Genetic Testing by Cancer Site: Breast

Identification of germline pathogenic variants in DNA damage repair genes by a next-generation sequencing multigene panel in BRCAX patients

BACKGROUND

Approximately 5-10% of breast carcinomas have been related to hereditary conditions and are attributable to pathogenic variants in the BRCA1 and BRCA2 genes, which is referred to as hereditary breast and ovarian cancer (HBOC) syndrome. The inclusion of additional genes that can be related to HBOC syndrome is under intense evaluation due to the high proportion of patients with HBOC criteria who do not present pathogenic mutations in BRCA genes, named BRCAX, despite having high clinical suspicion of hereditary cancer. The main aim is to identify new potentially pathogenic gene variants that may contribute to HBOC to improve the efficiency of routine diagnostic tests in this hereditary condition.

METHODS

A retrospective cohort of 77 HBOC BRCAX patients was analyzed by next-generation sequencing using a targeted multigene panel composed of 25 genes related to hereditary cancer and deficiencies in DNA repair pathways.

RESULTS

We found 9 variants in 7 different genes, which were confirmed by automated sequencing. Six variants were classified as pathogenic or likely pathogenic. Three of them were located in the PALB2 gene, one in the BRIP1 gene, one in the BARD1 gene and 1 in the RAD50 gene. In addition, three variants of uncertain significance (VUS) were detected in the TP53, CHEK2, and CDH1 genes.

CONCLUSIONS

We identified that 8% of BRCAX patients were carriers of pathogenic variants in genes other than BRCA1 and BRCA2. Therefore, wide gene panels, including clinically actionable genes, should be routinely used in the screening of HBOC in our population. We observed differences from other studies in the prevalence of mutated genes, most likely due to differences in the selection criteria of the probands and in the population analyzed. The high incidence of deleterious variant detection in PALB2 supports its significant role in breast cancer susceptibility and reinforces its inclusion in the HBOC genetic diagnostic process.

Prevalence of germline mutations in the TP53 gene in patients with early-onset breast cancer in the Mexican population

Background

Heterozygous germline TP53 gene mutations result in Li-Fraumeni Syndrome (LFS). Breast cancer (BC) is the most frequent tumor in young women with LFS. An important issue related to BC in the Mexican population is the average age at diagnosis, which is approximately 11 years younger than that of patients in the United States (U.S.) and Europe. The aim of this study was to determine the prevalence of germline mutations in TP53 among young Mexican BC patients.

Methods

We searched for germline mutations in the TP53 gene using targeted next-generation sequencing (NGS) in 78 BC patients younger than 45 years old (yo) who tested negative for BRCA1/2 mutations. A group of 509 Mexican women aged 45yo or older without personal or family BC history (parents/grandparents) was used as a control.

Results

We identified five patients with pathogenic variants in the TP53 gene, equivalent to 6.4% (5/78). Among patients diagnosed at age 36 or younger, 9.4% (5/55) had pathogenic TP53 mutations. Three of these variants were missense mutations (c.844C > T, c.517G > A, and c.604C > T), and the other two mutations were frameshifts (c.291delC and c.273dupC) and had not been reported previously. We also identified a variant of uncertain clinical significance (VUS), c.672G > A, which causes a putative splice donor site mutation. All patients with TP53 mutations had high-grade and HER2-positive tumors. None of the 509 patients in the healthy control group had mutations in TP53.

Conclusions

Among Mexican BC patients diagnosed at a young age, we identified a high proportion with germline mutations in the TP53 gene. All patients with the TP53 mutations had a family history suggestive of LFS. To establish the clinical significance of the VUS found, additional studies are needed. Pathogenic variants of TP53 may explain a substantial fraction of BC in young women in the Mexican population. Importantly, none of these mutations or other pathological variants in TP53 were found in the healthy control group.

BRCA1/BRCA2 Mutations Shaped by Ancient Consanguinity Practice in Southern Mediterranean Populations

The aim of this study is to investigate the involvement of consanguinity on BRCA1/2 mutation incidence in Southern Mediterranean populations and to confirm their low penetrance by comparison of their recurrence in sporadic and familial breast cancer in a context of ancient consanguinity practice. Our study comprises of two parts: First, a comparison of the consanguinity rates of the South Mediterranean countries in a relationship with the frequency of BRCA1 deleterious mutations in breast cancer families and the recurrence of these mutations. Second, we investigated 23patients with a family history of breast cancer, 51 patients without a family history of breast cancer using next-generation sequencing of BRCA2 and then confirmed by Sanger sequencing for the novel mutation. As results, we clearly show a strong relationship between the frequency of BRCA1 deleterious mutations in breast cancer families and rate of consanguinity, since they are significantly inversely correlated. Four deleterious mutations were found in BRCA2 gene including a novel frame-shift mutationc.9382_9383dup in a patient with familial breast cancer and three other frame-shift mutations c.6591_6592del, c.1310_1313del and c.7654dup in patients with sporadic breast cancer.These results are discussed in a context of selective pressure of ancient consanguinity practice. In conclusion, the study of BRCA1/2 gene in Southern Mediterranean countries revealed low penetrance recurrent mutations in sporadic and familial breast cancer. These mutations have been selected in a context of ancient consanguinity practice along with protective genetic and environmental factors.

Aberrant low expression of p85α in stromal fibroblasts promotes breast cancer cell metastasis through exosome-mediated paracrine Wnt10b

P85α, which acts as a tumour suppressor, is frequently found to be downregulated in various human cancers. However, the role of p85α in the tumour microenvironment is unknown. Here, we report that aberrantly low expression of p85α in breast cancer stroma is clinically relevant to breast cancer disease progression. Stromal fibroblasts can acquire the hallmarks of cancer-associated fibroblasts (CAFs) as a result of the loss of p85α expression. Paracrine Wnt10b from p85α-deficient fibroblasts can promote cancer progression via epithelial-to-mesenchymal transition (EMT) induced by the canonical Wnt pathway. Moreover, exosomes have a key role in paracrine Wnt10b transport from fibroblasts to breast cancer epithelial cells. Our results reveal that p85α expression in stromal fibroblasts haves a crucial role in regulating breast cancer tumourigenesis and progression by modifying stromal–epithelial crosstalk and remodelling the tumour microenvironment. Therefore, p85α can function as a tumour suppressor and represent a new candidate for diagnosis, prognosis and targeted therapy.

Risk reduction and survival benefit of prophylactic surgery in BRCA mutation carriers, a systematic review

BACKGROUND

Mutations in BRCA1 or BRCA2 genes results in an elevated risk for developing both breast and ovarian cancers over the lifetime of affected carriers. General surgeons may be faced with questions about surgical risk reduction and survival benefit of prophylactic surgery.

METHODS

A systematic literature review was performed using the electronic databases PubMed, OVID MEDLINE, and Scopus comparing prophylactic surgery vs observation with respect to breast and ovarian cancer risk reduction and mortality in BRCA mutation carriers.

RESULTS

Bilateral risk-reducing mastectomy provides a 90% to 95% risk reduction in BRCA mutation carriers, although the data do not demonstrate improved mortality. The reduction in ovarian and breast cancer risks using risk-reducing bilateral salpingo-oophorectomy has translated to improvement in survival.

CONCLUSIONS

Clinical management of patients at increased risk for breast cancer requires consideration of risk, patient preference, and quality of life.

Breast cancer risk associated with CHEK2 mutations

Most efforts to identify individuals who have a hereditary predisposition for developing breast cancer had focused on the BRCA1 and BRCA2 genes. Less common susceptibility genes also are associated with increased risk for developing breast cancer, but until recently have often gone undetected. With the advent of next generation sequencing (NGS), many families with suspected hereditary risk are undergoing testing for multiple genes associated with increased cancer risk (Mahon, 2013a). One gene that is commonly included on NGS hereditary breast cancer panels is CHEK2. Increasingly, oncology nurses will encounter patients and families affected with mutations on this gene and need to understand the implications it has for screening and treatment.

Personalized sequencing and the future of medicine: discovery, diagnosis and defeat of disease

The potential for personalized sequencing to individually optimize medical treatment in diseases such as cancer and for pharmacogenomic application is just beginning to be realized, and the utility of sequencing healthy individuals for managing health is also being explored. The data produced requires additional advancements in interpretation of variants of unknown significance to maximize clinical benefit. Nevertheless, personalized sequencing, only recently applied to clinical medicine, has already been broadly applied to the discovery and study of disease. It is poised to enable the earlier and more accurate diagnosis of disease risk and occurrence, guide prevention and individualized intervention as well as facilitate monitoring of healthy and treated patients, and play a role in the prevention and recurrence of future disease. This article documents the advancing capacity of personalized sequencing, reviews its impact on disease-oriented scientific discovery and anticipates its role in the future of medicine.

Health Promoting Life-Style Behaviors and Systemic Inflamma-tion in African American and Caucasian Women Prior to Chemo-therapy for Breast Cancer

BACKGROUND

Racial disparities in breast cancer outcomes persist, with differential adverse outcomes in African American women. Although research has ex-amined possible genetic differences, there has been little research on potentially modifiable characteristics such as health promoting behaviors. The purpose of this article is to describe the characteristics and to compare the differences by race in lifestyle factors and inflammatory biomarkers in African American and Caucasian women with breast cancer.

METHODS

This is a baseline descriptive analysis from an ongoing randomized controlled trial that includes 124 women diagnosed with early stage breast cancer prior to chemotherapy. Data sources included medical records, self-re-port questionnaires and a blood sample for measures of inflammation. The sta-tistical analysis included descriptive statistics and ANOVA models to determine differences between the two groups.

RESULTS

Overall, both groups had low levels of health promoting behaviors. African Americans had a significantly higher body mass index. Caucasian women consumed more alcohol. Levels of C-reactive protein and MIP-1β were significantly higher in African Americans.

CONCLUSION

Potentially modifiable factors such as nutrition, physical activity and levels of inflammation warrant further attention.

[Personalized medicine and breast cancer: anticipatory medicine, prognostic evaluation and therapeutic targeting]

Breast cancer is now considered as a large collection of distinct biological entities, the management of which is increasingly personalized. Personalized medicine - defined as a medicine, which uses molecular profiles, notably genetic profiles, from patients and/or tumors to tailor therapeutic decisions - is now introduced in the management of breast cancer at any stages: screening and prevention of hereditary forms, prognostic and predictive evaluation of early breast cancer, and, more recently, novel clinical trials in advanced breast cancer, where genetic characterization of tumor tissue based on genomics, including next-generation sequencing tools, is used to drive specific therapeutic targeting.

Multiplex genetic cancer testing identifies pathogenic mutations in TP53 and CDH1 in a patient with bilateral breast and endometrial adenocarcinoma

Background

Germline genetic testing for familial cancer syndromes is usually performed serially for the most likely genetic causes. In recent years the way genetic testing carried out has changed, as next generation sequencing now allows the simultaneous testing of multiple susceptibility genes at low costs.

Case presentation

Here, we present a female with bilateral breast cancer and endometrial adenocarcinoma. After simultaneous sequencing of 150 genes (890 kb) associated with hereditary cancer we identified pathogenic mutations in two high-penetrance genes, i.e. TP53 and CDH1 that would most likely not have been elucidated by serial screening of candidate genes.

Conclusion

As the two mutated genes are located on different chromosomes and cause different cancer syndromes these findings had a tremendous impact not only on genetic counseling of the index patient and her family but also on subsequent surveillance strategies.

ICO amplicon NGS data analysis: a Web tool for variant detection in common high-risk hereditary cancer genes analyzed by amplicon GS Junior next-generation sequencing

Next-generation sequencing (NGS) has revolutionized genomic research and is set to have a major impact on genetic diagnostics thanks to the advent of benchtop sequencers and flexible kits for targeted libraries. Among the main hurdles in NGS are the difficulty of performing bioinformatic analysis of the huge volume of data generated and the high number of false positive calls that could be obtained, depending on the NGS technology and the analysis pipeline. Here, we present the development of a free and user-friendly Web data analysis tool that detects and filters sequence variants, provides coverage information, and allows the user to customize some basic parameters. The tool has been developed to provide accurate genetic analysis of targeted sequencing of common high-risk hereditary cancer genes using amplicon libraries run in a GS Junior System. The Web resource is linked to our own mutation database, to assist in the clinical classification of identified variants. We believe that this tool will greatly facilitate the use of the NGS approach in routine laboratories.

Hereditary breast/ovarian cancer syndrome: a primer for obstetricians/gynecologists

An understanding of the diagnosis and clinical management of hereditary breast and ovarian cancer syndrome (HBOC) is essential for obstetricians/gynecologists. This article provides practical information regarding collecting a family history, cancer risk assessment and genetic testing, BRCA-associated cancer prognosis and treatment, screening recommendations, and prevention strategies. Through appropriate cancer risk assessment, women with BRCA1/2 mutations can be identified, and screening and prevention strategies can be used before a diagnosis of cancer occurs. Women's health providers with a strong working knowledge of HBOC are able to improve the quality of care for women and families impacted by BRCA1/2 mutations.

Breast cancer in the young: role of the geneticist

The genetics professional plays an important role in the care of young women with breast cancer by providing counseling on issues specific to these young women. The issues addressed in counseling include hereditary predisposition to cancer, fertility and reproductive options in the context of hereditary cancer, and the impact and implications of their history of early breast cancer on close family members. A thorough risk assessment and counseling session address the patient's personal and family history, with particular attention paid to benign and malignant findings that suggest the need for genetic testing. Genetics professionals, especially genetic counselors, also address the physical and emotional implications of an increased risk of cancer with patients and family members. This review highlights the unique aspects of care provided by these specialized healthcare providers.