Tumor Genetic Testing
Breast Cancer
In women, breast cancer accounts for 15% of cancer-related deaths. 10% of women affected by breast cancer have a family history of the disease. Compared with women without a family history, women with one first-degree relative with premenopausal breast cancer are at 3.3-fold greater risk, and women with two first-degree relatives with breast cancer are at 3.6-fold greater risk.
Hereditary forms account for approximately 5–10% of all human breast cancer. Mutations in the high-susceptibility genes BRCA1 and BRCA2 cause approximately 25–28% of the hereditary breast cancer cases. Mutations in other genes, with different levels of penetrance, account for about 20% of breast cancer cases. For more than 50% of hereditary breast cancer cases, no mutation has been identified yet. See the gene composition of our panel testing for hereditary breast and ovarian cancer here.
An important and large meta-analysis of pathogenic BRCA variants penetrance from 2007 states that carriers of BRCA1 and BRCA2 pathogenic mutations were shown to have a cumulative risk of 57 and 49%, respectively, for developing breast cancer by 70 years of age. These data were supported by a subsequent prospective epidemiological study in the UK (EMBRACE) in 2013, showing that carriers of BRCA1 and BRCA2 pathogenic mutations have a cumulative risk of 60 and 55%, respectively, for developing breast cancer by 70 years of age.
Due to the increased understanding of the molecular mechanisms underpinning the heterogeneity of breast cancer, it is possible to consider different genetically defined ‘intrinsic subtypes’.
- The luminal subtype, characterized by the expressions of the ESR1 (or ER, Estrogen Receptor gene) and of other genes that encode proteins characteristic of the luminal epithelial cells; up to 60% of breast cancers fall into this category. The luminal subtype can be divided in two different subgroups:
- The luminal A subgroup, characterized by high expression of the ESR1 gene but low expression of proliferation-related genes.
- The luminal B subgroup, characterized by lower expression of ESR1 and PGR (or PR, Progesterone Receptor gene) and higher expression of proliferation-related genes.
- The basal-like subtype, characterized by the expression of the genes characteristic of the basal-myoepithelial cells of the normal breast. It accounts for 15–20% of breast cancers. Even if a clear immunohistochemical profile for this subtype does not exist, the lack of expression of hormone receptor ERBB2 (or HER2, human epidermal growth factor receptor 2) is a typical feature. As the basal-like subtype tumors generally lack expression of ER and PR genes too, they are also known as triple-negative breast cancer.
- HER2-enriched subtype, characterized by high expression levels of genes located in the HER2 amplicon at 17q12. About 10–15% of breast cancers belong to this subtype.
This classification is not complete and must be seen more as a useful pragmatic clinical approach.
BRCA1-associated breast cancers are often high-grade and poorly differentiated infiltrating ductal carcinomas with special immunophenotypic features. These tumors are often triple-negative and express cytokeratins 5/6 (CK5/6), cyclinE and p53. They show a high frequency of necrotic areas and a higher proportion of continuous pushing margins and lymphocytic infiltration. In an important study published in 2012 from CIMBA, a group of researchers working on genetic modifiers of cancer risk in BRCA1 and BRCA2 mutation carriers, the authors observed in a large data set of 4,325 BRCA1 mutation carriers that 78% of the tumors were ER-negative; overexpression of HER2 could be shown in approximately 10% of the cases and 69% were triple-negative. In terms of the intrinsic subtypes, the majority of the BRCA1 breast cancers can thus be classified as basal-like. Furthermore, BRCA1 tumors more often stained p53 positive in comparison to sporadic tumors, probably reflecting the higher frequency of mutations in the TP53 gene found in BRCA1 tumors.
BRCA2-associated tumors are also mostly invasive ductal adenocarcinomas with moderate or poor differentiation, high mitotic counts, and continuous pushing margins. Immunohistochemically, BRCA2 tumors seem to be more similar to sporadic tumors. From the same aforementioned study, it was found that ER negativity was present in 23% of tumors arising in BRCA2 mutation carriers, HER2 overexpression in approximately 10%, and triple negativity in 16% when investigating a large collective of 2,568 BRCA2 mutation carriers. The overexpression of ER, PR, CK8, and CK18 assigns BRCA2 tumors to the luminal intrinsic subtype, with the vast majority belonging to the luminal B subtype.
BRCA-related breast cancer is characterized by a more aggressive phenotype than sporadic breast cancer, with BRCA1-related breast cancer being more frequently high grade and triple-negative, and BRCA2-related breast cancer being on average of a higher histological grade than sporadic cases. However, it is still controversial whether BRCA mutations in breast cancer are associated with a poor prognosis.
See our panels for hereditary breast and ovarian cancer:
Ovarian Cancer
Ovarian cancer has the highest mortality rate of all gynecological malignancies. It is the fifth most common cancer in European women with an estimated 65,500 cases and 42,700 deaths annually. Primary ovarian tumors can be classified into three major categories:
• epithelial ovarian tumors (include benign, borderline, and malignant tumors);
• germ cell tumors;
• sex cord-stromal tumors.
Malignant epithelial ovarian tumors or epithelial ovarian cancer are the most prevalent and they can be further classified histologically into serous (divided in a low grade- and high grade-serous), clear cell, endometrioid, mucinous, and undifferentiated tumors. Emerging evidence suggests that a significant proportion may have an extra-ovarian origin.
Several studies have estimated that approximately 13–15% of patients with ovarian cancer carry germ-line mutations in BRCA1 or BRCA2, with this frequency reaching 17% in patients with high-grade serous adenocarcinoma, whereas a recent study in 2016 estimates that approximately 6-25% of individuals affected by ovarian cancer have a BRCA1/BRCA2 germline mutation.
According to the aforementioned meta-analysis from 2007, carriers of BRCA1 and BRCA2 pathogenic mutations were shown to have a cumulative risk of 40 and 18%, respectively, for developing ovarian cancer by 70 years of age. The prospective epidemiological study in the UK (EMBRACE) in 2013, showed that carriers of BRCA1 and BRCA2 pathogenic mutations have a cumulative risk of 59 and 17%, respectively, for developing ovarian cancer by 70 years of age.
In unselected population studies, BRCA mutations are most frequently associated with high-grade serous ovarian cancer (17%) and to a lesser extent with low-grade serous carcinoma. Based on this evidence, and in line with the most recent guidelines, patients with invasive epithelial ovarian cancer (excluding borderline and mucinous), including fallopian tube and peritoneal cancers, irrespective of age, are recommended to be considered for BRCA genetic testing.
Carriers of BRCA1 and BRCA2 mutations have a very similar phenotype. Those with BRCA2 mutations tend to be diagnosed with ovarian cancer at a slightly older age than BRCA1 carriers (55–58 years and 49–53 years, respectively).
Currently, numerous studies have reported the association between BRCA mutations and ovarian cancer mortality, and the results are conflicting. Some investigators have found that ovarian cancer patients with BRCA mutations have more favorable outcomes, whereas others have indicated null results. In a recent study, including 386 BRCA1/2-associated epithelial ovarian cancer patients diagnosed between 1980 and 2015, parameters like progression-free survival, progression-free interval, overall survival and ovarian cancer-specific survival were compared between epithelial ovarian cancer patients with and without previous breast cancer. The results suggest that BRCA1/2-associated epithelial ovarian cancer patients with previous breast cancer have a worse outcome than patients without breast cancer, especially when treated with adjuvant chemotherapy.
Pancreatic Cancer
Pancreatic cancer is a highly lethal disease, and its mortality is almost equal to its incidence. Although advances have been made in the management of pancreatic cancer in recent years, the 5-year survival rate is still less than 6%.
Pancreatic cancer is the fourth leading cause of cancer death in the USA and leads to an estimated 227,000 deaths per year worldwide. The majority of pancreatic cancer are sporadic with a median age at diagnosis of 72 years. The male/female ratio is 1.3:1, and cigarette smoking accounts for approximately 20% of tumors. It has been estimated that approximately 7-10% of patients have one or more close relatives with pancreatic cancer and are therefore classified as having familial pancreatic cancer. In this case, relatives are at an increased risk of developing pancreatic cancer compared to the general population, and the risk rises with an increasing number of affected relatives and younger age at diagnosis.
Pancreatic cancer is reported to be the third most common cancer associated with BRCA mutations. Estimates of BRCA gene mutation prevalence in sporadic pancreatic cancer have ranged from 5.5 to 21.6% and from 4.9 to 26% in familial pancreatic cancer.
Recently, The Cancer Genome Atlas Research Network (TCGA) reported on whole-exome sequencing of a series of 333 localized pancreatic cancers. Seven subgroups were defined on the basis of certain gene fusions involving the ERG/ETS transcription factor family (ERG, ETV1/4, and FLI1) or recurrent mutations in specific genes (SPOP, FOXA1, and IDH1); these subgroups differ with regard to androgen receptor (AR) signaling activity, DNA methylation, and microRNA expression.
Intrapatient tumor heterogeneity represents a challenge for genomic stratification of PC in the clinic. Several studies have comprehensively observed an overall higher degree of heterogeneity within primary prostate tumors than in advanced disease. This is likely to be related to (1) bottlenecks in the metastatic process that limit metastatic spread and growth; (2) the capacity of metastatic tumor cells to seed other metastasis and even reseed the primary tumor; (3) the selection of resistant clones driven by treatment exposures.
In an international large study, 5,799 families with one or more cases of breast cancer tested for mutations in BRCA1 and/or BRCA2 were involved, in order to estimate the risk of pancreatic cancer in high-risk breast cancer families according to the BRCA mutation status. Their results confirmed the increased risk, with an estimation of a 4.11-fold higher risk of pancreatic cancer in BRCA1 carriers.
Prostate cancer
Prostate cancer is now one of the most serious oncological diseases in men with an incidence higher than that of all other solid tumors. It is the second most commonest tumor in men worldwide, with about 900,000 new cases diagnosed annually, although there is substantial variation in disease incidence across regions.
Prostate cancers can be divided for practical purposes into three groups – hereditary, familial, and sporadic. More than 85% of all prostate cancers are sporadic and only 10–15% of these cancers are genetically determined.
Meta-analyses of 33 epidemiological studies evaluating the familial risk of prostate cancer have shown that the relative risk of prostate cancer in a man with a brother or father with prostate cancer is 3.4 and 2.2, respectively. This risk is higher if there are more affected men in the first line than in the second line. Not only a family history of prostate cancer but also breast/ ovarian cancer increase the risk for men in a given familial line. In such case, the relative risk is 1.7 and in the case of incidence of prostate cancer together with breast or ovarian cancer, the risk is 5.8 but results from other studies differ.
For BRCA1 mutation carriers, the Breast Cancer Linkage Consortium reported an increase in prostate cancer risk in men aged <65 years with a relative risk of 1.82, but no risk increase was seen for men aged ≥65 years.
For BRCA2 mutation carriers, the same organization estimated the relative risk for developing prostate cancer as 4.65, rising to 7.33 for men aged <65 years. Two recent large studies reported a 3.5-fold and 8.6-fold increase in the risk of prostate cancer for BRCA1 and BRCA2 mutation carriers by age 65.
See our panels for hereditary breast and ovarian cancer:
