Pathogenic BRCA Variants as Biomarkers for Risk in Prostate Cancer

Studies have demonstrated that men with Prostate Cancer (PCa) harboring BRCA2/BRCA1 genetic aberrations, are more likely to have worse disease and a poorer prognosis. A mutation in BRCA2 is known to confer the highest risk of PCa for men (8.6 fold in men ≤65 years) making BRCA genes a conceivable genomic biomarker for risk in PCa. These genes have attracted a lot of research attention however their role in the clinical assessment and treatment of PCa remains complex. Multiple studies have been published examining the relationship between prostate cancer and BRCA mutations. Here BRCA mutations are explored specifically as a biomarker for risk in PCa. It is in this context, we examined the prognostic, clinical and therapeutic role of BRCA2/BRCA1 mutations across the evolution of PCa. The impact of the inclusion of BRCA genes on genetic screening will also be outlined.

Correlation between number of false positive variants and quality of results in Ion Torrent PGM Sequencing to screen BRCA genes

Introduction: Next Generation Sequencing (NGS) is cost-effective, capable to investigate the genes faster but the protocol has challenges throughout its steps. Objective: We investigated different adjustments of protocol to screen the BRCA genes using Ion Torrent PGM sequencing and correlate the results with number of False Positive (FP) variants. Material and methods: Library preparation process, number of FP InDels, library concentration, number of cycles in amplify targets step, purity of nucleic acid, input, and number of samples/Ion 314 chip were analyzed in association with the results obtained by NGS. Results: 51 reactions and 9 adjustments of protocols were done and 8 FP InDels were observed in homopolymer regions. No FP Single-Nucleotide Polymorphism variant was observed. Protocol variables jointly are associated in 67.5% with the quality of results obtained(p<0.05). The number of FP InDels decreased when the quality of results increased. Conclusion: Ion AmpliSeq BRCA1/BRCA2 Community Panel had better performance with 4 samples per Ion-314 chip instead of 8 and the number of cycles in the amplification step, even using DNA with high quality, was better with 23. We observed better results when the manual equalization process was done, without the Ion Library Equalizer kit. These adjustments provided higher coverage of the variants and fewer artifacts (6.7-fold). Laboratories must perform the internal validation because FP InDel variants can vary according to the quality of results. NGS assay must be validated with Sanger.

Study of the Genetic Variants in BRCA1/2 and Non-BRCA Genes in a Population-Based Cohort of 2155 Breast/Ovary Cancer Patients, Including 443 Triple-Negative Breast Cancer Patients, in Argentina

Gene/s sequencing in hereditary breast/ovary cancer (HBOC) in routine diagnosis is challenged by the analysis of panels. We aim to report a retrospective analysis of BRCA1/2 and non-BRCA gene sequencing in patients with breast/ovary cancer (BOC), including triple-negative breast cancer (TNBC), in our population. In total 2155 BOC patients (1900 analyzed in BRCA1/2 and 255 by multigenic panels) gave 372 (17.2.6%) and 107 (24.1%) likely pathogenic/pathogenic variants (LPVs/PVs), including BRCA and non-BRCA genes, for the total and TNBC patients, respectively. When BOC was present in the same proband, a 51.3% rate was found for LPVs/PVs in BRCA1/2. Most of the LPVs/PVs in the panels were in BRCA1/2; non-BRCA gene LPVs/PVs were in CDH1, CHEK2, CDKN2A, MUTYH, NBN, RAD51D, and TP53. TNBC is associated with BRCA1/2 at a higher rate than the rest of the breast cancer types. The more prevalent PVs in BRCA1/2 genes (mostly in BRCA1) do not rule out the importance to panels of genes, although they are certainly far from shedding light on the gap of the 85% predicted linkage association of BOC with BRCA1/2 and are still not elucidated.

Systematic review of family studies of heritable breast cancer in Africa.

e22508 Background: The incidence of breast cancer (BC) in Africa (40.4 per 100,000) is 49% that of Europe and North America (81.9 per 100,000) but the mortality rate is 42% higher (19.4 versus 13.7 per 100,000). The high mortality is due to lack of screening. However, more targeted screening based on genomic risks are also missed because of stigmatization, poor family history, and limited information on BC susceptibility gene mutations. Internationally based family members are influencing cultural attitudes to BC in Africa leading to reduced stigmatization, increased better family history and uptake of genomic screening. Family-based studies of BC in Africa would provide useful information on prevalence of mutations that can inform genomic screening panels. We conducted systemic review of all family-based studies of BC in Africa to document state of the art, identify barriers and facilitators of this research method and methods of advancing the science. Methods: Using a comprehensive research strategy, we reviewed articles indexed in PubMed and African Journals Online (AJOL) to identify studies of familial BC in Africa. Specifically, we searched for family-based, study design papers on BC in each country in Africa using the following keywords: breast cancer, family-studies, hereditary, genetic, gene, mutations, and Africa. We excluded case-control, and registry studies, and clinical trials. We extracted relevant information from each study using standardized criteria: number of first- and second-degree relatives affected by BC, mutations, genetic variations, and polymorphisms. Results: A total of 12 out of 727 studies met our inclusion criteria. 80% of these studies were published after the year 2010. There were 9 publications from North Africa evaluating 191 families in total. One study reported novel breast cancer candidate genes: MMS19, DNAH3, POLK and KATB6 and nine publications investigated the mutation spectrum of BRCA genes. One publication from West Africa and one publication from Southern Africa included 1 and 219 families, respectively. All the studies done in these two regions reported targeted genomic screening for only BRCA genes. No study was done in Central and East Africa. Conclusions: There is paucity of family-based studies of breast cancer in Africa. Given the high level of heterogeneity in African genomes, these types of studies may be needed to identify high penetrance, germline mutations to better understand hereditary BC risk and ultimately develop a multigene panel testing to for diagnosis of heritable BC in this population.

Mutational Landscape for Indian Hereditary Breast and Ovarian Cancer Cohort Suggests Need for Identifying Population Specific Genes and Biomarkers for Screening

BackgroundBreast and ovarian cancers are the most prevalent cancers and one of the leading causes of death in Indian women. The healthcare burden of breast and ovarian cancers and the rise in mortality rate are worrying and stress the need for early detection and treatment.MethodsWe performed amplicon sequencing of 144 cases who had breast/ovarian cancer disease (total 137 cases are patients and seven are tested for BRCA1/2 carrier) Using our custom designed gene panel consisting of 14 genes, that are associated with high to moderate risk of breast and ovarian cancers. Variants were called using Torrent Variant Caller and were annotated using ThermoFisher’s Ion Reporter software. Classification of variants and their clinical significance were identified by searching the variants against ClinVar database.ResultsFrom a total of 144 cases, we were able to detect 42 pathogenic mutations in [40/144] cases. Majority of pathogenic mutations (30/41) were detected in BRCA1 gene, while (7/41) pathogenic mutations were detected in BRCA2 gene, whereas, (2/41) pathogenic mutations were detected in TP53 gene and BRIP1, PALB2, and ATM genes respectively. So, BRCA genes contributed 88.09% of pathogenic mutations, whereas non-BRCA genes contributed 11.91% of pathogenic mutations. We were also able to detect 25 VUS which were predicted to be damaging by in silico prediction tools.ConclusionEarly detection of cancers in the Indian population can be done by genetic screening using customized multi-gene panels. Indications of our findings show that in the Indian population, apart from the common BRCA genes, there are other genes that are also responsible for the disease. High frequency mutations detected in the study and variants of uncertain significance predicted to be damaging by in silico pathogenicity prediction tools can be potential biomarkers of hereditary breast and ovarian cancer in Indian HBOC patients.