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Ricciardiello R, Forleo G, Cipolla L, van Winckel G, Marconi C, Nouspikel T, Halazonetis TD, Zgheib O, Sabbioneda S. Homozygous substitution of threonine 191 by proline in polymerase η causes Xeroderma pigmentosum variant. Sci Rep 2024; 14:1117. [PMID: 38212351 PMCID: PMC10784498 DOI: 10.1038/s41598-023-51120-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2023] [Accepted: 12/31/2023] [Indexed: 01/13/2024] Open
Abstract
DNA polymerase eta (Polη) is the only translesion synthesis polymerase capable of error-free bypass of UV-induced cyclobutane pyrimidine dimers. A deficiency in Polη function is associated with the human disease Xeroderma pigmentosum variant (XPV). We hereby report the case of a 60-year-old woman known for XPV and carrying a Polη Thr191Pro variant in homozygosity. We further characterize the variant in vitro and in vivo, providing molecular evidence that the substitution abrogates polymerase activity and results in UV sensitivity through deficient damage bypass. This is the first functional molecular characterization of a missense variant of Polη, whose reported pathogenic variants have thus far been loss of function truncation or frameshift mutations. Our work allows the upgrading of Polη Thr191Pro from 'variant of uncertain significance' to 'likely pathogenic mutant', bearing direct impact on molecular diagnosis and genetic counseling. Furthermore, we have established a robust experimental approach that will allow a precise molecular analysis of further missense mutations possibly linked to XPV. Finally, it provides insight into critical Polη residues that may be targeted to develop small molecule inhibitors for cancer therapeutics.
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Affiliation(s)
- Roberto Ricciardiello
- Istituto di Genetica Molecolare "Luigi Luca Cavalli-Sforza", CNR, Pavia, Italy
- Dipartimento di Biologia e Biotecnologie 'Lazzaro Spallanzani', Università degli Studi di Pavia, Pavia, Italy
| | - Giulia Forleo
- Istituto di Genetica Molecolare "Luigi Luca Cavalli-Sforza", CNR, Pavia, Italy
| | - Lina Cipolla
- Istituto di Genetica Molecolare "Luigi Luca Cavalli-Sforza", CNR, Pavia, Italy
| | - Geraldine van Winckel
- Division of Medical Genetics, Diagnostics Department, Geneva University Hospitals, Geneva, Switzerland
| | - Caterina Marconi
- Division of Medical Genetics, Diagnostics Department, Geneva University Hospitals, Geneva, Switzerland
| | - Thierry Nouspikel
- Division of Medical Genetics, Diagnostics Department, Geneva University Hospitals, Geneva, Switzerland
| | - Thanos D Halazonetis
- Department of Molecular and Cellular Biology, University of Geneva, Geneva, Switzerland
| | - Omar Zgheib
- Division of Medical Genetics, Diagnostics Department, Geneva University Hospitals, Geneva, Switzerland.
| | - Simone Sabbioneda
- Istituto di Genetica Molecolare "Luigi Luca Cavalli-Sforza", CNR, Pavia, Italy.
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Gimeno-Valiente F, Martín-Arana J, Tébar-Martínez R, Gambardella V, Martínez-Ciarpaglini C, García-Micó B, Martínez-Castedo B, Palomar B, García-Bartolomé M, Seguí V, Huerta M, Moro-Valdezate D, Pla-Martí V, Pérez-Santiago L, Roselló S, Roda D, Cervantes A, Tarazona N. Sequencing paired tumor DNA and white blood cells improves circulating tumor DNA tracking and detects pathogenic germline variants in localized colon cancer. ESMO Open 2023; 8:102051. [PMID: 37951129 PMCID: PMC10774972 DOI: 10.1016/j.esmoop.2023.102051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Accepted: 09/22/2023] [Indexed: 11/13/2023] Open
Abstract
BACKGROUND In the setting of localized colon cancer (CC), circulating tumor DNA (ctDNA) monitoring in plasma has shown potential for detecting minimal residual disease (MRD) and predicting a higher risk of recurrence. With the tumor-only sequencing approach, however, germline variants may be misidentified as somatic variations, precluding the possibility of tracking in up to 11% of patients due to a lack of known somatic mutations. In this study, we assess the potential value of adding white blood cells (WBCs) to tumor tissue sequencing to enhance the accuracy of sequencing results. PATIENTS AND METHODS A total of 148 patients diagnosed with localized CC were prospectively recruited at the Hospital Clínico Universitario in Valencia (Spain). Employing a custom 29-gene panel, sequencing was conducted on tumor tissue, plasma and corresponding WBCs. Droplet digital PCR and amplicon-based NGS were performed on plasma samples post-surgery to track MRD. Oncogenic somatic variants were identified by annotating with COSMIC, OncoKB and an internal repository of pathogenic mutations database. A variant prioritization analysis, mainly characterized by the match of oncogenic mutations with the evidence levels defined in OncoKB, was carried out to select specific targeted therapies. RESULTS Utilizing paired tumor and WBCs sequencing, we identified somatic mutations in all patients (100%) within our cohort, compared to 89% using only tumor tissue. Consequently, the top 10 most frequently mutated genes for plasma monitoring were altered. The sequencing of WBCs identified 9% of patients with pathogenic mutations in the germline, with APC and TP53 being the most frequently mutated genes. Additionally, mutations in genes related to clonal hematopoiesis of indeterminate potential were detected in 27% of the cohort, with TP53, KRAS, and KMT2C being the most frequently altered genes. There were no observed differences in the sensitivity of monitoring MRD using ddPCR or amplicon-based NGS (p = 1). Ultimately, 41% of the patients harbored potentially targetable alterations at diagnosis. CONCLUSION The germline testing method not only enhanced sequencing results and raised the proportion of patients eligible for plasma monitoring, but also uncovered the existence of pathogenic germline variations, thereby aiding in the identification of patients at a higher risk of hereditary cancer syndromes.
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Affiliation(s)
- F Gimeno-Valiente
- Cancer Evolution and Genome Instability Laboratory, University College London Cancer Institute, London, UK
| | - J Martín-Arana
- Department of Medical Oncology, INCLIVA Biomedical Research Institute, University of Valencia, Valencia; CIBERONC, Instituto de Salud Carlos III, Madrid
| | - R Tébar-Martínez
- Department of Medical Oncology, INCLIVA Biomedical Research Institute, University of Valencia, Valencia
| | - V Gambardella
- Department of Medical Oncology, INCLIVA Biomedical Research Institute, University of Valencia, Valencia
| | - C Martínez-Ciarpaglini
- CIBERONC, Instituto de Salud Carlos III, Madrid; Department of Pathology, INCLIVA Biomedical Research Institute, University of Valencia, Valencia
| | - B García-Micó
- Department of Medical Oncology, INCLIVA Biomedical Research Institute, University of Valencia, Valencia; CIBERONC, Instituto de Salud Carlos III, Madrid
| | - B Martínez-Castedo
- Department of Medical Oncology, INCLIVA Biomedical Research Institute, University of Valencia, Valencia; CIBERONC, Instituto de Salud Carlos III, Madrid
| | - B Palomar
- Department of Pathology, INCLIVA Biomedical Research Institute, University of Valencia, Valencia
| | - M García-Bartolomé
- Department of Medical Oncology, INCLIVA Biomedical Research Institute, University of Valencia, Valencia
| | - V Seguí
- Department of Medical Oncology, INCLIVA Biomedical Research Institute, University of Valencia, Valencia
| | - M Huerta
- Department of Medical Oncology, INCLIVA Biomedical Research Institute, University of Valencia, Valencia
| | - D Moro-Valdezate
- Colorectal Surgery Unit, INCLIVA Biomedical Research Institute, Hospital Clínico Universitario de Valencia, Department of Surgery, University of Valencia, Valencia, Spain
| | - V Pla-Martí
- Colorectal Surgery Unit, INCLIVA Biomedical Research Institute, Hospital Clínico Universitario de Valencia, Department of Surgery, University of Valencia, Valencia, Spain
| | - L Pérez-Santiago
- Colorectal Surgery Unit, INCLIVA Biomedical Research Institute, Hospital Clínico Universitario de Valencia, Department of Surgery, University of Valencia, Valencia, Spain
| | - S Roselló
- Department of Medical Oncology, INCLIVA Biomedical Research Institute, University of Valencia, Valencia; CIBERONC, Instituto de Salud Carlos III, Madrid
| | - D Roda
- Department of Medical Oncology, INCLIVA Biomedical Research Institute, University of Valencia, Valencia; CIBERONC, Instituto de Salud Carlos III, Madrid
| | - A Cervantes
- Department of Medical Oncology, INCLIVA Biomedical Research Institute, University of Valencia, Valencia; CIBERONC, Instituto de Salud Carlos III, Madrid.
| | - N Tarazona
- Department of Medical Oncology, INCLIVA Biomedical Research Institute, University of Valencia, Valencia; CIBERONC, Instituto de Salud Carlos III, Madrid.
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3
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Al-Kafaji G, Jassim G, AlHajeri A, Alawadhi AMT, Fida M, Sahin I, Alali F, Fadel E. Investigation of germline variants in Bahraini women with breast cancer using next-generation sequencing based-multigene panel. PLoS One 2023; 18:e0291015. [PMID: 37656691 PMCID: PMC10473515 DOI: 10.1371/journal.pone.0291015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Accepted: 08/20/2023] [Indexed: 09/03/2023] Open
Abstract
Germline variants in BRCA1 and BRCA2 (BRCA1/2) genes are the most common cause of hereditary breast cancer. However, a significant number of cases are not linked to these two genes and additional high-, moderate- and low-penetrance genes have been identified in breast cancer. The advent of next-generation sequencing (NGS) allowed simultaneous sequencing of multiple cancer-susceptibility genes and prompted research in this field. So far, cancer-predisposition genes other than BRCA1/2 have not been studied in the population of Bahrain. We performed a targeted NGS using a multi-panel covering 180 genes associated with cancer predisposition to investigate the spectrum and frequency of germline variants in 54 women with a positive personal and/or family history of breast cancer. Sequencing analysis revealed germline variants in 29 (53.7%) patients. Five pathogenic/likely pathogenic variants in four DNA repair pathway-related genes were identified in five unrelated patients (9.3%). Two BRCA1 variants, namely the missense variant c.287A>G (p.Asp96Gly) and the truncating variant c.1066C>T (p.Gln356Ter), were detected in two patients (3.7%). Three variants in non-BRCA1/2 genes were detected in three patients (1.85% each) with a strong family history of breast cancer. These included a monoallelic missense variant c.1187G>A (p.Gly396Asp) in MUTYH gene, and two truncating variants namely c.3343C>T (p.Arg1115Ter) in MLH3 gene and c.1826G>A (p.Trp609Ter) in PMS1 gene. Other variants of uncertain significance (VUS) were also detected, and some of them were found together with the deleterious variants. In this first application of NGS-based multigene testing in Bahraini women with breast cancer, we show that multigene testing can yield additional genomic information on low-penetrance genes, although the clinical significance of these genes has not been fully appreciated yet. Our findings also provide valuable epidemiological information for future studies and highlight the importance of genetic testing, and an NGS-based multigene analysis may be applied supplementary to traditional genetic counseling.
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Affiliation(s)
- Ghada Al-Kafaji
- Department of Molecular Medicine and Al-Jawhara Centre for Molecular Medicine, Genetics, and Inherited Disorders, College of Medicine and Medical Sciences, Arabian Gulf University, Manama, Kingdom of Bahrain
| | - Ghufran Jassim
- Department of Family Medicine, Royal College of Surgeons in Ireland-Bahrain, Manama, Kingdom of Bahrain
| | - Amani AlHajeri
- Department of Genetics, Salmaniya Medical Complex, Manama, Kingdom of Bahrain
| | | | - Mariam Fida
- Bahrain Oncology Center, King Hamad University Hospital, Manama, Kingdom of Bahrain
| | - Ibrahim Sahin
- Department of Molecular Medicine and Al-Jawhara Centre for Molecular Medicine, Genetics, and Inherited Disorders, College of Medicine and Medical Sciences, Arabian Gulf University, Manama, Kingdom of Bahrain
| | - Faisal Alali
- North western Hospital, Chicago Medical School, North Chicago, Illinois, United States of America
| | - Elias Fadel
- Bahrain Oncology Center, King Hamad University Hospital, Manama, Kingdom of Bahrain
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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.
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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
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BenAyed-Guerfali D, Kifagi C, BenKridis-Rejeb W, Ammous-Boukhris N, Ayedi W, Khanfir A, Daoud J, Mokdad-Gargouri R. The Identification by Exome Sequencing of Candidate Genes in BRCA-Negative Tunisian Patients at a High Risk of Hereditary Breast/Ovarian Cancer. Genes (Basel) 2022; 13:genes13081296. [PMID: 35893033 PMCID: PMC9331434 DOI: 10.3390/genes13081296] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 07/16/2022] [Accepted: 07/19/2022] [Indexed: 12/24/2022] Open
Abstract
(1) Background: Germline variants in BRCA1/BRCA2 genes explain about 20% of hereditary breast/ovarian cancer (HBOC) cases. In the present paper, we aim to identify genetic determinants in BRCA-negative families from the South of Tunisia. (2) Methods: Exome Sequencing (ES) was performed on the lymphocyte DNA of patients negative for BRCA mutations from each Tunisian family with a high risk of HBOC. (3) Results: We focus on the canonical genes associated with HBOC and identified missense variants in DNA damage response genes, such as ATM, RAD52, and RAD54; however, no variants in PALB2, Chek2, and TP53 genes were found. To identify novel candidate genes, we selected variants harboring a loss of function and identified 17 stop-gain and 11 frameshift variants in genes not commonly known to be predisposed to HBOC. Then, we focus on rare and high-impact genes shared by at least 3 unrelated patients from each family and selected 16 gene variants. Through combined data analysis from MCODE with gene ontology and KEGG pathways, a short list of eight candidate genes (ATM, EP300, LAMA1, LAMC2, TNNI3, MYLK, COL11A2, and LAMB3) was created. The impact of the 24 selected genes on survival was analyzed using the TCGA data resulting in a selection of five candidate genes (EP300, KMT2C, RHPN2, HSPG2, and CCR3) that showed a significant association with survival. (4) Conclusions: We identify novel candidate genes predisposed to HBOC that need to be validated in larger cohorts and investigated by analyzing the co-segregation of selected variants in affected families and the locus-specific loss of heterozygosity to highlight their relevance for HBOC risk.
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Affiliation(s)
- Dorra BenAyed-Guerfali
- Center of Biotechnology of Sfax, University of Sfax, Sidi Mansour Street Km 6, BP 1177, Sfax 3038, Tunisia; (D.B.-G.); (C.K.); (N.A.-B.); (W.A.)
| | - Chamseddine Kifagi
- Center of Biotechnology of Sfax, University of Sfax, Sidi Mansour Street Km 6, BP 1177, Sfax 3038, Tunisia; (D.B.-G.); (C.K.); (N.A.-B.); (W.A.)
| | - Wala BenKridis-Rejeb
- Department of Medical Oncology, Habib Bourguiba Hospital, Sfax 3002, Tunisia; (W.B.-R.); (A.K.)
| | - Nihel Ammous-Boukhris
- Center of Biotechnology of Sfax, University of Sfax, Sidi Mansour Street Km 6, BP 1177, Sfax 3038, Tunisia; (D.B.-G.); (C.K.); (N.A.-B.); (W.A.)
| | - Wajdi Ayedi
- Center of Biotechnology of Sfax, University of Sfax, Sidi Mansour Street Km 6, BP 1177, Sfax 3038, Tunisia; (D.B.-G.); (C.K.); (N.A.-B.); (W.A.)
| | - Afef Khanfir
- Department of Medical Oncology, Habib Bourguiba Hospital, Sfax 3002, Tunisia; (W.B.-R.); (A.K.)
| | - Jamel Daoud
- Department of Radiotherapy, Habib Bourguiba Hospital, Sfax 3002, Tunisia;
| | - Raja Mokdad-Gargouri
- Center of Biotechnology of Sfax, University of Sfax, Sidi Mansour Street Km 6, BP 1177, Sfax 3038, Tunisia; (D.B.-G.); (C.K.); (N.A.-B.); (W.A.)
- Correspondence: ; Tel./Fax: +216-748-744-49
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Feltes BC, Menck CFM. Current state of knowledge of human DNA polymerase eta protein structure and disease-causing mutations. MUTATION RESEARCH. REVIEWS IN MUTATION RESEARCH 2022; 790:108436. [PMID: 35952573 DOI: 10.1016/j.mrrev.2022.108436] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Revised: 06/29/2022] [Accepted: 07/31/2022] [Indexed: 01/01/2023]
Abstract
POLη, encoded by the POLH gene, is a crucial protein for replicating damaged DNA and the most studied specialized translesion synthesis polymerases. Mutations in POLη are associated with cancer and the human syndrome xeroderma pigmentosum variant, which is characterized by extreme photosensitivity and an increased likelihood of developing skin cancers. The myriad of structural information about POLη is vast, covering dozens of different mutants, numerous crucial residues, domains, and posttranslational modifications that are essential for protein function within cells. Since POLη is key vital enzyme for cell survival, and mutations in this protein are related to aggressive diseases, understanding its structure is crucial for biomedical sciences, primarily due to its similarities with other Y-family polymerases and its potential as a targeted therapy-drug for tumors. This work provides an up-to-date review on structural aspects of the human POLη: from basic knowledge about critical residues and protein domains to its mutant variants, posttranslational modifications, and our current understanding of therapeutic molecules that target POLη. Thus, this review provides lessons about POLη's structure and gathers critical discussions and hypotheses that may contribute to understanding this protein's vital roles within the cells.
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Affiliation(s)
- Bruno César Feltes
- Department of Theoretical Informatics, Institute of Informatics, Department of Theoretical Informatics, Federal University of Rio Grande do Sul, Porto Alegre, RS Brazil; Department of Genetics, Institute of Bioscience, Federal University of Rio Grande do Sul, Porto Alegre, RS, Brazil; Department of Biophysics, Institute of Bioscience, Federal University of Rio Grande do Sul, Porto Alegre, RS, Brazil
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Boujemaa M, Mighri N, Chouchane L, Boubaker MS, Abdelhak S, Boussen H, Hamdi Y. Health influenced by genetics: A first comprehensive analysis of breast cancer high and moderate penetrance susceptibility genes in the Tunisian population. PLoS One 2022; 17:e0265638. [PMID: 35333900 PMCID: PMC8956157 DOI: 10.1371/journal.pone.0265638] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Accepted: 03/04/2022] [Indexed: 12/03/2022] Open
Abstract
Significant advances have been made to understand the genetic basis of breast cancer. High, moderate and low penetrance variants have been identified with inter-ethnic variability in mutation frequency and spectrum. Genome wide association studies (GWAS) are widely used to identify disease-associated SNPs. Understanding the functional impact of these risk-SNPs will help the translation of GWAS findings into clinical interventions. Here we aim to characterize the genetic patterns of high and moderate penetrance breast cancer susceptibility genes and to assess the functional impact of non-coding SNPs. We analyzed BRCA1/2, PTEN, STK11, TP53, ATM, BRIP1, CHEK2 and PALB2 genotype data obtained from 135 healthy participants genotyped using Affymetrix Genome-Wide Human SNP-Array 6.0. Haplotype analysis was performed using Haploview.V4.2 and PHASE.V2.1. Population structure and genetic differentiation were assessed using principal component analysis (PCA) and fixation index (FST). Functional annotation was performed using In Silico web-based tools including RegulomeDB and VARAdb. Haplotype analysis showed distinct LD patterns with high levels of recombination and haplotype blocks of moderate to small size. Our findings revealed also that the Tunisian population tends to have a mixed origin with European, South Asian and Mexican footprints. Functional annotation allowed the selection of 28 putative regulatory variants. Of special interest were BRCA1_ rs8176318 predicted to alter the binding sites of a tumor suppressor miRNA hsa-miR-149 and PALB2_ rs120963 located in tumorigenesis-associated enhancer and predicted to strongly affect the binding of P53. Significant differences in allele frequencies were observed with populations of African and European ancestries for rs8176318 and rs120963 respectively. Our findings will help to better understand the genetic basis of breast cancer by guiding upcoming genome wide studies in the Tunisian population. Putative functional SNPs may be used to develop an efficient polygenic risk score to predict breast cancer risk leading to better disease prevention and management.
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Affiliation(s)
- Maroua Boujemaa
- Laboratory of Biomedical Genomics and Oncogenetics, Institut Pasteur de Tunis, University of Tunis El Manar, Tunis, Tunisia
| | - Najah Mighri
- Laboratory of Biomedical Genomics and Oncogenetics, Institut Pasteur de Tunis, University of Tunis El Manar, Tunis, Tunisia
| | - Lotfi Chouchane
- Department of Genetic Medicine, Weill Cornell Medicine, New York, New York, United States of America
- Department of Microbiology and Immunology, Weill Cornell Medicine, New York, New York, United States of America
- Laboratory of Genetic Medicine and Immunology, Weill Cornell Medicine-Qatar, Doha, Qatar
| | - Mohamed Samir Boubaker
- Laboratory of Biomedical Genomics and Oncogenetics, Institut Pasteur de Tunis, University of Tunis El Manar, Tunis, Tunisia
- Laboratory of Human and Experimental Pathology, Institut Pasteur de Tunis, Tunis, Tunisia
| | - Sonia Abdelhak
- Laboratory of Biomedical Genomics and Oncogenetics, Institut Pasteur de Tunis, University of Tunis El Manar, Tunis, Tunisia
| | - Hamouda Boussen
- Laboratory of Biomedical Genomics and Oncogenetics, Institut Pasteur de Tunis, University of Tunis El Manar, Tunis, Tunisia
- Medical Oncology Department, Abderrahman Mami Hospital, Faculty of Medicine Tunis, University Tunis El Manar, Tunis, Tunisia
| | - Yosr Hamdi
- Laboratory of Biomedical Genomics and Oncogenetics, Institut Pasteur de Tunis, University of Tunis El Manar, Tunis, Tunisia
- Laboratory of Human and Experimental Pathology, Institut Pasteur de Tunis, Tunis, Tunisia
- * E-mail:
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8
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Gómez-Flores-Ramos L, Barraza-Arellano AL, Mohar A, Trujillo-Martínez M, Grimaldo L, Ortiz-Lopez R, Treviño V. Germline Variants in Cancer Genes from Young Breast Cancer Mexican Patients. Cancers (Basel) 2022; 14:cancers14071647. [PMID: 35406420 PMCID: PMC8997148 DOI: 10.3390/cancers14071647] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2022] [Revised: 03/03/2022] [Accepted: 03/18/2022] [Indexed: 02/05/2023] Open
Abstract
Breast cancer (BC) is one of the most frequent cancer types in women worldwide. About 7% is diagnosed in young women (YBC) less than 40 years old. In Mexico, however, YBC reaches 15% suggesting a higher genetic susceptibility. There have been some reports of germline variants in YBC across the world. However, there is only one report from a Mexican population, which is not restricted by age and limited to a panel of 143 genes resulting in 15% of patients carrying putatively pathogenic variants. Nevertheless, expanding the analysis to whole exome involves using more complex tools to determine which genes and variants could be pathogenic. We used germline whole exome sequencing combined with the PeCanPie tool to analyze exome variants in 115 YBC patients. Our results showed that we were able to identify 49 high likely pathogenic variants involving 40 genes on 34% of patients. We noted many genes already reported in BC and YBC worldwide, such as BRCA1, BRCA2, ATM, CHEK2, PALB2, and POLQ, but also others not commonly reported in YBC in Latin America, such as CLTCL1, DDX3X, ERCC6, FANCE, and NFKBIE. We show further supporting and controversial evidence for some of these genes. We conclude that exome sequencing combined with robust annotation tools and further analysis, can identify more genes and more patients affected by germline mutations in cancer.
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Affiliation(s)
- Liliana Gómez-Flores-Ramos
- CONACYT/Center for Population Health Research, National Institute of Public Health, Universidad No. 655, Cuernavaca 62100, Morelos, Mexico; (L.G.-F.-R.); (L.G.)
| | - Angélica Leticia Barraza-Arellano
- School of Medicine, Tecnologico de Monterrey, Morones Prieto Av 3000, Los Doctores, Monterrey 64710, Nuevo Leon, Mexico; (A.L.B.-A.); (R.O.-L.)
| | - Alejandro Mohar
- Unidad de Investigación Biomédica en Cáncer, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Dirección de Investigación, Instituto Nacional de Cancerología, Av. San Fernando #22, Col. Sección XVI, Delegación Tlalpan, Mexico City 14080, Mexico;
| | - Miguel Trujillo-Martínez
- Instituto Mexicano del Seguro Social, Hospital General de Zona con Medicina Familiar No. 7, Cuautla 62780, Morelos, Mexico;
| | - Lizbeth Grimaldo
- CONACYT/Center for Population Health Research, National Institute of Public Health, Universidad No. 655, Cuernavaca 62100, Morelos, Mexico; (L.G.-F.-R.); (L.G.)
| | - Rocío Ortiz-Lopez
- School of Medicine, Tecnologico de Monterrey, Morones Prieto Av 3000, Los Doctores, Monterrey 64710, Nuevo Leon, Mexico; (A.L.B.-A.); (R.O.-L.)
- The Institute for Obesity Research, Tecnologico de Monterrey, Eugenio Garza Sada Av 2501, Monterrey 64849, Nuevo Leon, Mexico
| | - Víctor Treviño
- School of Medicine, Tecnologico de Monterrey, Morones Prieto Av 3000, Los Doctores, Monterrey 64710, Nuevo Leon, Mexico; (A.L.B.-A.); (R.O.-L.)
- The Institute for Obesity Research, Tecnologico de Monterrey, Eugenio Garza Sada Av 2501, Monterrey 64849, Nuevo Leon, Mexico
- Correspondence:
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9
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Ben Aissa-Haj J, Kabbage M, Othmen H, Saulnier P, Kettiti HT, Jaballah-Gabteni A, Ferah A, Medhioub M, Khsiba A, Mahmoudi M, Maaloul A, Ben Nasr S, Chelbi E, Abdelhak S, Boubaker MS, Azzouz MM, Rouleau E. CDH1 Germline Variants in a Tunisian Cohort with Hereditary Diffuse Gastric Carcinoma. Genes (Basel) 2022; 13:genes13030400. [PMID: 35327954 PMCID: PMC8950196 DOI: 10.3390/genes13030400] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Revised: 02/08/2022] [Accepted: 02/10/2022] [Indexed: 12/24/2022] Open
Abstract
Mutational screening of the CDH1 gene is a standard treatment for patients who fulfill Hereditary Diffuse Gastric Cancer (HDGC) testing criteria. In this framework, the classification of variants found in this gene is a crucial step for the clinical management of patients at high risk for HDGC. The aim of our study was to identify CDH1 as well as CTNNA1 mutational profiles predisposing to HDGC in Tunisia. Thirty-four cases were included for this purpose. We performed Sanger sequencing for the entire coding region of both genes and MLPA (Multiplex Ligation Probe Amplification) assays to investigate large rearrangements of the CDH1 gene. As a result, three cases, all with the HDGC inclusion criteria (8.82% of the entire cohort), carried pathogenic and likely pathogenic variants of the CDH1 gene. These variants involve a novel splicing alteration, a missense c.2281G > A detected by Sanger sequencing, and a large rearrangement detected by MLPA. No pathogenic CTNNA1 variants were found. The large rearrangement is clearly pathogenic, implicating a large deletion of two exons. The novel splicing variant creates a cryptic site. The missense variant is a VUS (Variant with Uncertain Significance). With ACMG (American College of Medical Genetics and Genomics) classification and the evidence available, we thus suggest a revision of its status to likely pathogenic. Further functional studies or cosegregation analysis should be performed to confirm its pathogenicity. In addition, molecular exploration will be needed to understand the etiology of the other CDH1- and CTNNA1-negative cases fulfilling the HDGC inclusion criteria.
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Affiliation(s)
- Jihenne Ben Aissa-Haj
- Department of Human and Experimental Pathology, Institut Pasteur de Tunis, Tunis 1002, Tunisia; (M.K.); (H.T.K.); (A.J.-G.); (A.M.); (M.S.B.)
- Laboratory of Biomedical Genomics and Oncogenetics, Institut Pasteur de Tunis, University of Tunis El Manar, Tunis 1002, Tunisia;
- Correspondence:
| | - Maria Kabbage
- Department of Human and Experimental Pathology, Institut Pasteur de Tunis, Tunis 1002, Tunisia; (M.K.); (H.T.K.); (A.J.-G.); (A.M.); (M.S.B.)
- Laboratory of Biomedical Genomics and Oncogenetics, Institut Pasteur de Tunis, University of Tunis El Manar, Tunis 1002, Tunisia;
| | - Houcemeddine Othmen
- Sydney Brenner Institute for Molecular Bioscience, University of the Witwatersrand, Johannesburg 2000, South Africa;
| | - Patrick Saulnier
- Genomic Platform Molecular Biopathology Unit, URA3655 Inserm, US23 CNRS, Gustave Roussy, 94805 Villejuif, France;
| | - Haifa Tounsi Kettiti
- Department of Human and Experimental Pathology, Institut Pasteur de Tunis, Tunis 1002, Tunisia; (M.K.); (H.T.K.); (A.J.-G.); (A.M.); (M.S.B.)
- Laboratory of Biomedical Genomics and Oncogenetics, Institut Pasteur de Tunis, University of Tunis El Manar, Tunis 1002, Tunisia;
| | - Amira Jaballah-Gabteni
- Department of Human and Experimental Pathology, Institut Pasteur de Tunis, Tunis 1002, Tunisia; (M.K.); (H.T.K.); (A.J.-G.); (A.M.); (M.S.B.)
- Laboratory of Biomedical Genomics and Oncogenetics, Institut Pasteur de Tunis, University of Tunis El Manar, Tunis 1002, Tunisia;
| | - Azer Ferah
- Laboratory of Venoms and Therapeutic Biomolecules, LR16IPT08 Institut Pasteur de Tunis, University of Tunis El Manar, Tunis 1002, Tunisia;
| | - Mouna Medhioub
- Gastroenterology Department, Mohamed Tahar Maamouri Hospital, Nabeul 8000, Tunisia; (M.M.); (A.K.); (M.M.); (M.M.A.)
- Faculty of Medicine Tunis, University of Tunis El Manar, Tunis 1068, Tunisia
| | - Amal Khsiba
- Gastroenterology Department, Mohamed Tahar Maamouri Hospital, Nabeul 8000, Tunisia; (M.M.); (A.K.); (M.M.); (M.M.A.)
- Faculty of Medicine Tunis, University of Tunis El Manar, Tunis 1068, Tunisia
| | - Moufida Mahmoudi
- Gastroenterology Department, Mohamed Tahar Maamouri Hospital, Nabeul 8000, Tunisia; (M.M.); (A.K.); (M.M.); (M.M.A.)
- Faculty of Medicine Tunis, University of Tunis El Manar, Tunis 1068, Tunisia
| | - Afifa Maaloul
- Department of Human and Experimental Pathology, Institut Pasteur de Tunis, Tunis 1002, Tunisia; (M.K.); (H.T.K.); (A.J.-G.); (A.M.); (M.S.B.)
| | - Sonia Ben Nasr
- Oncology Department, Military Hospital of Tunis, Tunis 1008, Tunisia;
| | - Emna Chelbi
- Department of Pathology, Mohamed Tahar Maamouri Hospital, Nabeul 8000, Tunisia;
| | - Sonia Abdelhak
- Laboratory of Biomedical Genomics and Oncogenetics, Institut Pasteur de Tunis, University of Tunis El Manar, Tunis 1002, Tunisia;
| | - M. Samir Boubaker
- Department of Human and Experimental Pathology, Institut Pasteur de Tunis, Tunis 1002, Tunisia; (M.K.); (H.T.K.); (A.J.-G.); (A.M.); (M.S.B.)
- Laboratory of Biomedical Genomics and Oncogenetics, Institut Pasteur de Tunis, University of Tunis El Manar, Tunis 1002, Tunisia;
| | - Mohamed Mousaddak Azzouz
- Gastroenterology Department, Mohamed Tahar Maamouri Hospital, Nabeul 8000, Tunisia; (M.M.); (A.K.); (M.M.); (M.M.A.)
- Faculty of Medicine Tunis, University of Tunis El Manar, Tunis 1068, Tunisia
| | - Etienne Rouleau
- Department of Biology and Pathology-Cancer Genetics Laboratory-Gustave Roussy, 94805 Villejuif, France;
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10
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Wu N, Wei L, Li L, Li F, Yu J, Liu J. Perspectives on the role of breast cancer susceptibility gene in breast cancer. Int J Clin Oncol 2022; 27:495-511. [PMID: 35064849 DOI: 10.1007/s10147-021-02098-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Accepted: 11/26/2021] [Indexed: 11/27/2022]
Abstract
PURPOSE Breast cancer susceptibility gene 1/2 can repair damaged DNA through homologous recombination. Besides, the local immune microenvironment of breast cancer is closely linked to the prognosis of patients. But the relationship of breast cancer susceptibility gene 1/2 expression and local immunosuppressive microenvironment in breast cancer is not clear. The aim of this study was to discuss the correlation between them. METHODS The fresh primary breast tumors and paired normal tissues of 156 cases of breast cancer patients as well as peripheral blood of 156 cases among them in Tianjin Medical University Cancer Institute and Hospital from January 2014 to October 2018 were collected. The association between breast cancer susceptibility gene 1/2 germline mutation and immune status of microenvironment in situ was analyzed. RESULTS The results indicated that the germline mutation of breast cancer susceptibility gene 1/2 was inconsistent with the breast cancer susceptibility gene 1/2 protein expression, and the proportion of immune cells in patients with negative expression of breast cancer susceptibility gene 1/2 protein was higher than patients with positive expression of breast cancer susceptibility gene 1/2 protein (p < 0.05). And the expression of programmed cell death protein 1, cytotoxic T-Lymphocyte Antigen 4, programmed death ligand-1 of CD3+ T cells in patients with negative expression of breast cancer susceptibility gene 1/2 protein was higher than patients with positive expression of breast cancer susceptibility gene 1/2 protein (p < 0.05). The breast cancer susceptibility gene 1 protein expression was significantly correlated with family history of breast cancer patients (p = 0.006), local lymph node metastases (p = 0.001), and TNM staging (p ≤ 0.001). The breast cancer susceptibility gene 2 protein expression was significantly related to local lymph node metastases (p ≤ 0.001), III stage rate(p = 0.003) and molecular subtyping (p ≤ 0.001). Besides, the 5 years disease free survival was worse for G1 group and pathological III stage patients than other groups and other TNM stage patients. CONCLUSION In short, the immune therapy may be a potential therapy method for breast cancer patients with negative expression of breast cancer susceptibility gene 1/2 protein.
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Affiliation(s)
- Nan Wu
- Cancer Prevention Center, Key Laboratory of Cancer Prevention and Therapy, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tiyuanbei, Huanhuxi Rode, Hexi District, Tianjin, 300060, China
| | - Lijuan Wei
- Cancer Prevention Center, Key Laboratory of Cancer Prevention and Therapy, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tiyuanbei, Huanhuxi Rode, Hexi District, Tianjin, 300060, China
| | - Lijuan Li
- Cancer Prevention Center, Key Laboratory of Cancer Prevention and Therapy, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tiyuanbei, Huanhuxi Rode, Hexi District, Tianjin, 300060, China
| | - Fangxuan Li
- Cancer Prevention Center, Key Laboratory of Cancer Prevention and Therapy, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tiyuanbei, Huanhuxi Rode, Hexi District, Tianjin, 300060, China
| | - Jinpu Yu
- The Molecular Diagnostics, Key Laboratory of Cancer Prevention and Therapy, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tiyuanbei, Huanhuxi Rode, Hexi District, Tianjin, 300060, China.
| | - Juntian Liu
- Cancer Prevention Center, Key Laboratory of Cancer Prevention and Therapy, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tiyuanbei, Huanhuxi Rode, Hexi District, Tianjin, 300060, China.
- The Second Department of Breast Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin, 300060, China.
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11
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Song Y, Zhao F, Ma W, Li G. Hotspots and trends in liver kinase B1 research: A bibliometric analysis. PLoS One 2021; 16:e0259240. [PMID: 34735498 PMCID: PMC8568265 DOI: 10.1371/journal.pone.0259240] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Accepted: 10/15/2021] [Indexed: 11/29/2022] Open
Abstract
Introduction In the past 22 years, a large number of publications have reported that liver kinase B1 (LKB1) can regulate a variety of cellular processes and play an important role in many diseases. However, there is no systematic bibliometric analysis on the publications of LKB1 to reveal the research hotspots and future direction. Methods Publications were retrieved from the Web of Science Core Collection (WoSCC), Scopus, and PubMed databases. CiteSpace and VOSviewer were used to analysis the top countries, institutions, authors, source journals, discipline categories, references, and keywords. Results In the past 22 years, the number of LKB1 publications has increased gradually by year. The country, institution, author, journals that have published the most articles and cited the most frequently were the United States, Harvard University, Prof. Benoit Viollet, Journal of Biochemistry and Plos One. The focused research hotspot was the molecular functions of LKB1. The emerging hotspots and future trends are the clinical studies about LKB1 and co-mutated genes as biomarkers in tumors, especially in lung adenocarcinoma. Conclusions Our research could provide knowledge base, frontiers, emerging hotspots and future trends associated with LKB1 for researchers in this field, and contribute to finding potential cooperation possibilities.
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Affiliation(s)
- Yaowen Song
- Department of Radiotherapy Oncology, The First Affiliated Hospital of China Medical University, Shenyan, China
| | - Fangkun Zhao
- Department of Ophthalmology, The Fourth Affiliated Hospital of China Medical University, Shenyang, China
| | - Wei Ma
- Department of Breast Surgery, The First Affiliated Hospital of China Medical University, Shenyang, China
| | - Guang Li
- Department of Radiotherapy Oncology, The First Affiliated Hospital of China Medical University, Shenyan, China
- * E-mail:
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12
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El Saghir NS, Ghanem H, El Karak F, Farhat F, Ghosn M, Makdessi J, Chouaib K, Debs J, Tabchy AB. Management of breast cancer patients with BRCA gene mutations in Lebanon of the Middle East: perspectives and challenges. Hosp Pract (1995) 2021; 49:325-329. [PMID: 34547975 DOI: 10.1080/21548331.2021.1974678] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
BACKGROUND This commentary explores and discusses the challenges oncologists face in diagnosing and managing breast cancer patients with BRCA gene mutations in Lebanon and the Middle East. METHODS Key opinion leaders shared their recommendations to achieve better patient outcomes and satisfaction based on evidence-based medicine and their clinical experience in BRCA management. RESULTS Challenges associated with BRCA management can be divided into four main levels: physicians, patients, test, and treatment factors. More genetic counselors are to be identified given their important role in the management of individuals with BRCA gene mutations. CONCLUSION Genetic counseling, continuing education, infrastructure, testing, expertise, and financial support are needed to fulfill the unmet needs in the management of BRCA mutation carriers.
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Affiliation(s)
- Nagi S El Saghir
- Division of Hematology Oncology, American University of Beirut Medical Center, Beirut, Lebanon
| | - Hady Ghanem
- Division of Hematology Oncology, Lebanese American University Medical Center - Rizk Hospital, Beirut, Lebanon
| | - Fadi El Karak
- Department of Oncology-Hematology, School of Medicine, Saint Joseph University, Beirut, Lebanon
| | - Fadi Farhat
- Division of Hematology Oncology, Hammoud Hospital University Medical Center, Saida, Lebanon
| | - Marwan Ghosn
- Hematology Oncology Department, Faculty of Medicine, Saint Joseph University, Beirut, Lebanon
| | - Joseph Makdessi
- Hematology and Oncology Department, Saint George Hospital University Medical Center, Beirut, Lebanon
| | - Khouloud Chouaib
- Oncology Department, Medical Affairs, Pfizer Africa - Middle East Region, Lebanon
| | - Jamil Debs
- Oncology Department, Medical Affairs, Pfizer Africa - Middle East Region, Lebanon
| | - Adel B Tabchy
- Department of Hematology/Oncology, Saint-Joseph University - School of Medicine, Beirut, Lebanon
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13
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Gianni P, Matenoglou E, Geropoulos G, Agrawal N, Adnani H, Zafeiropoulos S, Miyara SJ, Guevara S, Mumford JM, Molmenti EP, Giannis D. The Fanconi anemia pathway and Breast Cancer: A comprehensive review of clinical data. Clin Breast Cancer 2021; 22:10-25. [PMID: 34489172 DOI: 10.1016/j.clbc.2021.08.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2021] [Revised: 07/17/2021] [Accepted: 08/05/2021] [Indexed: 02/08/2023]
Abstract
The development of breast cancer depends on several risk factors, including environmental, lifestyle and genetic factors. Despite the evolution of DNA sequencing techniques and biomarker detection, the epidemiology and mechanisms of various breast cancer susceptibility genes have not been elucidated yet. Dysregulation of the DNA damage response causes genomic instability and increases the rate of mutagenesis and the risk of carcinogenesis. The Fanconi Anemia (FA) pathway is an important component of the DNA damage response and plays a critical role in the repair of DNA interstrand crosslinks and genomic stability. The FA pathway involves 22 recognized genes and specific mutations have been identified as the underlying defect in the majority of FA patients. A thorough understanding of the function and epidemiology of these genes in breast cancer is critical for the development and implementation of individualized therapies that target unique tumor profiles. Targeted therapies (PARP inhibitors) exploiting the FA pathway gene defects have been developed and have shown promising results. This narrative review summarizes the current literature on the involvement of FA genes in sporadic and familial breast cancer with a focus on clinical data derived from large cohorts.
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Affiliation(s)
- Panagiota Gianni
- Department of Internal Medicine III, Hematology, Oncology, Palliative Medicine, Rheumatology and Infectious Diseases, University Hospital Ulm, Germany
| | - Evangelia Matenoglou
- Medical School, Aristotle University of Thessaloniki, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Georgios Geropoulos
- Thoracic Surgery Department, University College London Hospitals NHS Foundation Trust, London
| | - Nirav Agrawal
- Feinstein Institutes for Medical Research at Northwell Health, Manhasset, New York, NY
| | - Harsha Adnani
- Feinstein Institutes for Medical Research at Northwell Health, Manhasset, New York, NY
| | - Stefanos Zafeiropoulos
- Feinstein Institutes for Medical Research at Northwell Health, Manhasset, New York, NY; Elmezzi Graduate School of Molecular Medicine, Northwell Health, Manhasset, New York, NY
| | - Santiago J Miyara
- Feinstein Institutes for Medical Research at Northwell Health, Manhasset, New York, NY; Elmezzi Graduate School of Molecular Medicine, Northwell Health, Manhasset, New York, NY
| | - Sara Guevara
- Department of Surgery, North Shore University Hospital, Manhasset, New York, NY
| | - James M Mumford
- Department of Family Medicine, Glen Cove Hospital, Glen Cove, New York, NY; Donald and Barbara Zucker School of Medicine at Hofstra/Northwell, Hempstead, New York, NY
| | - Ernesto P Molmenti
- Feinstein Institutes for Medical Research at Northwell Health, Manhasset, New York, NY; Department of Surgery, North Shore University Hospital, Manhasset, New York, NY; Donald and Barbara Zucker School of Medicine at Hofstra/Northwell, Hempstead, New York, NY
| | - Dimitrios Giannis
- Feinstein Institutes for Medical Research at Northwell Health, Manhasset, New York, NY.
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14
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Al-Shamsi HO, Abu-Gheida I, Abdulsamad AS, AlAwadhi A, Alrawi S, Musallam KM, Arun B, Ibrahim NK. Molecular Spectra and Frequency Patterns of Somatic Mutations in Arab Women with Breast Cancer. Oncologist 2021; 26:e2086-e2089. [PMID: 34327780 DOI: 10.1002/onco.13916] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Accepted: 07/12/2021] [Indexed: 11/07/2022] Open
Abstract
BACKGROUND The role of somatic mutations in breast cancer prognosis and management continues to be recognized. However, data on the molecular profiles of Arab women are limited. MATERIALS AND METHODS This was a cross-sectional study based on medical chart review of all Arab women diagnosed with breast cancer at a single institution between 2010 and 2018 who underwent next-generation sequencing with Ampliseq 46-Gene or 50-Gene. RESULTS A total of 78 Arab women were identified, with a median age at diagnosis of 52.3 years (range: 37-82 years; 38.5% ≤50 years). The majority of patients had stage III or IV disease (74.4%). Next-generation sequencing revealed the following somatic mutation rates: TP53, 23.1%; ATM, 2.6%; IDH1, 2.6%; IDH2, 3.8%; PTEN, 7.7%; PIK3CA, 15.4%; APC, 7.7%; NPM1, 2.5%; MPL, 1.3%; JAK2, 2.5%; KIT, 7.7%; KRAS, 3.8%; and NRAS, 3.8%. CONCLUSION Our study illustrates frequencies of somatic mutations in Arab women with breast cancer and suggests potential variations from estimates reported in the Western population. These data calls for larger epidemiologic studies considering the evolving role of such mutations in prognostication and personalized management.
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Affiliation(s)
- Humaid O Al-Shamsi
- Departments of Oncology, Burjeel Cancer Institute, Burjeel Medical City, Abu Dhabi, United Arab Emirates.,Departments of Radiation Oncology, Burjeel Cancer Institute, Burjeel Medical City, Abu Dhabi, United Arab Emirates.,Innovation and Research Center, Burjeel Cancer Institute, Burjeel Medical City, Abu Dhabi, United Arab Emirates.,College of Medicine, University of Sharjah, Sharjah, United Arab Emirates
| | - Ibrahim Abu-Gheida
- Departments of Radiation Oncology, Burjeel Cancer Institute, Burjeel Medical City, Abu Dhabi, United Arab Emirates.,Innovation and Research Center, Burjeel Cancer Institute, Burjeel Medical City, Abu Dhabi, United Arab Emirates.,College of Medicine and Health Sciences, United Arab Emirates University, Abu Dhabi, United Arab Emirates
| | | | | | - Sadir Alrawi
- Departments of Oncology, Burjeel Cancer Institute, Burjeel Medical City, Abu Dhabi, United Arab Emirates
| | - Khaled M Musallam
- Innovation and Research Center, Burjeel Cancer Institute, Burjeel Medical City, Abu Dhabi, United Arab Emirates
| | - Banu Arun
- Department of Breast Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Nuhad K Ibrahim
- Department of Breast Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
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15
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Martín-Morales L, Garre P, Lorca V, Cazorla M, Llovet P, Bando I, García-Barberan V, González-Morales ML, Esteban-Jurado C, de la Hoya M, Castellví-Bel S, Caldés T. BRIP1, a Gene Potentially Implicated in Familial Colorectal Cancer Type X. Cancer Prev Res (Phila) 2020; 14:185-194. [PMID: 33115781 DOI: 10.1158/1940-6207.capr-20-0316] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Revised: 08/17/2020] [Accepted: 10/15/2020] [Indexed: 11/16/2022]
Abstract
Familial colorectal cancer Type X (FCCTX) comprises a heterogeneous group of families with an increased risk of developing colorectal cancer and other related tumors, but with mismatch repair-proficient, microsatellite-stable (MSS) tumors. Unfortunately, the genetic basis underlying their cancer predisposition remains unknown. Although pathogenic germline variants in BRIP1 increase the risk of developing hereditary ovarian cancer, the involvement of BRIP1 in hereditary colorectal cancer is still not well known. In order to identify new BRIP1 variants associated with inherited colorectal cancer, affected and nonaffected individuals from 18 FCCTX or high-risk MSS colorectal cancer families were evaluated by whole-exome sequencing, and another 62 colorectal cancer patients from FCCTX or high-risk MSS colorectal cancer families were screened by a next-generation sequencing (NGS) multigene panel. The families were recruited at the Genetic Counseling Unit of Hospital Clínico San Carlos of Madrid. A total of three different BRIP1 mutations in three unrelated families were identified. Among them, there were two frameshift variants [c.1702_1703del, p.(Asn568TrpfsTer9) and c.903del, p.(Leu301PhefsTer2)] that result in the truncation of the protein and are thus classified as pathogenic (class 5). The remaining was a missense variant [c.2220G>T, p.(Gln740His)] considered a variant of uncertain significance (class 3). The segregation and loss-of-heterozygosity studies provide evidence linking the two BRIP1 frameshift variants to colorectal cancer risk, with suggestive but not definitive evidence that the third variant may be benign. The results here presented suggest that germline BRIP1 pathogenic variants could be associated with hereditary colorectal cancer predisposition.Prevention Relevance: We suggest that BRIP1 pathogenic germline variants may have a causal role in CRC as moderate cancer susceptibility alleles and be associated with hereditary CRC predisposition. A better understanding of hereditary CRC may provide important clues to disease predisposition and could contribute to molecular diagnostics, improved risk stratification, and targeted therapeutic strategies.
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Affiliation(s)
- Lorena Martín-Morales
- Molecular Oncology Laboratory, Hospital Clínico San Carlos, IdISSC, Centro de Investigación Biomédica en Red de Oncología (CIBERONC), Madrid, Spain
| | - Pilar Garre
- Molecular Oncology Laboratory, Hospital Clínico San Carlos, IdISSC, Centro de Investigación Biomédica en Red de Oncología (CIBERONC), Madrid, Spain
| | - Víctor Lorca
- Molecular Oncology Laboratory, Hospital Clínico San Carlos, IdISSC, Centro de Investigación Biomédica en Red de Oncología (CIBERONC), Madrid, Spain
| | - Marta Cazorla
- Molecular Oncology Laboratory, Hospital Clínico San Carlos, IdISSC, Centro de Investigación Biomédica en Red de Oncología (CIBERONC), Madrid, Spain
| | - Patricia Llovet
- Molecular Oncology Laboratory, Hospital Clínico San Carlos, IdISSC, Centro de Investigación Biomédica en Red de Oncología (CIBERONC), Madrid, Spain
| | - Inmaculada Bando
- Molecular Oncology Laboratory, Hospital Clínico San Carlos, IdISSC, Centro de Investigación Biomédica en Red de Oncología (CIBERONC), Madrid, Spain
| | - Vanesa García-Barberan
- Molecular Oncology Laboratory, Hospital Clínico San Carlos, IdISSC, Centro de Investigación Biomédica en Red de Oncología (CIBERONC), Madrid, Spain
| | | | - Clara Esteban-Jurado
- Gastroenterology Department, Hospital Clínic, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Barcelona, Spain
| | - Miguel de la Hoya
- Molecular Oncology Laboratory, Hospital Clínico San Carlos, IdISSC, Centro de Investigación Biomédica en Red de Oncología (CIBERONC), Madrid, Spain
| | - Sergi Castellví-Bel
- Gastroenterology Department, Hospital Clínic, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Barcelona, Spain
| | - Trinidad Caldés
- Molecular Oncology Laboratory, Hospital Clínico San Carlos, IdISSC, Centro de Investigación Biomédica en Red de Oncología (CIBERONC), Madrid, Spain.
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16
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Suszynska M, Kozlowski P. Summary of BARD1 Mutations and Precise Estimation of Breast and Ovarian Cancer Risks Associated with the Mutations. Genes (Basel) 2020; 11:genes11070798. [PMID: 32679805 PMCID: PMC7397132 DOI: 10.3390/genes11070798] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 07/13/2020] [Accepted: 07/14/2020] [Indexed: 12/12/2022] Open
Abstract
Over the last two decades, numerous BARD1 mutations/pathogenic variants (PVs) have been found in patients with breast cancer (BC) and ovarian cancer (OC). However, their role in BC and OC susceptibility remains controversial, and strong evidence-based guidelines for carriers are not yet available. Herein, we present a comprehensive catalog of BARD1 PVs identified in large cumulative cohorts of ~48,700 BC and ~20,800 OC cases (retrieved from 123 studies examining the whole coding sequence of BARD1). Using these resources, we compared the frequency of BARD1 PVs in the cases and ~134,100 controls from the gnomAD database and estimated the effect of the BARD1 PVs on BC and OC risks. The analysis revealed that BARD1 is a BC moderate-risk gene (odds ratio (OR) = 2.90, 95% CIs:2.25–3.75, p < 0.0001) but not an OC risk gene (OR = 1.36, 95% CIs:0.87–2.11, p = 0.1733). In addition, the BARD1 mutational spectrum outlined in this study allowed us to determine recurrent PVs and evaluate the variant-specific risk for the most frequent PVs. In conclusion, these precise estimates improve the understanding of the role of BARD1 PVs in BC and OC predisposition and support the need for BARD1 diagnostic testing in BC patients.
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Affiliation(s)
| | - Piotr Kozlowski
- Correspondence: ; Tel.: +48-618-528-503 (ext. 261); Fax: +48-618-520-532
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17
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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.
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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
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Al-Ajmi A, Shamsah S, Janicijevic A, Williams M, Al-Mulla F. Novel frameshift mutation in the SACS gene causing spastic ataxia of charlevoix-saguenay in a consanguineous family from the Arabian Peninsula: A case report and review of literature. World J Clin Cases 2020; 8:1477-1488. [PMID: 32368540 PMCID: PMC7190960 DOI: 10.12998/wjcc.v8.i8.1477] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Revised: 04/09/2020] [Accepted: 04/17/2020] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Familial cases of autosomal recessive spastic ataxia of charlevoix-saguenay have not been reported in the Arabian Peninsula, although the consanguineous marriage rate is very high. We report the first family from the Arabian Peninsula harboring a novel frameshift mutation in the SACS gene.
CASE SUMMARY A 33-year-old man presented to our neurology clinic with balance problems and weakness of distal upper and lower limbs. He was previously clinically diagnosed with Friedreich's ataxia. However, the severity of polyneuropathy and the electrodiagnostic studies (EDX) findings are atypical features of Friedreich’s ataxia, and the deterioration was attributed to diabetic neuropathy. Close examination of other family members identified cerebellar ataxia, lower-limb pyramidal signs, peripheral neuropathy, and magnetic resonance imaging findings characterized by pontine linear hypointensities. Genetic testing for Friedreich’s ataxia did not yield a diagnosis. Whole exome sequencing identified a novel frameshift germline mutation in the SACS gene termed c.5824_5827delTACT using the transcript NM_014363.5, which is predicted to cause premature termination of the sacsin protein at amino acid position 1942 (p.Tyr1942Metfs*9) and disrupts the sacsin SRR3 and domains downstream from it. The mutation segregated with the disease in the family.
CONCLUSION Our data add to the spectrum of mutations in the SACS gene and argues for a need to implement suitably integrated clinical and diagnostic services, including next generation sequencing technology, to better classify ataxia in this area of the world.
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Affiliation(s)
| | - Sarah Shamsah
- Faculty of Allied Health Sciences, Kuwait University, Kuwait City 13110, Kuwait
| | | | - Michayla Williams
- Department of Genetics, Genatak Center for Genomic Medicine, Kuwait City 12000, Kuwait
| | - Fahd Al-Mulla
- Department of Genetics, Genatak Center for Genomic Medicine, Kuwait City 12000, Kuwait
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Jalkh N, Mehawej C, Chouery E. Actionable Exomic Secondary Findings in 280 Lebanese Participants. Front Genet 2020; 11:208. [PMID: 32231684 PMCID: PMC7083077 DOI: 10.3389/fgene.2020.00208] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Accepted: 02/21/2020] [Indexed: 12/30/2022] Open
Abstract
The expanded use of NGS tests in genetic diagnosis enables the massive generation of data related to each individual, among which some findings are of medical value. Over the last three and a half years, 280 unrelated Lebanese patients, presenting a wide spectrum of genetic disorders were referred to our center for genetic evaluation by WES. Molecular diagnosis was established in 56% of the cases, as was previously reported. The current study evaluates secondary findings in these patients in 59 genes, linked to conditions mostly responsive to medical interventions, as per the ACMG guidelines. Our analysis allowed us to detect 19 pathogenic/likely pathogenic variants in 24 individuals from our cohort. Dominant actionable variants were found in 17 individuals representing 6% of the studied population. Genes associated with dominant cardiac diseases were the most frequently mutated: variants were found in 2.1% of our cohort. Genetic predisposition to cancer syndromes was observed in 1.07% of the cases. In parallel to dominant disease alleles, our analysis identified a recessive pathogenic disease allele in 2.5% of the individuals included in this study. Of interest, some variants were detected in different patients from our cohort thus urging the study of their prevalence in our population and the implementation, when needed, of specific genetic testing in the neonatal screening panel. In conclusion, here we report the first study estimating the actionable pathogenic variant load in the Lebanese population. Communicating current findings to the patients will enable them to benefit from a multi-disciplinary approach. Furthermore, tailoring the ACMG guidelines to the population is suggested, especially in highly consanguineous populations where the information related to recessive alleles might be highly beneficial to patients and their families.
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Affiliation(s)
- Nadine Jalkh
- Unité de Génétique Médicale, Faculty of Medicine, Saint Joseph University, Beirut, Lebanon
| | - Cybel Mehawej
- Unité de Génétique Médicale, Faculty of Medicine, Saint Joseph University, Beirut, Lebanon
| | - Eliane Chouery
- Unité de Génétique Médicale, Faculty of Medicine, Saint Joseph University, Beirut, Lebanon
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20
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Benavides J, Suárez J, Estrada A, Bohórquez M, Ramírez C, Olaya J, Sánchez Y, Mateus G, Carvajal L, Echeverry MM. Breast cancer in six families from Tolima and Huila: BRCA1 3450del4 mutation. BIOMEDICA : REVISTA DEL INSTITUTO NACIONAL DE SALUD 2020; 40:185-194. [PMID: 32220173 PMCID: PMC7357381 DOI: 10.7705/biomedica.4673] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Accepted: 07/31/2019] [Indexed: 12/22/2022]
Abstract
Introduction: Breast cancer is a worldwide public health problem; between 5% and 10% of the cases present familial aggregation explained by genes of high risk such as BRCA1 and BRCA2. The founding origin of the deletion BRCA1 3450del4 in Colombia has been previously reported. Objective: To carry out in six families from Tolima and Huila departments a descriptive analysis of the presence of the BRCA1 3450del4 mutation associated with breast cancer and familial aggregation. Materials and methods: We conducted a descriptive and cross-sectional study of six index cases with breast cancer positive for BRCA1 3450del4 that fulfilled three of the criteria established by Jalkh, et al. The genealogical trees were made using the information of the interview data (GenoPro™, version 2016). The mutation was typified in healthy and affected relatives who agreed to participate. Results: Thirty of the 78 individuals selected by convenience in the six families presented the mutation BRCA1 3450del4 six of whom developed breast cancer, one, ovarian cancer, one ovarian and breast cancer, and one prostate cancer; 21 did not present any type of neoplasm at the time of the study. Of the 30 individuals carrying the pathogenic variant, six were men, 24 were women, and 13 of these were under 30. Conclusions: In this study of families with the deletion BRCA1 3450del4 in Tolima and Huila we confirmed its association with familial aggregation of breast cancer.
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Affiliation(s)
- Jennyfer Benavides
- Grupo de Citogenética, Filogenia y Evolución de Poblaciones, Universidad del Tolima, Ibagué, Colombia.
| | - Jonh Suárez
- Grupo de Citogenética, Filogenia y Evolución de Poblaciones, Universidad del Tolima, Ibagué, Colombia.
| | - Ana Estrada
- Grupo de Citogenética, Filogenia y Evolución de Poblaciones, Universidad del Tolima, Ibagué, Colombia.
| | - Mábel Bohórquez
- Grupo de Citogenética, Filogenia y Evolución de Poblaciones, Universidad del Tolima, Ibagué, Colombia.
| | - Carolina Ramírez
- Grupo de Citogenética, Filogenia y Evolución de Poblaciones, Universidad del Tolima, Ibagué, Colombia.
| | - Justo Olaya
- Unidad de Oncología, Hospital Universitario Hernando Moncaleano Perdomo, Neiva, Colombia.
| | - Yesid Sánchez
- Grupo de Citogenética, Filogenia y Evolución de Poblaciones, Universidad del Tolima, Ibagué, Colombia; Programa de Medicina, Universidad del Tolima, Ibagué, Colombia.
| | - Gilbert Mateus
- Grupo de Citogenética, Filogenia y Evolución de Poblaciones, Universidad del Tolima, Ibagué, Colombia; Unidad de Oncología, Hospital Federico Lleras Acosta, Ibagué, Colombia.
| | - Luis Carvajal
- Grupo de Citogenética, Filogenia y Evolución de Poblaciones, Universidad del Tolima, Ibagué, Colombia; Genome Center and Department of Biochemistry and Molecular Medicine, University of California, Davis, USA; Unidad de Oncología, Fundación Genética y Genómica, Medellín, Colombia.
| | - María Magdalena Echeverry
- Grupo de Citogenética, Filogenia y Evolución de Poblaciones, Universidad del Tolima, Ibagué, Colombia.
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21
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Maciaszek JL, Oak N, Chen W, Hamilton KV, McGee RB, Nuccio R, Mostafavi R, Hines-Dowell S, Harrison L, Taylor L, Gerhardt EL, Ouma A, Edmonson MN, Patel A, Nakitandwe J, Pappo AS, Azzato EM, Shurtleff SA, Ellison DW, Downing JR, Hudson MM, Robison LL, Santana V, Newman S, Zhang J, Wang Z, Wu G, Nichols KE, Kesserwan CA. Enrichment of heterozygous germline RECQL4 loss-of-function variants in pediatric osteosarcoma. Cold Spring Harb Mol Case Stud 2019; 5:mcs.a004218. [PMID: 31604778 PMCID: PMC6824257 DOI: 10.1101/mcs.a004218] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2019] [Accepted: 08/28/2019] [Indexed: 02/07/2023] Open
Abstract
Patients harboring germline pathogenic biallelic variants in genes involved in the recognition and repair of DNA damage are known to have a substantially increased cancer risk. Emerging evidence suggests that individuals harboring heterozygous variants in these same genes may also be at heightened, albeit lesser, risk for cancer. Herein, we sought to determine whether heterozygous variants in RECQL4, the gene encoding an essential DNA helicase that is defective in children with the autosomal recessive cancer-predisposing condition Rothmund-Thomson syndrome (RTS), are associated with increased risk for childhood cancer. To address this question, we interrogated germline sequence data from 4435 pediatric cancer patients at St. Jude Children's Research Hospital and 1127 from the National Cancer Institute Therapeutically Applicable Research to Generate Effective Treatment (TARGET) database and identified 24 (0.43%) who harbored loss-of-function (LOF) RECQL4 variants, including five of 249 (2.0%) with osteosarcoma (OS). These RECQL4 variants were significantly overrepresented in children with OS, the cancer most frequently observed in patients with RTS, as compared to 134,187 noncancer controls in the Genome Aggregation Database (gnomAD v2.1; P = 0.00087, odds ratio [OR] = 7.1, 95% CI, 2.9-17). Nine of the 24 (38%) individuals possessed the same c.1573delT (p.Cys525Alafs) variant located in the highly conserved DNA helicase domain, suggesting that disruption of this domain is central to oncogenesis. Altogether these data expand our understanding of the genetic factors predisposing to childhood cancer and reveal a novel association between heterozygous RECQL4 LOF variants and development of pediatric OS.
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Affiliation(s)
- Jamie L Maciaszek
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, USA
| | - Ninad Oak
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, USA
| | - Wenan Chen
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, USA
| | - Kayla V Hamilton
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, USA
| | - Rose B McGee
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, USA
| | - Regina Nuccio
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, USA
| | - Roya Mostafavi
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, USA
| | - Stacy Hines-Dowell
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, USA
| | - Lynn Harrison
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, USA
| | - Leslie Taylor
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, USA
| | - Elsie L Gerhardt
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, USA
| | - Annastasia Ouma
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, USA
| | - Michael N Edmonson
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, USA
| | - Aman Patel
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, USA
| | - Joy Nakitandwe
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, USA
| | - Alberto S Pappo
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, USA
| | - Elizabeth M Azzato
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, USA
| | - Sheila A Shurtleff
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, USA
| | - David W Ellison
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, USA
| | - James R Downing
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, USA
| | - Melissa M Hudson
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, USA
| | - Leslie L Robison
- Department of Epidemiology and Cancer Control, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, USA
| | - Victor Santana
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, USA
| | - Scott Newman
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, USA
| | - Jinghui Zhang
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, USA
| | - Zhaoming Wang
- Department of Epidemiology and Cancer Control, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, USA
| | - Gang Wu
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, USA
| | - Kim E Nichols
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, USA
| | - Chimene A Kesserwan
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, USA
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22
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Fares MY, Salhab HA, Khachfe HH, Khachfe HM. Breast Cancer Epidemiology among Lebanese Women: An 11-Year Analysis. MEDICINA (KAUNAS, LITHUANIA) 2019; 55:E463. [PMID: 31405167 PMCID: PMC6723716 DOI: 10.3390/medicina55080463] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Revised: 07/20/2019] [Accepted: 08/08/2019] [Indexed: 02/06/2023]
Abstract
Background and Objectives: Breast cancer is the most prevalent cancer in women worldwide. Lebanon is a developing country in the Middle East with a prominent breast cancer incidence. The aim of our study was to explore the incidence rates of breast cancer in Lebanon from 2005 to 2015, and compare them to the rates of other countries. Materials and Methods: Breast cancer data for the years 2005-2015 was collected from the National Cancer Registry of Lebanon and stratified by gender and age group. Age-specific and age-standardized incidence rates were calculated and analyzed using joinpoint regression. Age-standardized incidence rates in the world population (ASR(w)) were obtained for other countries, from two online databases. Results: Breast cancer was found to be the most prevalent cancer in Lebanon, accounting for 20% of all cancer cases. The average ASR(w) was 96.5 per 100,000. Over the studied period, breast cancer ASR(w) in Lebanon showed a significantly increasing trend with an annual percent change (APC) of +4.6. Moreover, the APC of breast cancer age-specific rates significantly increased for the age groups 45-49 (p = 0.013), 50-54 (p < 0.001), 55-59 (p = 0.001), 60-64 (p = 0.002), 65-69 (p = 0.003), 70-74 (p < 0.001), and 75+ years (p < 0.001). Lebanon had the highest breast cancer ASR(w), when compared to other regional countries, and trailed only behind Denmark, when compared to selected countries from different parts of the world. Conclusions: Breast cancer incidence in Lebanon is among the highest in the world. Future studies should focus on exploring the genetic profile of the Lebanese population in an aim to extrapolate proper prevention guidelines.
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Affiliation(s)
- Mohamad Y Fares
- Faculty of Medicine, American University of Beirut, Beirut 1107, Lebanon.
- Neuroscience Research Center, Faculty of Medical Sciences, Lebanese University, Beirut 1102, Lebanon.
| | - Hamza A Salhab
- Faculty of Medicine, American University of Beirut, Beirut 1107, Lebanon
- Neuroscience Research Center, Faculty of Medical Sciences, Lebanese University, Beirut 1102, Lebanon
| | - Hussein H Khachfe
- Faculty of Medicine, American University of Beirut, Beirut 1107, Lebanon
- Neuroscience Research Center, Faculty of Medical Sciences, Lebanese University, Beirut 1102, Lebanon
| | - Hassan M Khachfe
- School of Arts and Sciences, and the Lebanese Institute for Biomedical Research and Application (LIBRA), Lebanese International University (LIU), Beirut 1105, Lebanon
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23
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Bermisheva MA, Gilyazova IR, Akhmadishina LZ, Gimalova GF, Zinnatullina GF, Khusnutdinova EK. A WRN Nonsense Mutation, p.R1406X, is Not a Risk Factor of Breast Cancer. RUSS J GENET+ 2019. [DOI: 10.1134/s1022795419070056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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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.
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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
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25
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Farra C, Dagher C, Badra R, Hammoud MS, Alameddine R, Awwad J, Seoud M, Abbas J, Boulos F, El Saghir N, Mukherji D. BRCA mutation screening and patterns among high-risk Lebanese subjects. Hered Cancer Clin Pract 2019; 17:4. [PMID: 30675319 PMCID: PMC6339325 DOI: 10.1186/s13053-019-0105-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2018] [Accepted: 01/15/2019] [Indexed: 01/01/2023] Open
Abstract
Background Previous studies have suggested that the prevalence of BRCA1 and 2 mutations in the Lebanese population is low despite the observation that the median age of breast cancer diagnosis is significantly lower than European and North American populations. We aimed at reviewing the rates and patterns of BRCA1/2 mutations found in individuals referred to the medical genetics unit at the American University of Beirut. We also evaluated the performance of clinical prediction tools. Methods We retrospectively reviewed the cases of all individuals undergoing BRCA mutation testing from April 2011 to May 2016. To put our findings in to context, we conducted a literature review of the most recently published data from the region. Results Two-hundred eighty one individuals were referred for testing. The prevalence of mutated BRCA1 or 2 genes were 6 and 1.4% respectively. Three mutations accounted for 54% of the pathogenic mutations found. The BRCA1 c.131G > T mutation was found among 5/17 (29%) unrelated subjects with BRCA1 mutation and is unique to the Lebanese and Palestinian populations. For patients tested between 2014 and 2016, all patients positive for mutations fit the NCCN guidelines for BRCA mutation screening. The Manchester Score failed to predict pathogenic mutations. Conclusion The BRCA1 c.131G > T mutation can be considered a founder mutation in the Lebanese population detected among 5/17 (29%) of individuals diagnosed with a mutation in BRCA1 and among 7/269 families in this cohort. On review of recently published data regarding the landscape of BRCA mutations in the Middle East and North Africa, each region appears to have a unique spectrum of mutations.
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Affiliation(s)
- Chantal Farra
- 1Medical Genetics Unit and Department of Pathology and Laboratory Medicine, American University of Beirut Medical Center, Beirut, Lebanon
| | - Christelle Dagher
- 2Division of Hematology-Oncology, Department of Internal Medicine, American University of Beirut Medical Center, Beirut, Lebanon
| | - Rebecca Badra
- 1Medical Genetics Unit and Department of Pathology and Laboratory Medicine, American University of Beirut Medical Center, Beirut, Lebanon
| | - Miza Salim Hammoud
- 2Division of Hematology-Oncology, Department of Internal Medicine, American University of Beirut Medical Center, Beirut, Lebanon
| | - Raafat Alameddine
- 2Division of Hematology-Oncology, Department of Internal Medicine, American University of Beirut Medical Center, Beirut, Lebanon
| | - Johnny Awwad
- 3Department of Obstetrics and Gynecology, American University of Beirut Medical Center, Beirut, Lebanon
| | - Muhieddine Seoud
- 3Department of Obstetrics and Gynecology, American University of Beirut Medical Center, Beirut, Lebanon
| | - Jaber Abbas
- 4Department of Surgery, American University of Beirut Medical Center, Beirut, Lebanon
| | - Fouad Boulos
- 1Medical Genetics Unit and Department of Pathology and Laboratory Medicine, American University of Beirut Medical Center, Beirut, Lebanon
| | - Nagi El Saghir
- 2Division of Hematology-Oncology, Department of Internal Medicine, American University of Beirut Medical Center, Beirut, Lebanon
| | - Deborah Mukherji
- 2Division of Hematology-Oncology, Department of Internal Medicine, American University of Beirut Medical Center, Beirut, Lebanon
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Girard E, Eon-Marchais S, Olaso R, Renault AL, Damiola F, Dondon MG, Barjhoux L, Goidin D, Meyer V, Le Gal D, Beauvallet J, Mebirouk N, Lonjou C, Coignard J, Marcou M, Cavaciuti E, Baulard C, Bihoreau MT, Cohen-Haguenauer O, Leroux D, Penet C, Fert-Ferrer S, Colas C, Frebourg T, Eisinger F, Adenis C, Fajac A, Gladieff L, Tinat J, Floquet A, Chiesa J, Giraud S, Mortemousque I, Soubrier F, Audebert-Bellanger S, Limacher JM, Lasset C, Lejeune-Dumoulin S, Dreyfus H, Bignon YJ, Longy M, Pujol P, Venat-Bouvet L, Bonadona V, Berthet P, Luporsi E, Maugard CM, Noguès C, Delnatte C, Fricker JP, Gesta P, Faivre L, Lortholary A, Buecher B, Caron O, Gauthier-Villars M, Coupier I, Servant N, Boland A, Mazoyer S, Deleuze JF, Stoppa-Lyonnet D, Andrieu N, Lesueur F. Familial breast cancer and DNA repair genes: Insights into known and novel susceptibility genes from the GENESIS study, and implications for multigene panel testing. Int J Cancer 2018; 144:1962-1974. [PMID: 30303537 PMCID: PMC6587727 DOI: 10.1002/ijc.31921] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2018] [Revised: 09/11/2018] [Accepted: 09/25/2018] [Indexed: 12/16/2022]
Abstract
Pathogenic variants in BRCA1 and BRCA2 only explain the underlying genetic cause of about 10% of hereditary breast and ovarian cancer families. Because of cost‐effectiveness, multigene panel testing is often performed even if the clinical utility of testing most of the genes remains questionable. The purpose of our study was to assess the contribution of rare, deleterious‐predicted variants in DNA repair genes in familial breast cancer (BC) in a well‐characterized and homogeneous population. We analyzed 113 DNA repair genes selected from either an exome sequencing or a candidate gene approach in the GENESIS study, which includes familial BC cases with no BRCA1 or BRCA2 mutation and having a sister with BC (N = 1,207), and general population controls (N = 1,199). Sequencing data were filtered for rare loss‐of‐function variants (LoF) and likely deleterious missense variants (MV). We confirmed associations between LoF and MV in PALB2, ATM and CHEK2 and BC occurrence. We also identified for the first time associations between FANCI, MAST1, POLH and RTEL1 and BC susceptibility. Unlike other associated genes, carriers of an ATM LoF had a significantly higher risk of developing BC than carriers of an ATM MV (ORLoF = 17.4 vs. ORMV = 1.6; pHet = 0.002). Hence, our approach allowed us to specify BC relative risks associated with deleterious‐predicted variants in PALB2, ATM and CHEK2 and to add MAST1, POLH, RTEL1 and FANCI to the list of DNA repair genes possibly involved in BC susceptibility. We also highlight that different types of variants within the same gene can lead to different risk estimates. What's new? Pathogenic variants in BRCA1 and BRCA2 only explain the genetic cause of about 10% of hereditary breast and ovarian cancer families, and the clinical usefulness of testing other genes following the recent introduction of cost‐effective multigene panel sequencing in diagnostics laboratories remains questionable. This large case‐control study describes genetic variation in 113 DNA repair genes and specifies breast cancer relative risks associated with rare deleterious‐predicted variants in PALB2, ATM, and CHEK2. Importantly, different types of variants within the same gene can lead to different risk estimates. The results may help improve risk prediction models and define gene‐specific consensus management guidelines.
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Affiliation(s)
- Elodie Girard
- Inserm, Paris, France.,Institut Curie, Paris, France.,Mines ParisTech, Fontainebleau, France.,PSL Research University, Paris, France
| | - Séverine Eon-Marchais
- Inserm, Paris, France.,Institut Curie, Paris, France.,Mines ParisTech, Fontainebleau, France.,PSL Research University, Paris, France
| | - Robert Olaso
- Centre National de Recherche en Génomique Humaine, Institut de Biologie François Jacob, CEA, Evry, France
| | - Anne-Laure Renault
- Inserm, Paris, France.,Institut Curie, Paris, France.,Mines ParisTech, Fontainebleau, France.,PSL Research University, Paris, France
| | | | - Marie-Gabrielle Dondon
- Inserm, Paris, France.,Institut Curie, Paris, France.,Mines ParisTech, Fontainebleau, France.,PSL Research University, Paris, France
| | - Laure Barjhoux
- Département de Biopathologie, Centre Léon Bérard, Lyon, France
| | - Didier Goidin
- Life Sciences and Diagnostics Group, Agilent Technologies France, Les Ulis, France
| | - Vincent Meyer
- Centre National de Recherche en Génomique Humaine, Institut de Biologie François Jacob, CEA, Evry, France
| | - Dorothée Le Gal
- Inserm, Paris, France.,Institut Curie, Paris, France.,Mines ParisTech, Fontainebleau, France.,PSL Research University, Paris, France
| | - Juana Beauvallet
- Inserm, Paris, France.,Institut Curie, Paris, France.,Mines ParisTech, Fontainebleau, France.,PSL Research University, Paris, France
| | - Noura Mebirouk
- Inserm, Paris, France.,Institut Curie, Paris, France.,Mines ParisTech, Fontainebleau, France.,PSL Research University, Paris, France
| | - Christine Lonjou
- Inserm, Paris, France.,Institut Curie, Paris, France.,Mines ParisTech, Fontainebleau, France.,PSL Research University, Paris, France
| | - Juliette Coignard
- Inserm, Paris, France.,Institut Curie, Paris, France.,Mines ParisTech, Fontainebleau, France.,PSL Research University, Paris, France.,Université Paris Sud, Paris, France
| | - Morgane Marcou
- Inserm, Paris, France.,Institut Curie, Paris, France.,Mines ParisTech, Fontainebleau, France.,PSL Research University, Paris, France
| | - Eve Cavaciuti
- Inserm, Paris, France.,Institut Curie, Paris, France.,Mines ParisTech, Fontainebleau, France.,PSL Research University, Paris, France
| | - Céline Baulard
- Centre National de Recherche en Génomique Humaine, Institut de Biologie François Jacob, CEA, Evry, France
| | - Marie-Thérèse Bihoreau
- Centre National de Recherche en Génomique Humaine, Institut de Biologie François Jacob, CEA, Evry, France
| | | | - Dominique Leroux
- Département de Génétique, CHU de Grenoble, Hôpital Couple-Enfant, Grenoble, France
| | - Clotilde Penet
- Consultation d'Oncogénétique, Institut Jean-Godinot & ICC Courlancy, Reims, France
| | | | - Chrystelle Colas
- Département de Génétique Groupe Hospitalier Pitié-Salpêtrière, APHP, Paris, France.,Service de Génétique, Institut Curie, Paris, France
| | - Thierry Frebourg
- Département de Génétique, Hôpital Universitaire de Rouen, Rouen, France
| | - François Eisinger
- Institut Paoli Calmette, Département d'Anticipation et de Suivi des Cancers, Oncogénétique Clinique, Institut Paoli-Calmettes & Aix Marseille Université, Inserm, IRD, SESSTIM, Marseille, France
| | - Claude Adenis
- Service de Génétique, Centre Oscar-Lambret, Lille, France
| | - Anne Fajac
- Service d'Oncogénétique, Hôpital Tenon, Paris, France
| | - Laurence Gladieff
- Service d'Oncologie Médicale, Institut Claudius Regaud - IUCT-Oncopole, Toulouse, France
| | - Julie Tinat
- Département de Génétique, Hôpital Universitaire de Rouen, Rouen, France
| | | | | | - Sophie Giraud
- Service de Génétique, Hospices Civils de Lyon, Groupement Hospitalier EST, Bron, France
| | | | | | | | | | - Christine Lasset
- Université Claude Bernard Lyon 1, Villeurbanne; CNRS UMR 5558, Unité de Prévention et Epidémiologie Génétique, Lyon, Centre, Léon Bérard, France
| | | | - Hélène Dreyfus
- Clinique Sainte Catherine, Avignon & CHU de Grenoble, Département de Génétique, Hôpital Couple-Enfant, Grenoble, France
| | - Yves-Jean Bignon
- Université Clermont Auvergne; Inserm, U1240, Centre Jean Perrin, Clermont-Ferrand, France
| | | | - Pascal Pujol
- Service de Génétique Médicale et Oncogénétique, Hôpital Arnaud de Villeneuve, CHU Montpellier & INSERM 896, CRCM Val d'Aurelle, Montpellier, France
| | | | - Valérie Bonadona
- Université Claude Bernard Lyon 1, Villeurbanne; CNRS UMR 5558, Unité de Prévention et Epidémiologie Génétique, Lyon, Centre, Léon Bérard, France
| | - Pascaline Berthet
- Unité de Pathologie Gynécologique, Centre François Baclesse, Caen, France
| | - Elisabeth Luporsi
- Service de Génétique UF4128 CHR Metz-Thionville, Hôpital de Mercy, Metz, France
| | - Christine M Maugard
- Hôpitaux Universitaires de Strasbourg, UF1422 Oncogénétique moléculaire, Laboratoire d'Oncobiologie & UF6948 Oncogénétique Evaluation familiale et suivi, Strasbourg, France
| | - Catherine Noguès
- Institut Paoli Calmette, Département d'Anticipation et de Suivi des Cancers, Oncogénétique Clinique, Institut Paoli-Calmettes & Aix Marseille Université, Inserm, IRD, SESSTIM, Marseille, France
| | - Capucine Delnatte
- Unité d'Oncogénétique, Centre René Gauducheau, Nantes, Saint Herblain, France
| | | | - Paul Gesta
- Service d'Oncogénétique Régional Poitou-Charentes, Niort, France
| | - Laurence Faivre
- Institut GIMI, CHU de Dijon, Hôpital d'Enfants, Oncogénétique & Centre de Lutte contre le Cancer Georges François Leclerc, Dijon, France
| | - Alain Lortholary
- Service d'Oncologie Médicale, Centre Catherine de Sienne, Nantes, France
| | | | - Olivier Caron
- Gustave Roussy, Université Paris-Saclay, Département de Médecine Oncologique, Villejuif, France
| | | | - Isabelle Coupier
- Service de Génétique Médicale et Oncogénétique, Hôpital Arnaud de Villeneuve, CHU Montpellier & INSERM 896, CRCM Val d'Aurelle, Montpellier, France
| | - Nicolas Servant
- Inserm, Paris, France.,Institut Curie, Paris, France.,Mines ParisTech, Fontainebleau, France.,PSL Research University, Paris, France
| | - Anne Boland
- Centre National de Recherche en Génomique Humaine, Institut de Biologie François Jacob, CEA, Evry, France
| | - Sylvie Mazoyer
- Inserm, U1028, CNRS UMR5292, Centre de Recherche en Neurosciences de Lyon, France
| | - Jean-François Deleuze
- Centre National de Recherche en Génomique Humaine, Institut de Biologie François Jacob, CEA, Evry, France
| | - Dominique Stoppa-Lyonnet
- Service de Génétique, Institut Curie, Paris, France.,Inserm, U830, Institut Curie, Paris, France.,Université Paris Descartes, Paris, France
| | - Nadine Andrieu
- Inserm, Paris, France.,Institut Curie, Paris, France.,Mines ParisTech, Fontainebleau, France.,PSL Research University, Paris, France
| | - Fabienne Lesueur
- Inserm, Paris, France.,Institut Curie, Paris, France.,Mines ParisTech, Fontainebleau, France.,PSL Research University, Paris, France
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Fortuno C, James PA, Spurdle AB. Current review of TP53 pathogenic germline variants in breast cancer patients outside Li-Fraumeni syndrome. Hum Mutat 2018; 39:1764-1773. [PMID: 30240537 DOI: 10.1002/humu.23656] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2018] [Revised: 08/31/2018] [Accepted: 09/19/2018] [Indexed: 12/16/2022]
Abstract
Pathogenic germline variants in TP53 predispose carriers to the multi-cancer Li-Fraumeni syndrome (LFS). Widespread multigene panel testing is identifying TP53 pathogenic variants in breast cancer patients outside the strict clinical criteria recommended for LFS testing. We aimed to assess frequency and clinical implications of TP53 pathogenic variants in breast cancer cohorts ascertained outside LFS. Classification of TP53 germline variants reported in 59 breast cancer studies, and publicly available population control sets was reviewed and identified evidence for misclassification of variants. TP53 pathogenic variant frequency was determined for: breast cancer studies grouped by ascertainment characteristics; breast cancer cohorts undergoing panel testing; and population controls. Early age of breast cancer onset, regardless of family history or BRCA1/BRCA2 previous testing, had the highest pick-up rate for TP53 carriers. Patients at risk of hereditary breast cancer unselected for features of LFS carried TP53 pathogenic variants at a frequency comparable to that of other non-BRCA1/2 breast cancer predisposing genes, and ∼threefold more than reported in population controls. These results have implications for the implementation of TP53 testing in broader clinical settings, and suggest urgent need to investigate cancer risks associated with TP53 pathogenic variants in individuals outside the LFS spectrum.
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Affiliation(s)
- Cristina Fortuno
- QIMR Berghofer Medical Research Institute, Herston, Brisbane, Australia
| | - Paul A James
- Peter MacCallum Cancer Centre and Royal Melbourne Hospital Familial Cancer Centre, Melbourne, Australia
| | - Amanda B Spurdle
- QIMR Berghofer Medical Research Institute, Herston, Brisbane, Australia
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28
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El Shamieh S, Saleh F, Moussa S, Kattan J, Farhat F. RICTOR gene amplification is correlated with metastasis and therapeutic resistance in triple-negative breast cancer. Pharmacogenomics 2018; 19:757-760. [PMID: 29790419 DOI: 10.2217/pgs-2018-0019] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Triple-negative breast cancer (TNBC) is characterized by its aggressive behavior, metastasis and lack of targeted therapies. Herein, we discuss the clinical, histopathological and genetic profile of a woman diagnosed with TNBC. Since the patient had no durable response to chemotherapy, a genetic profiling was carried out. Next-generation sequencing analysis of 592 genes showed a missense mutation, p.E545A in PIK3CA, thus the patient was started on the mTOR inhibitor everolimus, in combination with exemestane, which controlled her pain; however, the disease progressed aggressively. More importantly, next-generation sequencing analysis showed a RICTOR gene amplification (eight copies) suggesting that RICTOR promotes the genesis of TNBC. We conclude that determining regulators of RICTOR and furthermore, their inhibitors might decrease cancer cells proliferation rate in patients with TNBC.
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Affiliation(s)
- Said El Shamieh
- Department of Medical Laboratory Sciences, Faculty of Health Sciences, Beirut Arab University, Beirut, Lebanon
| | - Fatima Saleh
- Department of Medical Laboratory Sciences, Faculty of Health Sciences, Beirut Arab University, Beirut, Lebanon
| | - Salim Moussa
- Department of Medical Laboratory Sciences, Faculty of Health Sciences, Beirut Arab University, Beirut, Lebanon
| | - Joseph Kattan
- Department of Hematology-Oncology, Saint Joseph Faculty of Medicine, Beirut, Lebanon
| | - Fadi Farhat
- Department of Hematology-Oncology, Saint Joseph Faculty of Medicine, Beirut, Lebanon.,Department of Hematology & Oncology, Hammoud Hospital UMC, Saida, Lebanon
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29
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Surowy H, Varga D, Burwinkel B, Marmé F, Sohn C, Luedeke M, Rinckleb A, Maier C, Deissler H, Volcic M, Wiesmüller L, Hasenburg A, Klar M, Hoegel J, Vogel W. A low-frequency haplotype spanning SLX4/FANCP constitutes a new risk locus for early-onset breast cancer (<60 years) and is associated with reduced DNA repair capacity. Int J Cancer 2017; 142:757-768. [PMID: 29044504 DOI: 10.1002/ijc.31105] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Revised: 08/31/2017] [Accepted: 09/25/2017] [Indexed: 01/21/2023]
Abstract
Only a fraction of breast cancer (BC) cases can be yet explained by mutations in genes or genomic variants discovered in linkage, genome-wide association and sequencing studies. The known genes entailing medium or high risk for BC are strongly enriched for a function in DNA double strand repair. Thus, aiming at identifying low frequency variants conferring an intermediate risk, we here investigated 17 variants (MAF: 0.01-0.1) in 10 candidate genes involved in DNA repair or cell cycle control. In an exploration cohort of 437 cases and 1189 controls, we show the variant rs3810813 in the SLX4/FANCP gene to be significantly associated with both BC (≤60 years; OR = 2.6(1.6-3.9), p = 1.6E-05) and decreased DNA repair capacity (≤60 years; beta = 37.8(17.9-57.8), p = 5.3E-4). BC association was confirmed in a verification cohort (N = 2441). Both associations were absent from cases diagnosed >60 years and stronger the earlier the diagnosis. By imputation we show that rs3810813 tags a haplotype with 5 additional variants with the same allele frequency (R2 > 0.9), and a pattern of association very similar for both phenotypes (cases <60 years, p < 0.001, the Bonferroni threshold derived from unlinked variants in the region). In young cases (≤60 years) carrying the risk haplotype, micronucleus test results are predictive for BC (AUC > 0.9). Our findings propose a risk variant with high penetrance on the haplotype spanning SLX4/FANCP to be functionally associated to BC predisposition via decreased repair capacity and suggest this variant is carried by a fraction of these haplotypes that is enriched in early onset BC cases.
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Affiliation(s)
- Harald Surowy
- Institute of Human Genetics, University of Ulm, Albert-Einstein-Allee 11, Ulm, D-89081, Germany.,Division of Molecular Biology of Breast Cancer, Department of Obstetrics and Gynecology, University of Heidelberg, Im Neuenheimer Feld 440, Heidelberg, D-69120, Germany.,Molecular Epidemiology, C080, German Cancer Research Center, Im Neuenheimer Feld 581, Heidelberg, D-69120, Germany.,Harald Surowy's current address is: Institute of Human Genetics, University of Duesseldorf, Universitaetsstr. 1, Duesseldorf, 40225, Germany
| | - Dominic Varga
- Department of Obstetrics and Gynecology, Ulm University, Prittwitzstr. 43, Ulm, D-89075, Germany.,Dominic Varga's current address is: Department of Gynecology, Donauklinik, Krankenhausstr 11, Neu-Ulm, 89231, Germany
| | - Barbara Burwinkel
- Division of Molecular Biology of Breast Cancer, Department of Obstetrics and Gynecology, University of Heidelberg, Im Neuenheimer Feld 440, Heidelberg, D-69120, Germany.,Molecular Epidemiology, C080, German Cancer Research Center, Im Neuenheimer Feld 581, Heidelberg, D-69120, Germany
| | - Frederik Marmé
- Division of Molecular Biology of Breast Cancer, Department of Obstetrics and Gynecology, University of Heidelberg, Im Neuenheimer Feld 440, Heidelberg, D-69120, Germany.,National Centre for Tumor Diseases, Heidelberg, D-69120, Germany
| | - Christof Sohn
- Division of Molecular Biology of Breast Cancer, Department of Obstetrics and Gynecology, University of Heidelberg, Im Neuenheimer Feld 440, Heidelberg, D-69120, Germany
| | - Manuel Luedeke
- Institute of Human Genetics, University of Ulm, Albert-Einstein-Allee 11, Ulm, D-89081, Germany
| | - Antje Rinckleb
- Institute of Human Genetics, University of Ulm, Albert-Einstein-Allee 11, Ulm, D-89081, Germany
| | - Christiane Maier
- Institute of Human Genetics, University of Ulm, Albert-Einstein-Allee 11, Ulm, D-89081, Germany
| | - Helmut Deissler
- Department of Obstetrics and Gynecology, Ulm University, Prittwitzstr. 43, Ulm, D-89075, Germany.,Helmut Deissler's current address is: HD/U Biomedical Services, Im Wiblinger Hart 62, Ulm, 89079, Germany
| | - Meta Volcic
- Department of Obstetrics and Gynecology, Ulm University, Prittwitzstr. 43, Ulm, D-89075, Germany
| | - Lisa Wiesmüller
- Department of Obstetrics and Gynecology, Ulm University, Prittwitzstr. 43, Ulm, D-89075, Germany
| | - Annette Hasenburg
- Department of Obstetrics and Gynecology, University of Freiburg, Hugstetter Straße 55, Freiburg, D-79106, Germany.,Annete Hasenburg's current address is: Klinik und Poliklinik für Geburtshilfe und Frauengesundheit, University of Mainz, Langenbeckstr. 1, Mainz, 55131, Germany
| | - Maximilian Klar
- Department of Obstetrics and Gynecology, University of Freiburg, Hugstetter Straße 55, Freiburg, D-79106, Germany
| | - Josef Hoegel
- Institute of Human Genetics, University of Ulm, Albert-Einstein-Allee 11, Ulm, D-89081, Germany
| | - Walther Vogel
- Institute of Human Genetics, University of Ulm, Albert-Einstein-Allee 11, Ulm, D-89081, Germany
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30
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Inherited predisposition to breast and ovarian cancer in non-Jewish populations in Israel. Breast Cancer Res Treat 2017; 166:881-885. [DOI: 10.1007/s10549-017-4474-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2017] [Accepted: 08/19/2017] [Indexed: 11/26/2022]
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31
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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.
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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
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