Screening of exon 11 of BRCA1 gene using the high resolution melting approach for diagnosis in Moroccan breast cancer patients

Analysis of BRCA1 germline variants (exons 5, 11 and 20) in breast cancer families from Libya

Breast cancer (BC) is a leading cause of cancer deaths in Libyan women. BRCA1 variants differ globally due to the diversity of genetic makeup and populations history. Their distribution, prevalence, and significance in Libyans remain largely unexplored. This study investigated the characteristics and distribution of BRCA1 variants in exons 5, 11, and 20 in Libyan families with BC. Thirty-six BC patients at ≤ 45 years, between 46-50 years and with a family history of breast, ovarian, pancreatic or prostate cancer in close relatives, or with triple-negative BC, were selected from 33 unrelated families during 2018-2020 at the National Cancer Institute, Sabratha, Libya. From these 33 families, 20 women (18 BC patients and two unaffected) were screened for BRCA1 exons 5, 11 and 20 using Sanger sequencing. All families completed an epidemiology and family history questionnaire. Twenty-seven variants (26 in exon 11 and 1 in exon 20, minor allele frequency of < 0.01) were detected in 10 of 18 unrelated families (55.6%.) Among the 27 variants, 26 (96%) were heterozygous. A frameshift pathogenic variant, c.2643del, and one novel variant c.1366A>G were identified. Furthermore, seven variants with unknown clinical significance were detected: c.1158T>A, c.1346C>G, c.1174C>G, c.3630 G>T, c.3599A>T, and c.3400 G>C in exon 11, and c.5244T>A in exon 20. Six variants with conflicting pathogenicity interpretations, c. 3460T>A, c. 3572 G>A, c. 3700 G>C, c. 1246C>G, c. 1344C>G, and c. 1054 G>A, were also identified. Twelve benign/likely benign variants were identified. Rare BRCA1 variants that have not been reported in North Africa were found in Libyan patients. These findings provide preliminary insights into the BRCA1 variants that could contribute to hereditary BC risk in Libyans. Further functional, computational, and population analyses are essential to determine their significance and potential impact on BC risk, which could ultimately lead to more personalized management strategies.

Prevalence of Clinically Relevant Germline BRCA Variants in a Large Unselected South African Breast and Ovarian Cancer Cohort: A Public Sector Experience

Breast cancer is a multifaceted disease that currently represents a leading cause of death in women worldwide. Over the past two decades (1998–2020), the National Health Laboratory Service’s Human Genetics Laboratory in central South Africa screened more than 2,974 breast and/or ovarian cancer patients for abnormalities characteristic of the widely known familial breast cancer genes, Breast Cancer gene 1 (BRCA1) and Breast Cancer gene 2 (BRCA2). Patients were stratified according to the presence of family history, age at onset, stage of the disease, ethnicity and mutation status relative to BRCA1/2. Collectively, 481 actionable (likely-to pathogenic) variants were detected in this cohort among the different ethnic/racial groups. A combination of old (pre-2014) and new (post-2014) laboratory techniques was used to identify these variants. Additionally, targeted genotyping was performed as translational research revealed the first three recurrent South African pathogenic variants, namely BRCA1 c.1374del (legacy name 1493delC), BRCA1 c.2641G&gt;T (legacy name E881X) and BRCA2 c.7934del (legacy name 8162delG). This initial flagship study resulted in a cost-effective diagnostic test that enabled screening of a particular ethnic group for these variants. Since then, various non-Afrikaner frequent variants were identified that were proven to represent recurrent variants. These include BRCA2 c.5771_5774del (legacy name 5999del4) and BRCA2 c.582G&gt;A, both Black African founder mutations. By performing innovative translational research, medical science in South Africa can adopt first-world technologies into its healthcare context as a developing country. Over the past two decades, the progress made in the public sector enabled a pivotal shift away from population-directed genetic testing to the screening of potentially all breast and ovarian cancer patients, irrespective of ethnicity, family history or immunohistochemical status. The modifications over the years complied with international standards and guidelines aimed at universal healthcare for all. This article shares all the cohort stratifications and the likely-to pathogenic variants detected.

A review on the genetic polymorphisms and susceptibility of cancer patients in Bangladesh

Cancer is one of the major health burdens worldwide, and genetic polymorphisms in individuals are closely associated with cancer susceptibility. Like in many other developing countries, the risk of cancer is increasing among Bangladeshi population. Genetic polymorphisms in xenobiotic metabolic enzymes (CYP1A1, CYP2A6, CYP3A4, CYP3A5, NAT2, SULT1A), cell cycle regulatory proteins (TP53, HER2, MDM2, miR-218-2, TGFB), cell signaling protein (CDH1), DNA repair proteins (BRCA1, BRCA2, EXO1, RAD51, XRCC2, ECCR1, ERCC4, XPC, ERCC2), and others (HLA-DRB1, INSIG2, GCNT1P5) have been found to be associated with various cancers like cancers of breast, bladder, cervix, colon, lung, prostate, etc. in different studies with Bangladeshi population. In this review article, we have discussed these gene polymorphisms associated with cancers in the Bangladeshi population, and also made a comparison with other ethnic groups. This will probably be helpful in understanding drug effects, drug resistance, and personalized medicine in the population of this region.

Prevalence of specific and recurrent/founder pathogenic variants in BRCA genes in breast and ovarian cancer in North Africa

Background

Elucidation of specific and recurrent/founder pathogenic variants (PVs) in BRCA (BRCA1 and BRCA2) genes can make the genetic testing, for breast cancer (BC) and/or ovarian cancer (OC), affordable for developing nations.

Methods

To establish the knowledge about BRCA PVs and to determine the prevalence of the specific and recurrent/founder variants in BRCA genes in BC and/or OC women in North Africa, a systematic review was conducted in Morocco, Algeria, and Tunisia.

Results

Search of the databases yielded 25 relevant references, including eleven studies in Morocco, five in Algeria, and nine in Tunisia. Overall, 15 studies investigated both BRCA1 and BRCA2 genes, four studies examined the entire coding region of the BRCA1 gene, and six studies in which the analysis was limited to a few BRCA1 and/or BRCA2 exons. Overall, 76 PVs (44 in BRCA1 and32 in BRCA2) were identified in 196 BC and/or OC patients (129 BRCA1 and 67 BRCA2 carriers). Eighteen of the 76 (23.7%) PVs [10/44 (22.7%) in BRCA1 and 8/32 (25%) in BRCA2] were reported for the first time and considered to be novel PVs. Among those identified as unlikely to be of North African origin, the BRCA1 c.68_69del and BRCA1 c.5266dupC Jewish founder alleles and PVs that have been reported as recurrent/founder variants in European populations (ex: BRCA1 c.181T>G, BRCA1 c1016dupA). The most well characterized PVs are four in BRCA1 gene [c.211dupA (14.7%), c.798_799detTT (14%), c.5266dup (8.5%), c.5309G>T (7.8%), c.3279delC (4.7%)] and one in BRCA2 [c.1310_1313detAAGA (38.9%)]. The c.211dupA and c.5309G>T PVs were identified as specific founder variants in Tunisia and Morocco, accounting for 35.2% (19/54) and 20.4% (10/49) of total established BRCA1 PVs, respectively. c.798_799delTT variant was identified in 14% (18/129) of all BRCA1 North African carriers, suggesting a founder allele. A broad spectrum of recurrent variants including BRCA1 3279delC, BRCA1 c.5266dup and BRCA2 c.1310_1313detAAGA was detected in 42 patients. BRCA1 founder variants explain around 36.4% (47/129) of BC and outnumber BRCA2 founder variants by a ratio of ≈3:1.

Conclusions

Testing BC and/or OC patients for the panel of specific and recurrent/founder PVs might be the most cost-effective molecular diagnosis strategy.

BRCA1 gene polymorphism and finger dermatoglyphic patterns in Ghanaian breast cancer patients: a quantitative cross-sectional approach

Introduction

breast cancer development is linked to mutant single nucleotide polymorphism of breast cancer type 1 (BRCA1) gene usually harboured within exon 11. It has also been linked to finger dermatoglyphics where certain patterns have been associated with breast cancer. This study suggests a possible relationship between finger dermatoglyphic patterns and single nucleotide polymorphism of BRCA1 gene.

Methods

in a quantitative cross-sectional approach, finger dermatoglyphic patterns were obtained using the ink method from 70 female breast cancer patients and 70 age-matched apparently healthy females. Approximately 5 ml of venous blood was obtained from each participant from which DNA was extracted from the white blood cells collected after centrifugation. DNA was amplified and sequenced and the data aligned with the wildtype template of BRCA1 gene. Fingerprint patterns were analyzed with Chi-square. Mean frequency of fingerprint patterns was analyzed with independent student's t-test. Differences in data set with p<0.05 were statistically significant.

Results

luminal B was the predominant breast cancer molecular subtype among the patients. The predominant fingerprint pattern among breast cancer participants was the loop. Six or more loops had higher frequency among breast cancer females. The predominant BRCA1 gene variant locations were c.34311, c.34320, and c.34321 with c.34311A>C being the predominant variant. Higher percentage frequency of six or more loops in relation to c.34311A>C was observed in apparently healthy females compared to breast cancer females.

Conclusion

the study reports for the very first time in Ghana, BRCA1 gene variants and finger dermatoglyphics among breast cancer patients. Although the results are preliminary and inconclusive it creates an avenue for extended studies.

A Review of Cancer Genetics and Genomics Studies in Africa

Cancer is the second leading cause of death globally and is projected to overtake infectious disease as the leading cause of mortality in Africa within the next two decades. Cancer is a group of genomic diseases that presents with intra- and inter-population unique phenotypes, with Black populations having the burden of morbidity and mortality for most types. At large, the prevention and treatment of cancers have been propelled by the understanding of the genetic make-up of the disease of mostly non-African populations. By the same token, there is a wide knowledge gap in understanding the underlying genetic causes of, and genomic alterations associated with, cancer among black Africans. Accordingly, we performed a review of the literature to survey existing studies on cancer genetics/genomics and curated findings pertaining to publications across multiple cancer types conducted on African populations. We used PubMed MeSH terms to retrieve the relevant publications from 1990 to December 2019. The metadata of these publications were extracted using R text mining packages: RISmed and Pubmed.mineR. The data showed that only 0.329% of cancer publications globally were on Africa, and only 0.016% were on cancer genetics/genomics from Africa. Although the most prevalent cancers in Africa are cancers of the breast, cervix, uterus, and prostate, publications representing breast, colorectal, liver, and blood cancers were the most frequent in our review. The most frequently reported cancer genes were BRCA1, BRCA2, and TP53. Next, the genes reported in the reviewed publications’ abstracts were extracted and annotated into three gene ontology classes. Genes in the cellular component class were mostly associated with cell part and organelle part, while those in biological process and molecular function classes were mainly associated with cell process, biological regulation, and binding, and catalytic activity, respectively. Overall, this review highlights the paucity of research on cancer genomics on African populations, identified gaps, and discussed the need for concerted efforts to encourage more research on cancer genomics in Africa.

Fluorometric determination of the breast cancer 1 gene based on the target-induced conformational change of a DNA template for copper nanoclusters

The breast cancer 1 (BRCA1) gene is a tumor suppressor gene, whose mutation is closely related to breast cancer. Therefore, the sensitive detection of the BRCA1 gene is extremely important for human health, particularly for women. In this study, a label-free fluorescent method based on hairpin DNA-templated copper nanoclusters (CuNCs) was for the first time developed for the detection of the BRCA1 gene. In the absence of target DNA, the detection system showed a strong red emission and produced a high emission peak. However, in the presence of the BRCA1 gene, the DNA probe hybridized with the BRCA1 gene and conformation of the DNA probe changed. As a result, the amount of produced CuNCs decreased and a low emission peak was obtained. The fluorescence intensity of the detection system was linearly correlated with the concentration of the BRCA1 gene ranging from 2 nM to 600 nM. The detectable limit was 2 nM for the BRCA1 gene assay, which was comparable with those reported by other non-amplifying sensors. Moreover, the developed method showed satisfactory recoveries for the BRCA1 gene assay in the bovine serum. The DNA-templated CuNC-based fluorescent assay thus offered a promising platform for the diagnosis of a breast cancer biomarker.

Screening of BRCA1/2 genes mutations and copy number variations in patients with high risk for hereditary breast and ovarian cancer syndrome (HBOC)

Background

Hereditary breast and ovarian cancer (HBOC) is an autosomal dominant inherited cancer susceptibility disorder. Both BRCA1 and BRCA2 genes are considered as high penetrance genes of this syndrome. The identification of BRCA1/2 genetic alterations before cancer development, grant patients the chance to benefit from various medical cancer prevention approaches. Therefore, the appearance of recent advanced technologies in molecular analysis such as next generation sequencing has simplified full BRCA1/2 analysis.

Many attempts took place in hope of understanding the molecular germline spectrum of these two genes in Moroccan HBOC patients. However, most of the past projects focused only on young breast cancer cases, lacked ovarian cancer cases in their cohort and only a limited number of these studies were able to analyze the entire exons or copy number variations for both genes.

In attempt of gaining more information regarding the molecular profile of BRCA1/2 in HBOC, we conducted a study in which we analyze their molecular profile on selected Moroccan patients suspected of having HBOC syndrome.

Methods

In this study we obtained blood samples from 64 selected Moroccan patients, who suffered from Breast and/or ovarian cancer and had a strong family history for cancer. To analyze BRCA1/2 punctual variants and copy number variations, we used the Ion Personal Genome Machine (PGM) and Oncomine BRCA1/2 research assay panel. Afterward, we correlated the molecular results with the clinic-pathologic data using IBM SPSS Statistics ver 2.

Results

From the 64 selected cases, Forty-six had breast cancer, fifteen had ovarian cancer and three had both breast and ovarian cancer. The molecular analysis revealed that 18 patients from the 64 harbored a pathogenic variant (28%). Twelve had six different BRCA1 pathogenic variants and six had six different BRCA2 pathogenic variants. In this study, we report four pathogenic variants that to the best of our knowledge has never been reported in the Moroccan population before. Regarding copy number variation analysis, No CNV was detected in both genes for all the 64 successfully sequenced and analyzed patients in our cohort.

Conclusion

Work like the present has an important implication on public health and science. It is critical that molecular profiling studies are performed on underserved and understudied population like Morocco.

Identification of Mutation in Exon11 of BRCA1 Gene in Bangladeshi Patients with Breast Cancer

Background:

Worldwide, breast cancer is the leading cause of cancer death in female, in Bangladesh breast cancer is the second leading cancer in both sexes, and in women it occupied the top position. Highly penetrant mutations in BRCA1 gene constitute high risk of breast cancer. The spectrum of BRCA1 gene mutations varies in different population. The objective of this study was to identify mutation in exon11 of BRCA1 gene in Bangladeshi breast cancer patients.

Methods:

Genomic DNA was extracted from the histopathologically diagnosed formalin fixed paraffin embedded (FFPE) breast cancer tissues of 65 adult female patients. Two regions of exon11 of the BRCA1 gene were amplified and the amplicons were sequenced using Sanger sequencing. The sequenced nucleotides were analyzed and blast using NCBI nucleoblast. Selected demographic, reproductive and medical histories were collected and analyzed using SPSS version 20.

Results:

The mean age of the patients was 46 years and the mean age at diagnosis was 44.64 years. The patients were married and had 2.65 ± 1.22 children except one was nulliparous, the mean age of menarche was 12.67 years. All patients had children, breastfed the babies for an average 1.5 years. Only 13.6% of the patients had hypertension and the rest had no comorbidity. The family history for cancer (breast and other cancer) was negative. Three novel mutations were found in a patient. Two among the three mutant sequences had effect on amino acid coding (DNA sequence change g.852G>C and g.709G>A and amino acid changes p.Gln284His and p.Glu237Lys respectively).

Conclusion:

We found three novel mutations in Bangladeshi breast cancer patients. This finding indicates the necessity to study the mutation profile of whole BRCA1 gene in our population for cancer risk prediction.

High-resolution melting analysis for rapid and sensitive NOTCH1 screening in chronic lymphocytic leukemia

Chronic lymphocytic leukemia (CLL) is a biological and clinical heterogeneous disease. Activating mutations of NOTCH1 have been implicated to be associated with adverse prognosis in CLL. The objective of the present study was to develop an effective high-resolution melting (HRM) assay for detecting NOTCH1 mutations. Genomic DNA (gDNA) extracted from 133 CLL patients was screened by HRM assay, and the results were compared with the data obtained using direct sequencing. The relative sensitivity of the HRM assay and direct sequencing was evaluated using diluted gDNA with different NOTCH1 mutational frequencies. The HRM assay was able to detect and discriminate samples with NOTCH1 mutations from the wild-type template in CLL. Eight of the 133 CLL patients (6.02%) were scored positively for NOTCH1 mutations in the HRM assay. The results of the NOTCH1 mutations detected by HRM analysis achieved 100% concordance with those determined from direct sequencing. HRM had a higher sensitivity (1%) and shorter turn-around time (TAT), compared to direct sequencing. In conclusion, the HRM assay developed by us was confirmed to be a rapid, sensitive, and promising approach for high-throughput prognostic NOTCH1 screening in CLL. It enables real-time NOTCH1 evaluation, which is of great significance in clinical practice and may facilitate the decision-making of clinicians in CLL.

Identification of gene mutation in patients with osteogenesis imperfect using high resolution melting analysis

Osteogenesis imperfecta (OI), a congenital bone disorder, is caused by mutations in COL1A1 and COL1A2 genes, leading to deficiency of type I collagen. The high resolution melting (HRM) analysis has been used for detecting mutations, polymorphisms and epigenetic alteration in double-stranded DNAs. This study was to evaluate the potential application of HRM analysis for identifying gene mutations in patients with OI. This study included four children with OI and their parents and fifty normal people as controls. Blood samples were collected for HRM analysis of PCR-amplified exons and flanking DNA sequences of COL1A1 and COL1A2 genes. Direct gene sequencing was performed to validate HRM-identified gene mutations. As compared to controls, HRM analysis of samples form children with OI showed abnormal melting curves in exons 11 and 33–34 of the COL1A1 gene and exons 19 and 48 of the COL1A2 gene, which indicates the presence of heterozygous mutations in COL1A1 and COL1A2 genes. In addition to two known mutations in the COL1A2 gene, c.982G > A and c.3197G > T, sequencing analysis identified two novel mutations in the COL1A1 gene, c.2321delC and c.768dupC mutations, which function as premature stop codons. These results support future studies of applying HRM analysis as a diagnostic approach for OI.