Detection of Germline Variants in 450 Breast/Ovarian Cancer Families with a Multi-Gene Panel Including Coding and Regulatory Regions

• Main Authors: Chiara Guglielmi, Rosa Scarpitta, Gaetana Gambino, Eleonora Conti, Francesca Bellè, Mariella Tancredi, Tiziana Cervelli, Elisabetta Falaschi, Cinzia Cosini, Paolo Aretini, Caterina Congregati, Marco Marino, Margherita Patruno, Brunella Pilato, Francesca Spina, Luisa Balestrino, Elena Tenedini, Ileana Carnevali, Laura Cortesi, Enrico Tagliafico, Maria Grazia Tibiletti, Stefania Tommasi, Matteo Ghilli, Caterina Vivanet, Alvaro Galli, Maria Adelaide Caligo
• Format: Article
• Language: English
• Published: MDPI AG 2021-07-01
• Series: International Journal of Molecular Sciences
• Subjects: hereditary breast and ovarian cancer; BRCA1/2; breast cancer predisposition genes; coding variants; non-coding variants; regulatory regions
• Online Access: https://www.mdpi.com/1422-0067/22/14/7693

With the progress of sequencing technologies, an ever-increasing number of variants of unknown functional and clinical significance (VUS) have been identified in both coding and non-coding regions of the main Breast Cancer (BC) predisposition genes. The aim of this study is to identify a mutational profile of coding and intron-exon junction regions of 12 moderate penetrance genes (<i>ATM</i>, <i>BRIP1</i>, <i>CDH1</i>, <i>CHEK2</i>, <i>NBN</i>, <i>PALB2</i>, <i>PTEN</i>, <i>RAD50</i>, <i>RAD51C</i>, <i>RAD51D</i>, <i>STK11</i>, <i>TP53</i>) in a cohort of 450 Italian patients with Hereditary Breast/Ovarian Cancer Syndrome, <i>wild type</i> for germline mutation in <i>BRCA1/2</i> genes. The analysis was extended to 5′UTR and 3′UTR of all the genes listed above and to the BRCA1 and BRCA2 known regulatory regions in a subset of 120 patients. The screening was performed through NGS target resequencing on the Illumina platform MiSeq. 8.7% of the patients analyzed is carriers of class 5/4 coding variants in the <i>ATM</i> (3.6%), <i>BRIP1</i> (1.6%), <i>CHEK2</i> (1.8%), <i>PALB2</i> (0.7%), <i>RAD51C</i> (0.4%), <i>RAD51D</i> (0.4%), and <i>TP53</i> (0.2%) genes, while variants of uncertain pathological significance (VUSs)/class 3 were identified in 9.1% of the samples. In intron-exon junctions and in regulatory regions, variants were detected respectively in 5.1% and in 32.5% of the cases analyzed. The average age of disease onset of 44.4 in non-coding variant carriers is absolutely similar to the average age of disease onset in coding variant carriers for each proband’s group with the same cancer type. Furthermore, there is not a statistically significant difference in the proportion of cases with a tumor onset under age of 40 between the two groups, but the presence of multiple non-coding variants in the same patient may affect the aggressiveness of the tumor and it is worth underlining that 25% of patients with an aggressive tumor are carriers of a <i>PTEN</i> 3′UTR-variant. This data provides initial information on how important it might be to extend mutational screening to the regulatory regions in clinical practice.