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Demir O, Saglam KA, Yilmaz M, Apuhan T, Cebi AH, Turkyilmaz A. Secondary findings in genes related to cancer phenotypes in Turkish exome sequencing data from 2020 individuals. Am J Med Genet A 2024:e63806. [PMID: 38940262 DOI: 10.1002/ajmg.a.63806] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2024] [Revised: 05/24/2024] [Accepted: 06/20/2024] [Indexed: 06/29/2024]
Abstract
Big data generated from exome sequencing (ES) and genome sequencing (GS) analyses can be used to detect actionable and high-penetrance variants that are not directly associated with the primary diagnosis of patients but can guide their clinical follow-up and treatment. Variants that are classified as pathogenic/likely pathogenic and are clinically significant but not directly associated with the primary diagnosis of patients are defined as secondary findings (SF). The aim of this study was to examine the frequency and variant spectrum of cancer-related SF in 2020 Turkish ES data and to discuss the importance of the presence of cancer-related SF in at-risk family members in terms of genetic counseling and follow-up. A total of 2020 patients from 2020 different families were evaluated by ES. SF were detected in 28 unrelated cases (1.38%), and variants in BRCA2 (11 patients) and MLH1 (4 patients) genes were observed most frequently. A total of 21 different variants were identified, with 4 of them (c.9919_9932del and c.3653del in the BRCA2 gene, c.2002A>G in the MSH2 gene, c.26_29del in the TMEM127 gene) being novel variations. In three different families, c.1189C>T (p.Gln397*) variation in BRCA2 gene was detected, suggesting that this may be a common variant in the Turkish population. This study represents the largest cohort conducted in the Turkish population, examining the frequency and variant spectrum of cancer-related SF. With the identification of frequent variations and the detection of novel variations, the findings of this study have contributed to the variant spectrum. Genetic testing conducted in family members is presented as real-life data, showcasing the implications in terms of counseling, monitoring, and treatment through case examples.
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Affiliation(s)
- Oguzhan Demir
- Department of Medical Genetics, Faculty of Medicine, Karadeniz Technical University, Trabzon, Turkey
| | - Kubra Adanur Saglam
- Department of Medical Genetics, Faculty of Medicine, Karadeniz Technical University, Trabzon, Turkey
| | - Mustafa Yilmaz
- Department of Medical Genetics, Faculty of Medicine, Karadeniz Technical University, Trabzon, Turkey
| | - Tuna Apuhan
- Department of Medical Genetics, Faculty of Medicine, Karadeniz Technical University, Trabzon, Turkey
| | - Alper Han Cebi
- Department of Medical Genetics, Faculty of Medicine, Karadeniz Technical University, Trabzon, Turkey
| | - Ayberk Turkyilmaz
- Department of Medical Genetics, Faculty of Medicine, Karadeniz Technical University, Trabzon, Turkey
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Yin X, Richardson M, Laner A, Shi X, Ognedal E, Vasta V, Hansen TVO, Pineda M, Ritter D, den Dunnen JT, Hassanin E, Lyman Lin W, Borras E, Krahn K, Nordling M, Martins A, Mahmood K, Nadeau EAW, Beshay V, Tops C, Genuardi M, Pesaran T, Frayling IM, Capellá G, Latchford A, Tavtigian SV, Maj C, Plon SE, Greenblatt MS, Macrae FA, Spier I, Aretz S. Systematic large-scale application of ClinGen InSiGHT APC -specific ACMG/AMP variant classification criteria substantially alleviates the burden of variants of uncertain significance in ClinVar and LOVD databases. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.05.03.24306761. [PMID: 38746299 PMCID: PMC11092726 DOI: 10.1101/2024.05.03.24306761] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
Background Pathogenic constitutional APC variants underlie familial adenomatous polyposis, the most common hereditary gastrointestinal polyposis syndrome. To improve variant classification and resolve the interpretative challenges of variants of uncertain significance (VUS), APC-specific ACMG/AMP variant classification criteria were developed by the ClinGen-InSiGHT Hereditary Colorectal Cancer/Polyposis Variant Curation Expert Panel (VCEP). Methods A streamlined algorithm using the APC -specific criteria was developed and applied to assess all APC variants in ClinVar and the InSiGHT international reference APC LOVD variant database. Results A total of 10,228 unique APC variants were analysed. Among the ClinVar and LOVD variants with an initial classification of (Likely) Benign or (Likely) Pathogenic, 94% and 96% remained in their original categories, respectively. In contrast, 41% ClinVar and 61% LOVD VUS were reclassified into clinically actionable classes, the vast majority as (Likely) Benign. The total number of VUS was reduced by 37%. In 21 out of 36 (58%) promising APC variants that remained VUS despite evidence for pathogenicity, a data mining-driven work-up allowed their reclassification as (Likely) Pathogenic. Conclusions The application of APC -specific criteria substantially reduced the number of VUS in ClinVar and LOVD. The study also demonstrated the feasibility of a systematic approach to variant classification in large datasets, which might serve as a generalisable model for other gene-/disease-specific variant interpretation initiatives. It also allowed for the prioritization of VUS that will benefit from in-depth evidence collection. This subset of APC variants was approved by the VCEP and made publicly available through ClinVar and LOVD for widespread clinical use.
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Güleç Ceylan G, Arslan Satılmış SB, Çavdarlı B, Semerci Gündüz CN. Contribution of Inherited Variants to Hereditary Cancer Syndrome Predisposition. TOHOKU J EXP MED 2022; 258:319-325. [PMID: 36288950 DOI: 10.1620/tjem.2022.j087] [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: 11/22/2022]
Abstract
Cancer is a clonal disease that develops as a result of the changes on the genetic material by various factors in micro/macro environment. It has a multi-step development process. In some cancer types, genetic factors allow this multi-step process to proceed easily. These cancer types are also called hereditary cancer syndromes. Targeted gene panels are important diagnostic methods in hereditary cancer syndromes to detect the causative variants associated with these hereditary cancer syndromes. We reviewed the data of 94 patients who applied to Ankara City Hospital Genetic Diseases Evaluation Center from March 2019 to July 2021. Qiagen familial cancer susceptibility gene panel kit was used for next generation sequencing to detect the single nucleotide variants for the targeted genes. Sixty-one genes which are associated with increased cancer risk or well characterized hereditary cancer syndromes were included to this panel. Twenty five patients (27%), including 8 males and 17 females, had pathogenic/likely pathogenic variants in 13 of the 61 genes analyzed. Forty patients (43%) had variants which were assessed as variant of unknown significant. In our study, targeted multi-gene panel was diagnostic in nearly one third of the patients with personal/familial cancer syndromes. Molecular diagnosis in familial cancer syndromes is important in terms of predictive diagnosis and family screening, as well as patient follow-up and early prophylactic surgery. The predisposition for hereditary cancer syndromes can be determined according to pre-test evaluation, figuring out the inheritance type with pedigree analysis, cancer type and the genetic analysis for appropriate susceptibility genes.
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Affiliation(s)
- Gülay Güleç Ceylan
- Department of Medical Genetics, Ankara City Hospital.,Department of Medical Genetics, Ankara Yıldırım Beyazıt University
| | | | | | - C Nur Semerci Gündüz
- Department of Medical Genetics, Ankara City Hospital.,Department of Medical Genetics, Ankara Yıldırım Beyazıt University
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Zavaleta E, Solis N, Palacios MI, Zevallos-Escobar LE, Corales EV, Bazo-Alvarez JC, Dominguez-Barrera C, Campos A, Wernhoff P, Ekstrøm PO, Møller P, Visnovska T, Hovig E, Balazar-Palacios J, Alvarez-Valenzuela K, Nakken S, Dominguez-Valentin M. Genetic Characterization in High-Risk Individuals from a Low-Resource City of Peru. Cancers (Basel) 2022; 14:cancers14225603. [PMID: 36428697 PMCID: PMC9688598 DOI: 10.3390/cancers14225603] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Accepted: 11/09/2022] [Indexed: 11/17/2022] Open
Abstract
Background: Genetic testing for hereditary cancers is inconsistently applied within the healthcare systems in Latin America. In Peru, the prevalence and spectrum of cancer-predisposing germline variants is thus poorly characterized. Purpose: To determine the spectrum and prevalence of cancer-predisposing germline variants and variants of uncertain significance (VUS) in high-risk individuals located in a Peruvian low-resource setting city. Methods: Individuals presenting clinical criteria for hereditary cancer syndromes or being unaffected with familial history of cancer were included in the study. Samples from a total of 84 individuals were subjected to a high-throughput DNA sequencing assay that targeted a panel of 94 cancer predisposition genes. The pathogenicity of detected germline variants was classified according to the established American College of Medical Genetics and Genomics (ACMG) criteria. All pathogenic variants were validated by cycling temperature capillary electrophoresis. Results: We identified a total of eight pathogenic variants, found in 19 out of 84 individuals (23%). Pathogenic variants were identified in 24% (10/42) of unaffected individuals with family history of cancer and in 21% (9/42) of individuals with a cancer diagnosis. Pathogenic variants were identified in eight genes: RET (3), BRCA1 (3), SBDS (2), SBDS/MLH1 (4), MLH1 (4), TP53 (1), FANCD2 (1), DDB2/FANCG (1). In cancer cases, all colon cancer cases were affected by pathogenic variants in MLH1 and SBDS genes, while 20% (2/10) of the thyroid cancer cases by RET c.1900T>C variants were affected. One patient with endometrial cancer (1/3) had a double heterozygous pathogenic variant in DDB2 and FANCG genes, while one breast cancer patient (1/14) had a pathogenic variant in TP53 gene. Overall, each individual presented at least 17 VUS, totaling 1926 VUS for the full study population. Conclusion: We describe the first genetic characterization in a low-resource setting population where genetic testing is not yet implemented. We identified multiple pathogenic germline variants in clinically actionable predisposition genes, that have an impact on providing an appropriate genetic counselling and clinical management for individuals and their relatives who carry these variants. We also reported a high number of VUS, which may indicate variants specific for this population and may require a determination of their clinical significance.
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Affiliation(s)
| | - Nelly Solis
- Hospital La Caleta, Ministerio de Salud, Chimbote 02803, Peru
| | | | | | | | - Juan Carlos Bazo-Alvarez
- Research Department of Primary Care and Population Health, University College London, London WC1H 0NN, UK
- Escuela de Medicina, Universidad Cesar Vallejo, Piura 20001, Peru
| | | | | | - Patrik Wernhoff
- Department of Medical Genetics, Institute of Clinical Medicine, University of Oslo and Oslo University Hospital, 0450 Oslo, Norway
| | - Per Olaf Ekstrøm
- Department of Tumor Biology, Institute for Cancer Research, Oslo University Hospital, 0450 Oslo, Norway
| | - Pål Møller
- Department of Tumor Biology, Institute for Cancer Research, Oslo University Hospital, 0450 Oslo, Norway
| | - Tina Visnovska
- Bioinformatics Core Facility, Oslo University Hospital, 0450 Oslo, Norway
| | - Eivind Hovig
- Department of Tumor Biology, Institute for Cancer Research, Oslo University Hospital, 0450 Oslo, Norway
- Centre for Bioinformatics, Department of Informatics, University of Oslo, 0450 Oslo, Norway
| | | | | | - Sigve Nakken
- Department of Tumor Biology, Institute for Cancer Research, Oslo University Hospital, 0450 Oslo, Norway
- Centre for Bioinformatics, Department of Informatics, University of Oslo, 0450 Oslo, Norway
- Centre for Cancer Cell Reprogramming, Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, 0450 Oslo, Norway
| | - Mev Dominguez-Valentin
- Department of Tumor Biology, Institute for Cancer Research, Oslo University Hospital, 0450 Oslo, Norway
- Correspondence:
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