1
|
Azim HA, Loutfy SA, Azim HA, Kamal NS, Abdel Fattah NF, Elberry MH, Abdelaziz MR, Abdelsalam M, Aziz M, Shohdy KS, Kassem L. The Landscape of BRCA Mutations among Egyptian Women with Breast Cancer. Oncol Ther 2023; 11:445-459. [PMID: 37731153 PMCID: PMC10673778 DOI: 10.1007/s40487-023-00240-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Accepted: 08/09/2023] [Indexed: 09/22/2023] Open
Abstract
BACKGROUND Deleterious germline mutations in BRCA1 and BRCA2 genes are associated with a high risk of breast and ovarian cancer. In many developing countries, including Egypt, the prevalence of BRCA1/2 mutations among women with breast cancer (BC) is unknown. AIM We aimed to determine the prevalence of deleterious germline BRCA mutations in Egyptian patients with breast cancer. METHODS We report the results of a cohort study of 81 Egyptian patients with breast cancer who were tested for germline BRCA1/2 mutations during routine clinical practice, mostly for their young age of presentation, BC subtype, or presence of family history. In addition, we searched five databases to retrieve studies that reported the prevalence of BRCA1/2 mutation status in Egyptian women with BC. A systematic review of the literature was performed, including prospective and retrospective studies. RESULTS In our patient cohort study, 12 patients (14.8%) were positive for either BRCA1/2 deleterious mutations. Moreover, 13 (16.1%) patients had a variant of unknown significance (VUS) of BRCA1/2 genes. Twelve studies were eligible for the systematic review, including 610 patients. A total of 19 deleterious germline mutations in BRCA1/2 were identified. The pooled prevalence of BRCA1/2 mutations was 40% (95% confidence interval 1-80%). CONCLUSION The reported prevalence was highly variable among the small-sized published studies that adopted adequate techniques. In our patient cohort, there was a high incidence of VUS in BRCA1/2 genes. Accordingly, there is an actual demand to conduct a prospective well-designed national study to accurately estimate the prevalence of BRCA1/2 mutations among patients with BC in Egypt.
Collapse
Affiliation(s)
- Hamdy A Azim
- Clinical Oncology Department, Kasr Alainy School of Medicine, Cairo University, Cairo, Egypt
- Medical Oncology Unit, Cairo Oncology Center, Cairo, Egypt
| | - Samah A Loutfy
- Virology and Immunology Unit, Cancer Biology Department, National Cancer Institute, Cairo University, Cairo, Egypt
- Nanotechnology Research Center, BUE, Cairo, Egypt
| | - Hatem A Azim
- Medical Oncology Unit, Cairo Oncology Center, Cairo, Egypt
| | - Nermin S Kamal
- Medical Oncology Unit, Cairo Oncology Center, Cairo, Egypt
| | - Nasra F Abdel Fattah
- Virology and Immunology Unit, Cancer Biology Department, National Cancer Institute, Cairo University, Cairo, Egypt
| | - Mostafa H Elberry
- Virology and Immunology Unit, Cancer Biology Department, National Cancer Institute, Cairo University, Cairo, Egypt
| | | | | | - Madonna Aziz
- Clinical Research Unit, Cairo Oncology Center, Cairo, Egypt
| | - Kyrillus S Shohdy
- Clinical Oncology Department, Kasr Alainy School of Medicine, Cairo University, Cairo, Egypt
- Division of Cancer Sciences, The University of Manchester, Manchester, UK
| | - Loay Kassem
- Clinical Oncology Department, Kasr Alainy School of Medicine, Cairo University, Cairo, Egypt.
- Medical Oncology Unit, Cairo Oncology Center, Cairo, Egypt.
| |
Collapse
|
2
|
Nassar A, Zekri ARN, Kamel MM, Elberry MH, Lotfy MM, Seadawy MG, Hassan ZK, Soliman HK, Lymona AM, Youssef ASED. Frequency of Pathogenic Germline Mutations in Early and Late Onset Familial Breast Cancer Patients Using Multi-Gene Panel Sequencing: An Egyptian Study. Genes (Basel) 2022; 14:106. [PMID: 36672847 PMCID: PMC9858960 DOI: 10.3390/genes14010106] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Revised: 11/23/2022] [Accepted: 12/08/2022] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND Precision oncology has been increasingly used in clinical practice and rapidly evolving in the oncology field. Thus, this study was performed to assess the frequency of germline mutations in early and late onset familial breast cancer (BC) Egyptian patients using multi-gene panel sequencing to better understand the contribution of the inherited germline mutations in BC predisposition. Moreover, to determine the actionable deleterious mutations associated with familial BC that might be used as biomarker for early cancer detection. METHODS Whole blood samples were collected from 101 Egyptian patients selected for BC family history, in addition to 50 age-matched healthy controls. A QIAseq targeted DNA panel (human BC panel) was used to assess the frequency of germline mutations. RESULTS A total of 58 patients (57.4%) out of 101 were found to have 27 deleterious germline mutations in 11 cancer susceptibility genes. Of them, 32 (31.6%) patients carried more than one pathogenic mutation and each one carried at least one pathogenic mutation. The major genes harboring the pathogenic mutations were: ATM, BRCA2, BRCA1, VHL, MSH6, APC, CHEK2, MSH2, MEN1, PALB2, and MUTYH. Thirty-one patients (30.6%) had BRCA2 mutations and twenty (19.8%) had BRCA1 mutations. Our results showed that exon 10 and exon 11 harbored 3 and 5 mutations, respectively, in BRCA1 and BRCA2 genes. Our analysis also revealed that the VHL gene significantly co-occurred with each of the BRCA2 gene (p = 0.003, event ratio 11/21), the MSH2 gene (p = 0.01, 4/10), the CHEK2 gene (p = 0.02, 4/11), and the MSH6 gene (p = 0.04, 4/12). In addition, the APC gene significantly co-occurred with the MSH2 gene (p = 0.01, 3/7). Furthermore, there was a significant mutually exclusive event between the APC gene and the ATM gene (p = 0.04, 1/36). Interestingly, we identified population specific germline mutations in genes showing potentials for targeted therapy to meet the need for incorporating precision oncology into clinical practice. For example, the mutations identified in the ATM, APC, and MSH2 genes. CONCLUSIONS Multi-gene panel sequencing was used to detect the deleterious mutations associated with familial BC, which in turns mitigate the essential need for implementing next generation sequencing technologies in precision oncology to identify cancer predisposing genes. Moreover, identifying DNA repair gene mutations, with focus on non-BRCA genes, might serve as candidates for targeted therapy and will be increasingly used in precision oncology.
Collapse
Affiliation(s)
- Auhood Nassar
- Virology and Immunology Unit, Cancer Biology Department, National Cancer Institute, Cairo University, Cairo 11976, Egypt
| | - Abdel-Rahman N. Zekri
- Virology and Immunology Unit, Cancer Biology Department, National Cancer Institute, Cairo University, Cairo 11976, Egypt
| | - Mahmoud M. Kamel
- Clinical Pathology Department, National Cancer Institute, Cairo University, Cairo 11976, Egypt
- Baheya Centre for Early Detection and Treatment of Breast Cancer, Giza 3546211, Egypt
| | - Mostafa H. Elberry
- Virology and Immunology Unit, Cancer Biology Department, National Cancer Institute, Cairo University, Cairo 11976, Egypt
| | - Mai M. Lotfy
- Virology and Immunology Unit, Cancer Biology Department, National Cancer Institute, Cairo University, Cairo 11976, Egypt
| | - Mohamed G. Seadawy
- Biological Prevention Department, Chemical Warfare, 4.5 km Suez-Cairo Rd, Almaza, Cairo 11351, Egypt
| | - Zeinab K. Hassan
- Virology and Immunology Unit, Cancer Biology Department, National Cancer Institute, Cairo University, Cairo 11976, Egypt
| | - Hany K. Soliman
- Virology and Immunology Unit, Cancer Biology Department, National Cancer Institute, Cairo University, Cairo 11976, Egypt
| | - Ahmed M. Lymona
- Surgical Oncology Department, National Cancer Institute, Cairo University, Cairo 11976, Egypt
| | - Amira Salah El-Din Youssef
- Virology and Immunology Unit, Cancer Biology Department, National Cancer Institute, Cairo University, Cairo 11976, Egypt
| |
Collapse
|
3
|
Said MB, Ayed IB, Elloumi I, Hasnaoui M, Souissi A, Idriss N, Aloulou H, Chabchoub I, Maâlej B, Driss D, Masmoudi S. Custom Next-Generation Sequencing Identifies Novel Mutations Expanding the Molecular and clinical spectrum of isolated Hearing Impairment or along with defects of the retina, the thyroid, and the kidneys. Mol Genet Genomic Med 2022; 10:e1868. [PMID: 34997822 PMCID: PMC8830811 DOI: 10.1002/mgg3.1868] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Revised: 12/16/2021] [Accepted: 12/28/2021] [Indexed: 11/28/2022] Open
Abstract
Background In the Tunisian population, the molecular analysis of hearing impairment remains based on conventional approaches, which makes the task laborious and enormously expensive. Exploration of the etiology of Hearing Impairment and the early diagnosis of causal mutations by next‐generation sequencing help significantly alleviate social and economic problems. Methods We elaborated a custom SureSelectQXT panel for next‐generation sequencing of the coding sequences of 42 genes involved in isolated hearing impairment or along with defects of the retina, the thyroid, and the kidneys. Results We report eight pathogenic variants, four of which are novel in patients with isolated hearing impairment, hearing impairment, and renal tubular acidosis, Usher syndrome and Pendred syndrome. Functional studies using molecular modeling showed the severe impact of the novel missense mutations on the concerned proteins. Basically, we identified mutations in nuclear as well as mitochondrial genes in a Tunisian family with isolated hearing impairment, which explains definitely the phenotype detected since 2006. Conclusion Our results expanded the mutation spectrum and genotype‒phenotype correlation of isolated and syndromic hearing loss and also emphasized the importance of combining both targeted next‐generation sequencing and detailed clinical evaluation to elaborate a more accurate diagnosis for hearing impairment and related phenotypes especially in North African populations.
Collapse
Affiliation(s)
- Mariem Ben Said
- Laboratory of Molecular and Cellular Screening Processes, Center of Biotechnology of Sfax, University of Sfax, Sfax, Tunisia
| | - Ikhlas Ben Ayed
- Laboratory of Molecular and Cellular Screening Processes, Center of Biotechnology of Sfax, University of Sfax, Sfax, Tunisia.,Medical Genetics Department, Hedi Chaker University Hospital of Sfax, Sfax, Tunisia
| | - Ines Elloumi
- Laboratory of Molecular and Cellular Screening Processes, Center of Biotechnology of Sfax, University of Sfax, Sfax, Tunisia
| | - Mehdi Hasnaoui
- Department of Otorhinolaryngology, Tahar Sfar University Hospital of Mahdia, Sfax, Tunisia
| | - Amal Souissi
- Laboratory of Molecular and Cellular Screening Processes, Center of Biotechnology of Sfax, University of Sfax, Sfax, Tunisia
| | - Nabil Idriss
- Department of Otorhinolaryngology, Tahar Sfar University Hospital of Mahdia, Sfax, Tunisia
| | - Hajer Aloulou
- Pediatric Department, Hedi Chaker Hospital, Sfax, Tunisia
| | - Imen Chabchoub
- Pediatric Department, Hedi Chaker Hospital, Sfax, Tunisia
| | - Bayen Maâlej
- Pediatric Department, Hedi Chaker Hospital, Sfax, Tunisia
| | - Dorra Driss
- Laboratory of Molecular and Cellular Screening Processes, Center of Biotechnology of Sfax, University of Sfax, Sfax, Tunisia
| | - Saber Masmoudi
- Laboratory of Molecular and Cellular Screening Processes, Center of Biotechnology of Sfax, University of Sfax, Sfax, Tunisia
| |
Collapse
|
4
|
Saied MH, Elkaffash D, Fadl R, Haleem RA, Refeat A, Ibrahim I, Tahoun M, Elkayal A, Tayae E. Preliminary results of targeted sequencing of BRCA1 and BRCA2 in a cohort of breast cancer families: New insight into pathogenic variants in patients and at‑risk relatives. Mol Med Rep 2021; 24:678. [PMID: 34296289 DOI: 10.3892/mmr.2021.12317] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Accepted: 05/24/2021] [Indexed: 11/06/2022] Open
Abstract
Breast cancer (BC) is the most commonly diagnosed cancer worldwide and a major health concern in Egypt. There is a known association between pathogenic variants identified in breast cancer susceptibility gene (BRCA)1 and 2 and the risk of developing BC. However, the number of studies investigating mutations in BRCA1 and BRCA2 in Egypt remains limited. Thus, the aim of the present study was to investigate the frequency of BRCA1 and BRCA2 variants in patients with BC and their relatives. For this purpose, 11 families (11 patients and 16 relatives) were included in the present study. BRCA1 and BRCA2 variants were investigated using the Ion S5 next‑generation sequencer. It was found that pathogenic variants were more frequent in patients with familial BC (FBC) than in those with sporadic BC, with 71% of variants in BRCA2, including the first reported identification of c.9089del, c.5583_5584dup, c.8243G>A and c.7976G>A pathogenic variants in Egyptian patients with BC. Pathogenic variants in relatives were confined to FBC c.1278delA, c.1960_1961del, and c.1224delT, with a higher incidence of variants of uncertain significance (VUS), such as BRCA2 intron 2 c.68‑16delT. Of note, two cold spot benign variants, c.3113A>G and c.4837A>G, were repeatedly found (67%) in patients and relatives. In conclusion, to the best of our knowledge, novel pathogenic variants and VUS in Egyptian patients with BC and their high‑risk relatives were identified for the first time in the present study. These findings should be integrated with other genomic data concerning Egyptian families and carefully interpreted during genetic counseling.
Collapse
Affiliation(s)
- Marwa H Saied
- Department of Clinical Pathology, Faculty of Medicine, Alexandria University, Alexandria 21131, Egypt
| | - Dalal Elkaffash
- Department of Clinical Pathology, Faculty of Medicine, Alexandria University, Alexandria 21131, Egypt
| | - Reham Fadl
- Department of Clinical Pathology, Faculty of Medicine, Alexandria University, Alexandria 21131, Egypt
| | - Reham Abdel Haleem
- Department of Clinical Pathology, Faculty of Medicine, Alexandria University, Alexandria 21131, Egypt
| | - Amal Refeat
- Department of Clinical Pathology, Faculty of Medicine, Alexandria University, Alexandria 21131, Egypt
| | - Inas Ibrahim
- Department of Pathology, Faculty of Medicine, Alexandria University, Alexandria 21131, Egypt
| | - Mona Tahoun
- Department of Clinical Pathology, Faculty of Medicine, Alexandria University, Alexandria 21131, Egypt
| | - Alyaa Elkayal
- Department of Clinical Pathology, Faculty of Medicine, Alexandria University, Alexandria 21131, Egypt
| | - Eman Tayae
- Department of Clinical Pathology, Faculty of Medicine, Alexandria University, Alexandria 21131, Egypt
| |
Collapse
|
5
|
Rotimi SO, Rotimi OA, Salhia B. A Review of Cancer Genetics and Genomics Studies in Africa. Front Oncol 2021; 10:606400. [PMID: 33659210 PMCID: PMC7917259 DOI: 10.3389/fonc.2020.606400] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Accepted: 12/14/2020] [Indexed: 12/24/2022] Open
Abstract
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.
Collapse
Affiliation(s)
- Solomon O Rotimi
- Department of Translational Genomics, Keck School of Medicine, University of Southern California, Los Angeles, CA, United States.,Department of Biochemistry, Covenant University, Ota, Nigeria
| | - Oluwakemi A Rotimi
- Department of Translational Genomics, Keck School of Medicine, University of Southern California, Los Angeles, CA, United States.,Department of Biochemistry, Covenant University, Ota, Nigeria
| | - Bodour Salhia
- Department of Translational Genomics, Keck School of Medicine, University of Southern California, Los Angeles, CA, United States.,Norris Comprehensive Cancer Centre, University of Southern California, Los Angeles, CA, United States
| |
Collapse
|
6
|
AbdelHamid SG, Zekri ARN, AbdelAziz HM, El-Mesallamy HO. BRCA1 and BRCA2 truncating mutations and variants of unknown significance in Egyptian female breast cancer patients. Clin Chim Acta 2020; 512:66-73. [PMID: 33278427 DOI: 10.1016/j.cca.2020.11.023] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Revised: 11/24/2020] [Accepted: 11/26/2020] [Indexed: 12/24/2022]
Abstract
BACKGROUND Breast cancer is the most common malignancy among women worldwide and the leading cause of cancer death in economically developing countries. We sought to study the contribution of BRCA1/2 mutations to the burden of breast cancer in Egypt. PATIENTS AND METHODS 103 Egyptian female breast cancer patients, unselected for age of onset or family history, were included in the study. Mutational screening of some exons of BRCA1/2 genes was performed using High Resolution Melting analysis followed by direct sequencing of detected variants. RESULTS Twenty sequence variants were identified. According to the American College of Medical Genetics and Genomics and the Association for Molecular Pathology (ACMG/AMP) guidelines, 8 variants were classified as pathogenic (Class 5), 1 as likely pathogenic and 11 as variants of unknown significance (Class 3). The pathogenic variants comprised 5 novel frameshift mutations; BRCA1 c.5205delA and BRCA2 (c.3641delT, c.3291dupT, c.3292delA, and c.787dupA) mutations; 1 novel nonsense mutation (BRCA2 c.3280A>T) and 2 previously described missense mutations (BRCA1 c.117T>G, c.110C>A). CONCLUSION This study provides the results of our attempt to delineate the genetic aspect of breast cancer among the Egyptian population and emphasizes the necessity of implementing screening strategies for early diagnosis and counseling for breast cancer in Egypt.
Collapse
Affiliation(s)
- Sherihan G AbdelHamid
- Department of Biochemistry, Faculty of Pharmacy, Ain Shams University, Cairo, Egypt.
| | - Abdel-Rahman N Zekri
- Virology and Immunology Unit, Cancer Biology Department, National Cancer Institute, Cairo University, Giza, Egypt
| | - Hany M AbdelAziz
- Department of Clinical Oncology, Faculty of Medicine, Ain Shams University, Cairo, Egypt
| | - Hala O El-Mesallamy
- Department of Biochemistry, Faculty of Pharmacy, Ain Shams University, Cairo, Egypt; Dean of Faculty of Pharmacy, Sinai University, Egypt
| |
Collapse
|
7
|
Wang Y, Chen Y, Xiao S, Fu K. Integrated Analysis of the Functions and Prognostic Values of RNA-Binding Proteins in Colorectal Cancer. Front Cell Dev Biol 2020; 8:595605. [PMID: 33224957 PMCID: PMC7674310 DOI: 10.3389/fcell.2020.595605] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Accepted: 10/08/2020] [Indexed: 01/10/2023] Open
Abstract
Colorectal cancer (CRC) is one of the most common malignant tumors. Selecting effective treatment for CRC patients, especially in the early stages, remains a challenge because of the lack of adequate biomarkers. Recent evidence suggests that RNA-binding proteins (RBPs) play a vital role in development and progression of carcinogenesis. However, their mechanisms in cancer progression are still limited. The role of RBPs in CRC has been poorly understood. There were 1,542 reported RBPs analyzed between CRC tissues and normal tissues using the Wilcoxon test to identify differentially expressed RBPs (DE RBPs). Then, the potential functions and the prognostic value of these DE RBPs were explored through systematic bioinformatics analysis. There were 177 DE RBPs identified between CRC tissues and normal tissues. A protein–protein interaction network was constructed based on DE RBPs, and critical modules were screened. A regulatory network between prognostic DE RBPs and differentially expressed transcription factors was constructed. Besides, a risk signature was built based on prognostic DE RBPs, which is able to predict overall survival of CRC patients with high accuracy. In conclusion, the results provided a comprehensive understanding of the functions of RBPs in CRC, as well as an RBP-related prognostic signature.
Collapse
Affiliation(s)
- Ya Wang
- Institute of Molecular Precision Medicine and Hunan Key Laboratory of Molecular Precision Medicine, Xiangya Hospital, Central South University, Changsha, China.,Department of General Surgery, Xiangya Hospital, Central South University, Changsha, China
| | - Yuqiao Chen
- Institute of Molecular Precision Medicine and Hunan Key Laboratory of Molecular Precision Medicine, Xiangya Hospital, Central South University, Changsha, China.,Department of General Surgery, Xiangya Hospital, Central South University, Changsha, China
| | - Shuai Xiao
- Department of Gastrointestinal Surgery and Institute of Clinical Medicine, The First Affiliated Hospital, University of South China, Hengyang, China
| | - Kai Fu
- Institute of Molecular Precision Medicine and Hunan Key Laboratory of Molecular Precision Medicine, Xiangya Hospital, Central South University, Changsha, China.,Department of General Surgery, Xiangya Hospital, Central South University, Changsha, China.,Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, China.,Hunan Key Laboratory of Animal Models for Human Diseases, Central South University, Changsha, China
| |
Collapse
|
8
|
Rotunno M, Barajas R, Clyne M, Hoover E, Simonds NI, Lam TK, Mechanic LE, Goldstein AM, Gillanders EM. A Systematic Literature Review of Whole Exome and Genome Sequencing Population Studies of Genetic Susceptibility to Cancer. Cancer Epidemiol Biomarkers Prev 2020; 29:1519-1534. [PMID: 32467344 DOI: 10.1158/1055-9965.epi-19-1551] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2019] [Revised: 03/17/2020] [Accepted: 05/13/2020] [Indexed: 01/03/2023] Open
Abstract
The application of next-generation sequencing (NGS) technologies in cancer research has accelerated the discovery of somatic mutations; however, progress in the identification of germline variation associated with cancer risk is less clear. We conducted a systematic literature review of cancer genetic susceptibility studies that used NGS technologies at an exome/genome-wide scale to obtain a fuller understanding of the research landscape to date and to inform future studies. The variability across studies on methodologies and reporting was considerable. Most studies sequenced few high-risk (mainly European) families, used a candidate analysis approach, and identified potential cancer-related germline variants or genes in a small fraction of the sequenced cancer cases. This review highlights the importance of establishing consensus on standards for the application and reporting of variants filtering strategies. It also describes the progress in the identification of cancer-related germline variation to date. These findings point to the untapped potential in conducting studies with appropriately sized and racially diverse families and populations, combining results across studies and expanding beyond a candidate analysis approach to advance the discovery of genetic variation that accounts for the unexplained cancer heritability.
Collapse
Affiliation(s)
- Melissa Rotunno
- National Cancer Institute, National Institutes of Health, U.S. Department of Health and Human Services, Bethesda, Maryland.
| | - Rolando Barajas
- National Cancer Institute, National Institutes of Health, U.S. Department of Health and Human Services, Bethesda, Maryland
| | - Mindy Clyne
- National Cancer Institute, National Institutes of Health, U.S. Department of Health and Human Services, Bethesda, Maryland
| | - Elise Hoover
- National Cancer Institute, National Institutes of Health, U.S. Department of Health and Human Services, Bethesda, Maryland
| | | | - Tram Kim Lam
- National Cancer Institute, National Institutes of Health, U.S. Department of Health and Human Services, Bethesda, Maryland
| | - Leah E Mechanic
- National Cancer Institute, National Institutes of Health, U.S. Department of Health and Human Services, Bethesda, Maryland
| | - Alisa M Goldstein
- National Cancer Institute, National Institutes of Health, U.S. Department of Health and Human Services, Bethesda, Maryland
| | - Elizabeth M Gillanders
- National Cancer Institute, National Institutes of Health, U.S. Department of Health and Human Services, Bethesda, Maryland
| |
Collapse
|
9
|
Al Hannan F, Keogh MB, Taha S, Al Buainain L. Characterization of BRCA1 and BRCA2 genetic variants in a cohort of Bahraini breast cancer patients using next-generation sequencing. Mol Genet Genomic Med 2019; 7:e00771. [PMID: 31131559 PMCID: PMC6625152 DOI: 10.1002/mgg3.771] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Revised: 01/16/2019] [Accepted: 04/18/2019] [Indexed: 12/29/2022] Open
Abstract
Background Breast cancer is the most common malignancy in women worldwide. About 5%–10% are due to hereditary predisposition. The contribution of BRCA1/2 mutations to familial breast cancer in Bahrain has not been explored. The objective of this study was to investigate the spectrum of BRCA1/2 genetic variants and estimate their frequencies in familial breast cancer. We also aim to test the efficiency of the next‐generation sequencing (NGS) as a powerful tool for detecting genetic variation within BRCA1/2 genes. Methods Twenty‐five unrelated female patients diagnosed with familial breast cancer were screened for BRCA1/2 variants. All targeted coding exons and exon–intron boundaries of BRCA1/2 genes were amplified with 167 pairs of primers by NGS. Results We have identified two deleterious BRCA1/2 variants in two patients, one in BRCA1 gene (c.4850C>A) and other in BRCA2 gene (c.67+2T>C). In addition to the deleterious variants, we identified 24 distinct missense variants of uncertain significance, 10 of them are seen to confer minor but cumulatively significant risk of breast cancer. Conclusion Our data suggest that BRCA1/2 variants may contribute to the pathogenesis of familial breast cancer in Bahrain. It also shows that NGS is useful tool for screening BRCA1/2 genetic variants of probands and unaffected relatives.
Collapse
Affiliation(s)
- Fatima Al Hannan
- Department of Basic Medical Sciences, Royal College of Surgeons in Ireland, Busaiteen, Bahrain
| | - Michael B Keogh
- Department of Basic Medical Sciences, Royal College of Surgeons in Ireland, Busaiteen, Bahrain
| | - Safa Taha
- Al Jawhara Centre for Molecular Medicine & Inherited Disorders, Arabian Gulf University, Manama, Bahrain
| | | |
Collapse
|
10
|
Hamdi Y, Boujemaa M, Ben Rekaya M, Ben Hamda C, Mighri N, El Benna H, Mejri N, Labidi S, Daoud N, Naouali C, Messaoud O, Chargui M, Ghedira K, Boubaker MS, Mrad R, Boussen H, Abdelhak S. Family specific genetic predisposition to breast cancer: results from Tunisian whole exome sequenced breast cancer cases. J Transl Med 2018; 16:158. [PMID: 29879995 PMCID: PMC5992876 DOI: 10.1186/s12967-018-1504-9] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2018] [Accepted: 05/03/2018] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND A family history of breast cancer has long been thought to indicate the presence of inherited genetic events that predispose to this disease. In North Africa, many specific epidemio-genetic characteristics have been observed in breast cancer families when compared to Western populations. Despite these specificities, the majority of breast cancer genetics studies performed in North Africa remain restricted to the investigation of the BRCA1 and BRCA2 genes. Thus, comprehensive data at a whole exome or whole genome level from local patients are lacking. METHODS A whole exome sequencing (WES) of seven breast cancer Tunisian families have been performed using a family-based approach. We focused our analysis on BC-TN-F001 family that included two affected members that have been sequenced using WES. Relevant variants identified in BC-TN-F001 have been confirmed using Sanger sequencing. Then, we conducted an integrative analysis by combining our results with those from other WES studies in order to figure out the genetic transmission model of the newly identified genes. Biological network construction and protein-protein interactions analyses have been performed to decipher the molecular mechanisms likely accounting for the role of these genes in breast cancer risk. RESULTS Sequencing, filtering strategies, and validation analysis have been achieved. For BC-TN-F001, no deleterious mutations have been identified on known breast cancer genes. However, 373 heterozygous, exonic and rare variants have been identified on other candidate genes. After applying several filters, 12 relevant high-risk variants have been selected. Our results showed that these variants seem to be inherited in a family specific model. This hypothesis has been confirmed following a thorough analysis of the reported WES studies. Enriched biological process and protein-protein interaction networks resulted in the identification of four novel breast cancer candidate genes namely MMS19, DNAH3, POLK and KATB6. CONCLUSIONS In this first WES application on Tunisian breast cancer patients, we highlighted the impact of next generation sequencing technologies in the identification of novel breast cancer candidate genes which may bring new insights into the biological mechanisms of breast carcinogenesis. Our findings showed that the breast cancer predisposition in non-BRCA families may be ethnic and/or family specific.
Collapse
Affiliation(s)
- Yosr Hamdi
- Laboratory of Biomedical Genomics and Oncogenetics, LR16IPT05, Institut Pasteur de Tunis, University of Tunis El Manar, 13, Place Pasteur-BP 74, 1002 Tunis, Tunisia
| | - Maroua Boujemaa
- Laboratory of Biomedical Genomics and Oncogenetics, LR16IPT05, Institut Pasteur de Tunis, University of Tunis El Manar, 13, Place Pasteur-BP 74, 1002 Tunis, Tunisia
| | - Mariem Ben Rekaya
- Laboratory of Biomedical Genomics and Oncogenetics, LR16IPT05, Institut Pasteur de Tunis, University of Tunis El Manar, 13, Place Pasteur-BP 74, 1002 Tunis, Tunisia
| | - Cherif Ben Hamda
- Laboratory of Bioinformatics, Biomathematics and Biostatistics, LR16IPT09, Institut Pasteur de Tunis, University of Tunis El Manar, Tunis, Tunisia
- Faculty of Sciences of Bizerte, Carthage University, Tunis, Tunisia
| | - Najah Mighri
- Laboratory of Biomedical Genomics and Oncogenetics, LR16IPT05, Institut Pasteur de Tunis, University of Tunis El Manar, 13, Place Pasteur-BP 74, 1002 Tunis, Tunisia
| | - Houda El Benna
- Department of Medical Oncology, Abderrahmane Mami Hospital, Ariana, Tunisia
| | - Nesrine Mejri
- Department of Medical Oncology, Abderrahmane Mami Hospital, Ariana, Tunisia
| | - Soumaya Labidi
- Department of Medical Oncology, Abderrahmane Mami Hospital, Ariana, Tunisia
| | - Nouha Daoud
- Department of Medical Oncology, Abderrahmane Mami Hospital, Ariana, Tunisia
| | - Chokri Naouali
- Laboratory of Biomedical Genomics and Oncogenetics, LR16IPT05, Institut Pasteur de Tunis, University of Tunis El Manar, 13, Place Pasteur-BP 74, 1002 Tunis, Tunisia
| | - Olfa Messaoud
- Laboratory of Biomedical Genomics and Oncogenetics, LR16IPT05, Institut Pasteur de Tunis, University of Tunis El Manar, 13, Place Pasteur-BP 74, 1002 Tunis, Tunisia
| | - Mariem Chargui
- Laboratory of Biomedical Genomics and Oncogenetics, LR16IPT05, Institut Pasteur de Tunis, University of Tunis El Manar, 13, Place Pasteur-BP 74, 1002 Tunis, Tunisia
| | - Kais Ghedira
- Laboratory of Bioinformatics, Biomathematics and Biostatistics, LR16IPT09, Institut Pasteur de Tunis, University of Tunis El Manar, Tunis, Tunisia
| | - Mohamed Samir Boubaker
- Laboratory of Biomedical Genomics and Oncogenetics, LR16IPT05, Institut Pasteur de Tunis, University of Tunis El Manar, 13, Place Pasteur-BP 74, 1002 Tunis, Tunisia
| | - Ridha Mrad
- Department of Human Genetics, Charles Nicolle Hospital, Tunis, Tunisia
| | - Hamouda Boussen
- Department of Medical Oncology, Abderrahmane Mami Hospital, Ariana, Tunisia
| | - Sonia Abdelhak
- Laboratory of Biomedical Genomics and Oncogenetics, LR16IPT05, Institut Pasteur de Tunis, University of Tunis El Manar, 13, Place Pasteur-BP 74, 1002 Tunis, Tunisia
| | - the PEC Consortium
- Department of Medical Oncology, Abderrahmane Mami Hospital, Ariana, Tunisia
| |
Collapse
|
11
|
Torrezan GT, de Almeida FGDSR, Figueiredo MCP, Barros BDDF, de Paula CAA, Valieris R, de Souza JES, Ramalho RF, da Silva FCC, Ferreira EN, de Nóbrega AF, Felicio PS, Achatz MI, de Souza SJ, Palmero EI, Carraro DM. Complex Landscape of Germline Variants in Brazilian Patients With Hereditary and Early Onset Breast Cancer. Front Genet 2018; 9:161. [PMID: 29868112 PMCID: PMC5949367 DOI: 10.3389/fgene.2018.00161] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2017] [Accepted: 04/17/2018] [Indexed: 12/11/2022] Open
Abstract
Pathogenic variants in known breast cancer (BC) predisposing genes explain only about 30% of Hereditary Breast Cancer (HBC) cases, whereas the underlying genetic factors for most families remain unknown. Here, we used whole-exome sequencing (WES) to identify genetic variants associated to HBC in 17 patients of Brazil with familial BC and negative for causal variants in major BC risk genes (BRCA1/2, TP53, and CHEK2 c.1100delC). First, we searched for rare variants in 27 known HBC genes and identified two patients harboring truncating pathogenic variants in ATM and BARD1. For the remaining 15 negative patients, we found a substantial vast number of rare genetic variants. Thus, for selecting the most promising variants we used functional-based variant prioritization, followed by NGS validation, analysis in a control group, cosegregation analysis in one family and comparison with previous WES studies, shrinking our list to 23 novel BC candidate genes, which were evaluated in an independent cohort of 42 high-risk BC patients. Rare and possibly damaging variants were identified in 12 candidate genes in this cohort, including variants in DNA repair genes (ERCC1 and SXL4) and other cancer-related genes (NOTCH2, ERBB2, MST1R, and RAF1). Overall, this is the first WES study applied for identifying novel genes associated to HBC in Brazilian patients, in which we provide a set of putative BC predisposing genes. We also underpin the value of using WES for assessing the complex landscape of HBC susceptibility, especially in less characterized populations.
Collapse
Affiliation(s)
- Giovana T Torrezan
- Laboratory of Genomics and Molecular Biology, International Research Center, CIPE/A.C. Camargo Cancer Center, São Paulo, Brazil.,National Institute for Science and Technology in Oncogenomics and Therapeutic Innovation, São Paulo, Brazil
| | | | - Márcia C P Figueiredo
- Laboratory of Genomics and Molecular Biology, International Research Center, CIPE/A.C. Camargo Cancer Center, São Paulo, Brazil
| | - Bruna D de Figueiredo Barros
- Laboratory of Genomics and Molecular Biology, International Research Center, CIPE/A.C. Camargo Cancer Center, São Paulo, Brazil
| | - Cláudia A A de Paula
- Laboratory of Genomics and Molecular Biology, International Research Center, CIPE/A.C. Camargo Cancer Center, São Paulo, Brazil
| | - Renan Valieris
- Laboratory of Bioinformatics and Computational Biology, International Research Center, CIPE/A.C. Camargo Cancer Center, São Paulo, Brazil
| | - Jorge E S de Souza
- Instituto de Bioinformática e Biotecnologia-2bio, Natal, Brazil.,Instituto Metrópole Digital, Federal University of Rio Grande do Norte, Natal, Brazil.,Bioinformatics Multidisciplinary Environment, Federal University of Rio Grande do Norte, Natal, Brazil
| | - Rodrigo F Ramalho
- Laboratory of Genomics and Molecular Biology, International Research Center, CIPE/A.C. Camargo Cancer Center, São Paulo, Brazil
| | - Felipe C C da Silva
- Laboratory of Genomics and Molecular Biology, International Research Center, CIPE/A.C. Camargo Cancer Center, São Paulo, Brazil
| | - Elisa N Ferreira
- Laboratory of Genomics and Molecular Biology, International Research Center, CIPE/A.C. Camargo Cancer Center, São Paulo, Brazil.,Research and Development, Fleury Group, São Paulo, Brazil
| | | | - Paula S Felicio
- Molecular Oncology Research Center, Barretos Cancer Hospital, São Paulo, Brazil
| | - Maria I Achatz
- Oncogenetics Department, A.C. Camargo Cancer Center, São Paulo, Brazil.,Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department of Health and Human Services, Bethesda, MD, United States
| | - Sandro J de Souza
- National Institute for Science and Technology in Oncogenomics and Therapeutic Innovation, São Paulo, Brazil.,Bioinformatics Multidisciplinary Environment, Federal University of Rio Grande do Norte, Natal, Brazil.,Brain Institute, Federal University of Rio Grande do Norte, Natal, Brazil
| | - Edenir I Palmero
- Molecular Oncology Research Center, Barretos Cancer Hospital, São Paulo, Brazil.,Barretos School of Health Sciences, Dr. Paulo Prata - FACISB, Barretos, Brazil
| | - Dirce M Carraro
- Laboratory of Genomics and Molecular Biology, International Research Center, CIPE/A.C. Camargo Cancer Center, São Paulo, Brazil.,National Institute for Science and Technology in Oncogenomics and Therapeutic Innovation, São Paulo, Brazil
| |
Collapse
|
12
|
Lin YY, Yu MW, Lin SM, Lee SD, Chen CL, Chen DS, Chen PJ. Genome-wide association analysis identifies a GLUL haplotype for familial hepatitis B virus-related hepatocellular carcinoma. Cancer 2017; 123:3966-3976. [PMID: 28662289 DOI: 10.1002/cncr.30851] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2017] [Revised: 05/02/2017] [Accepted: 05/08/2017] [Indexed: 12/24/2022]
Abstract
BACKGROUND A family history of liver cancer increases the risk of developing hepatocellular carcinoma (HCC) by 2-fold to 10-fold among patients with chronic hepatitis B virus (HBV). Previous genome-wide association studies have identified many possible susceptible loci associated with sporadic HBV-related HCC. However, despite family history being a well-known risk factor for HBV-related HCC, to the authors' knowledge its genetic mechanisms and associating loci remain largely unknown or unexplored, most likely due to the relative rarity of familial HCC and the difficulty of sample collection. METHODS The authors conducted a genome-wide association study with 139 male cases with familial HBV-related HCC and 139 non-HCC male controls with chronic HBV. The results were corroborated further with an independent cohort of 101 patients with familial HBV-related HCC and comparison with both the 1000 Genomes Project and the Taiwan Biobank. RESULTS A total of 51 risk single-nucleotide polymorphisms (P≤1E-04) were identified in the association analyses, which included 2 clusters of associated single-nucleotide polymorphisms and haplotypes at 1q25.3 (glutamate-ammonia ligase [GLUL]/transmembrane epididymal protein 1 [TEDDM1]/long intergenic non-protein-coding RNA 272 [LINC00272]/regulator of G-protein signaling-like 1 [RGSL1]) and 17q11.2 (solute carrier family 13 member 2 [SLC13A2]/forkhead box N1 [FOXN1]). Both the GLUL and SLC13A2/FOXN1 haplotypes have large effect sizes and were found to be different from those found from genome-wide association studies of sporadic HCCs. CONCLUSIONS To the authors' knowledge, the current study is the first genome-wide association study to identify genetic factors for familial HBV-related HCC. The results identified 2 large effect susceptible haplotypes located at GLUL and SLC13A2/FOXN1. The current study findings also suggest different genetic susceptibility between familial and sporadic HBV-related HCC. Cancer 2017;123:3966-76. © 2017 American Cancer Society.
Collapse
Affiliation(s)
- You-Yu Lin
- Graduate Institute of Clinical Medicine, National Taiwan University, Taipei, Taiwan
| | - Ming-Whei Yu
- Institute of Epidemiology and Preventive Medicine, National Taiwan University, Taipei, Taiwan
| | - Shi-Ming Lin
- Liver Research Unit, Chang Gung Memorial Hospital, Chang Gung University College of Medicine, Taipei, Taiwan
| | - Shou-Dong Lee
- Faculty of Medicine, National Yang-Ming University School of Medicine, Taipei, Taiwan.,Division of Gastroenterology, Department of Medicine, Cheng Hsin General Hospital, Taipei, Taiwan
| | - Chih-Ling Chen
- Graduate Institute of Clinical Medicine, National Taiwan University, Taipei, Taiwan
| | - Ding-Shinn Chen
- Hepatitis Research Center, National Taiwan University, Taipei, Taiwan
| | - Pei-Jer Chen
- Graduate Institute of Clinical Medicine, National Taiwan University, Taipei, Taiwan
| |
Collapse
|