2 variant carriers diagnosed with in situ melanoma and clear cell renal cell carcinoma (ccRCC), respectively. Extended testing beyond BRCA1/2 identified PVs and LPVs in a further 2.9% of BC patients. In conclusion, panel testing yields more accurate genetic information for appropriate counselling, risk management, and preventive options than assessing BRCA1/2 alone.

Keywords: ATM; CHEK2; PALB2; RAD51C; RAD51D; breast cancer; moderate-penetrance genes.

Figure 1

Distribution of germline PVs/LPVs in BC susceptibility genes detected with NGS multi-gene panel test in 15 BC patients. The heatmap displays the mutational spectrum identified. The graph shows both SNVs and CNVs: missense mutations, splicing mutations, and truncating mutations are represented by green, salmon pink, and light blue rectangles, respectively; exonic deletions (CHEK2, ATM) are represented by purple rectangles.

Figure 2

Germline PVs/LPVs identified in CHEK2 gene. Lolliplot shows deleterious germline variants throughout the whole protein sequence of CHEK2. The horizontal scale bar represents the length (amino acids) of the protein sequence, and the light-blue bar below represents the corresponding exons. The vertical bar represents the number of patients affected by the specific mutation (#). Each variant identified in this study is depicted by a lolliplot. In detail, the orange lolliplot identifies the splicing mutation, the green lolliplot indicates missense variants, and the black lolliplot displays a frameshift mutation. Deletion of exon 9 is represented by the grey triangle. The lolliplot graph was obtained by the informatics tool Mutation Mapper (https://www.cbioportal.org/ (accessed on 30 May 2023) and modified.

Figure 3

Germline PVs/LPVs identified in ATM and PALB2 genes. Lolliplots show deleterious germline variants throughout the whole protein sequences of ATM (above) and PALB2 (below). The horizontal scale bar represents the length (amino acids) of the protein sequence, and the light-blue bar below represents the corresponding exons. The vertical bar represents the number of patients affected by the specific mutation (#). Each variant identified in this study is depicted by a lolliplot. In detail, the orange lolliplot identifies the splicing mutation, and the black ones display non-sense mutations. Deletion of exon 29 in ATM is represented by the grey triangle. The lolliplot graph was obtained by the informatics tool Mutation Mapper (https://www.cbioportal.org/ (accessed on 30 May 2023) and modified.

Figure 4

Germline PVs/LPVs identified in RAD51C and RAD51D genes. Lolliplot shows deleterious germline variants throughout the whole protein sequences of RAD51C (above) and RAD51D (below). The horizontal scale bar represents the length (amino acids) of the protein sequence, the light blue bar below represents the corresponding exons. The vertical bar represents the number of patients affected by the specific mutation (#). Each variant identified in this study is depicted by a lolliplot. In detail, the orange lolliplot identifies the splicing mutation, and the black ones display non-sense mutation. The lolliplot graph was obtained by the informatics tool Mutation Mapper (https://www.cbioportal.org/ (accessed on 30 May 2023) and modified.

Figure 5

Figure illustrates three family trees showing segregation of PVs and LPVs in affected relatives. The arrows indicate the probands from each family. Panel (A) depicts the segregation of the CHEK2 c.793-1G>A in a patient diagnosed with ccRCC; panel (B) displays the finding of the CHEK2 p.(Ile157Thr) in an in situ melanoma case. The third family tree (C) illustrates the ATM p.(Tyr2100*) in the mother’s proband suffering from BC.