1
|
Lebedeva A, Veselovsky E, Kavun A, Belova E, Grigoreva T, Orlov P, Subbotovskaya A, Shipunov M, Mashkov O, Bilalov F, Shatalov P, Kaprin A, Shegai P, Diuzhev Z, Migiaev O, Vytnova N, Mileyko V, Ivanov M. Untapped Potential of Poly(ADP-Ribose) Polymerase Inhibitors: Lessons Learned From the Real-World Clinical Homologous Recombination Repair Mutation Testing. World J Oncol 2024; 15:562-578. [PMID: 38993246 PMCID: PMC11236374 DOI: 10.14740/wjon1820] [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: 01/17/2024] [Accepted: 04/29/2024] [Indexed: 07/13/2024] Open
Abstract
Background Testing for homologous recombination deficiency (HRD) mutations is pivotal to assess individual risk, to proact preventive measures in healthy carriers and to tailor treatments for cancer patients. Increasing prominence of poly(ADP-ribose) polymerase (PARP) inhibitors with remarkable impact on molecular-selected patient survival across diverse nosologies, ingrains testing for BRCA genes and beyond in clinical practice. Nevertheless, testing strategies remain a question of debate. While several pathogenic BRCA1/2 gene variants have been described as founder pathogenic mutations frequently found in patients from Russia, other homologous recombination repair (HRR) genes have not been sufficiently explored. In this study, we present real-world data of routine HRR gene testing in Russia. Methods We evaluated clinical and sequencing data from cancer patients who had germline/somatic next-generation sequencing (NGS) HRR gene testing in Russia (BRCA1/2/ATM/CHEK2, or 15 HRR genes). The primary objectives of this study were to evaluate the frequency of BRCA1/2 and non-BRCA gene mutations in real-world unselected patients from Russia, and to determine whether testing beyond BRCA1/2 is feasible. Results Data of 2,032 patients were collected from February 2021 to February 2023. Most had breast (n = 715, 35.2%), ovarian (n = 259, 12.7%), pancreatic (n = 85, 4.2%), or prostate cancer (n = 58, 2.9%). We observed 586 variants of uncertain significance (VUS) and 372 deleterious variants (DVs) across 487 patients, with 17.6% HRR-mutation positivity. HRR testing identified 120 (11.8%) BRCA1/2-positive, and 172 (16.9%) HRR-positive patients. With 51 DVs identified in 242 formalin-fixed paraffin-embedded (FFPE), testing for variant origin clarification was required in one case (0.4%). Most BRCA1/2 germline variants were DV (121 DVs, 26 VUS); in non-BRCA1/2 genes, VUS were ubiquitous (53 DVs, 132 VUS). In silico prediction identified additional 4.9% HRR and 1.2% BRCA1/2/ATM/CHEK2 mutation patients. Conclusions Our study represents one of the first reports about the incidence of DV and VUS in HRR genes, including genes beyond BRCA1/2, identified in cancer patients from Russia, assessed by NGS. In silico predictions of the observed HRR gene variants suggest that non-BRCA gene testing is likely to result in higher frequency of patients who are candidates for PARP inhibitor therapy. Continuing sequencing efforts should clarify interpretation of frequently observed non-BRCA VUS.
Collapse
Affiliation(s)
- Alexandra Lebedeva
- OncoAtlas LLC, Moscow, Russia
- Sechenov First Moscow State Medical University, Moscow, Russia
| | - Egor Veselovsky
- OncoAtlas LLC, Moscow, Russia
- Department of Evolutionary Genetics of Development, Koltzov Institute of Developmental Biology of the Russian Academy of Sciences, Moscow, Russia
| | | | - Ekaterina Belova
- OncoAtlas LLC, Moscow, Russia
- Sechenov First Moscow State Medical University, Moscow, Russia
- Lomonosov Moscow State University, Moscow, Russia
| | - Tatiana Grigoreva
- OncoAtlas LLC, Moscow, Russia
- Sechenov First Moscow State Medical University, Moscow, Russia
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Pavel Orlov
- The Federal Research Center for Fundamental and Translational Medicine (NIIECM FRC FTM), Novosibirsk, Russia
| | - Anna Subbotovskaya
- The Federal Research Center for Fundamental and Translational Medicine (NIIECM FRC FTM), Novosibirsk, Russia
| | - Maksim Shipunov
- The Federal Research Center for Fundamental and Translational Medicine (NIIECM FRC FTM), Novosibirsk, Russia
| | - Oleg Mashkov
- State Budgetary Institution of Healthcare Republican Medical Genetic Center, Ufa, Russia
| | - Fanil Bilalov
- State Budgetary Institution of Healthcare Republican Medical Genetic Center, Ufa, Russia
| | - Peter Shatalov
- National Medical Research Radiological Centre of the Ministry of Health of the Russian Federation, Obninsk, Russia
| | - Andrey Kaprin
- National Medical Research Radiological Centre of the Ministry of Health of the Russian Federation, Obninsk, Russia
| | - Peter Shegai
- National Medical Research Radiological Centre of the Ministry of Health of the Russian Federation, Obninsk, Russia
| | | | | | | | - Vladislav Mileyko
- OncoAtlas LLC, Moscow, Russia
- Sechenov First Moscow State Medical University, Moscow, Russia
| | - Maxim Ivanov
- OncoAtlas LLC, Moscow, Russia
- Sechenov First Moscow State Medical University, Moscow, Russia
- Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, Russia
| |
Collapse
|
2
|
Grigore LG, Radoi VE, Serban A, Mihai AD, Stoica I. The Molecular Detection of Germline Mutations in the BRCA1 and BRCA2 Genes Associated with Breast and Ovarian Cancer in a Romanian Cohort of 616 Patients. Curr Issues Mol Biol 2024; 46:4630-4645. [PMID: 38785549 PMCID: PMC11119367 DOI: 10.3390/cimb46050281] [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: 04/15/2024] [Revised: 05/07/2024] [Accepted: 05/10/2024] [Indexed: 05/25/2024] Open
Abstract
The objective of this study was to identify and classify the spectrum of mutations found in the BRCA1 and BRCA2 genes associated with breast and ovarian cancer in female patients in Romania. Germline BRCA1 and BRCA2 mutations were investigated in a cohort of 616 female patients using NGS and/or MLPA methods followed by software-based data analysis and classification according to international guidelines. Out of the 616 female patients included in this study, we found that 482 patients (78.2%) did not have any mutation present in the two genes investigated; 69 patients (11.2%) had a BRCA1 mutation, 34 (5.5%) had a BRCA2 mutation, and 31 (5%) presented different type of mutations with uncertain clinical significance, moderate risk or a large mutation in the BRCA1 gene. Our investigation indicates the most common mutations in the BRCA1 and BRCA2 genes, associated with breast and ovarian cancer in the Romanian population. Our results also bring more data in support of the frequency of the c.5266 mutation in the BRCA1 gene, acknowledged in the literature as a founder mutation in Eastern Europe. We consider that the results of our study will provide necessary data regarding BRCA1 and BRCA2 mutations that would help to create a genetic database for the Romanian population.
Collapse
Affiliation(s)
- Liliana-Georgiana Grigore
- Doctoral School of Biology, Faculty of Biology, University of Bucharest, 030018 Bucharest, Romania
- Personal Genetics, 010987 Bucharest, Romania
| | - Viorica-Elena Radoi
- Department of Medical Genetics, “Carol Davila” University of Medicine and Pharmacy, 020021 Bucharest, Romania
- “Alessandrescu-Rusescu” National Institute for Maternal and Child Health, 20382 Bucharest, Romania
| | | | | | - Ileana Stoica
- Department of Genetics, Faculty of Biology, University of Bucharest, 030018 Bucharest, Romania
| |
Collapse
|
3
|
Zawadzka A, Brzozowska B, Matyjanka A, Mikula M, Reszczyńska J, Tartas A, Fornalski KW. The Risk Function of Breast and Ovarian Cancers in the Avrami-Dobrzyński Cellular Phase-Transition Model. Int J Mol Sci 2024; 25:1352. [PMID: 38279352 PMCID: PMC10816518 DOI: 10.3390/ijms25021352] [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: 12/08/2023] [Revised: 01/11/2024] [Accepted: 01/16/2024] [Indexed: 01/28/2024] Open
Abstract
Specifying the role of genetic mutations in cancer development is crucial for effective screening or targeted treatments for people with hereditary cancer predispositions. Our goal here is to find the relationship between a number of cancerogenic mutations and the probability of cancer induction over the lifetime of cancer patients. We believe that the Avrami-Dobrzyński biophysical model can be used to describe this mechanism. Therefore, clinical data from breast and ovarian cancer patients were used to validate this model of cancer induction, which is based on a purely physical concept of the phase-transition process with an analogy to the neoplastic transformation. The obtained values of model parameters established using clinical data confirm the hypothesis that the carcinogenic process strongly follows fractal dynamics. We found that the model's theoretical prediction and population clinical data slightly differed for patients with the age below 30 years old, and that might point to the existence of an ancillary protection mechanism against cancer development. Additionally, we reveal that the existing clinical data predict breast or ovarian cancers onset two years earlier for patients with BRCA1/2 mutations.
Collapse
Affiliation(s)
- Anna Zawadzka
- Maria Skłodowska-Curie National Research Institute of Oncology (NIO-MSCI), 02-781 Warsaw, Poland; (A.Z.)
| | - Beata Brzozowska
- Faculty of Physics, University of Warsaw, 02-093 Warsaw, Poland; (B.B.)
| | - Anna Matyjanka
- Faculty of Physics, Warsaw University of Technology, 00-662 Warsaw, Poland
| | - Michał Mikula
- Maria Skłodowska-Curie National Research Institute of Oncology (NIO-MSCI), 02-781 Warsaw, Poland; (A.Z.)
| | - Joanna Reszczyńska
- Mossakowski Medical Research Institute, Polish Academy of Sciences (IMDiK PAN), 02-106 Warsaw, Poland;
| | - Adrianna Tartas
- Faculty of Physics, University of Warsaw, 02-093 Warsaw, Poland; (B.B.)
| | - Krzysztof W. Fornalski
- Faculty of Physics, Warsaw University of Technology, 00-662 Warsaw, Poland
- National Centre for Nuclear Research (NCBJ), 05-400 Otwock-Świerk, Poland
| |
Collapse
|
4
|
Madar L, Majoros V, Szűcs Z, Nagy O, Babicz T, Butz H, Patócs A, Balogh I, Koczok K. Double Heterozygosity for Rare Deleterious Variants in the BRCA1 and BRCA2 Genes in a Hungarian Patient with Breast Cancer. Int J Mol Sci 2023; 24:15334. [PMID: 37895014 PMCID: PMC10607119 DOI: 10.3390/ijms242015334] [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: 09/06/2023] [Revised: 10/13/2023] [Accepted: 10/17/2023] [Indexed: 10/29/2023] Open
Abstract
Hereditary breast cancer is most commonly attributed to germline BRCA1 and BRCA2 gene variants. The vast majority of BRCA1 and BRCA2 mutation carriers are single heterozygotes, and double heterozygosity (DH) is a very rare finding. Here, we describe the case of a BRCA1/BRCA2 double heterozygous female proband diagnosed with breast cancer. Genetic testing for hereditary breast and ovarian cancer revealed two pathogenic variants in the BRCA1 (c.5095C>T, p.(Arg1699Trp)) and in BRCA2 genes (c.658_659delGT, p.(Val220Ilefs*4)) in heterozygous form. None of the variants were founder Jewish mutations; to our knowledge, these rare deleterious variants have not been previously described in DH patients in the literature. The patient had triple-negative unilateral breast cancer at the age of 36 and 44 years. Based on family studies, the BRCA1 variant was maternally inherited.
Collapse
Affiliation(s)
- László Madar
- Department of Laboratory Medicine, Faculty of Medicine, University of Debrecen, 4032 Debrecen, Hungary; (L.M.); (V.M.); (Z.S.); (O.N.)
- Doctoral School of Molecular Cell and Immune Biology, University of Debrecen, 4032 Debrecen, Hungary
| | - Viktória Majoros
- Department of Laboratory Medicine, Faculty of Medicine, University of Debrecen, 4032 Debrecen, Hungary; (L.M.); (V.M.); (Z.S.); (O.N.)
| | - Zsuzsanna Szűcs
- Department of Laboratory Medicine, Faculty of Medicine, University of Debrecen, 4032 Debrecen, Hungary; (L.M.); (V.M.); (Z.S.); (O.N.)
- Doctoral School of Molecular Cell and Immune Biology, University of Debrecen, 4032 Debrecen, Hungary
| | - Orsolya Nagy
- Department of Laboratory Medicine, Faculty of Medicine, University of Debrecen, 4032 Debrecen, Hungary; (L.M.); (V.M.); (Z.S.); (O.N.)
| | - Tamás Babicz
- Department of Oncoradiology, Nyíregyházi Jósa András Tagkórház, Szabolcs—Szatmár—Bereg County Teaching Hospital, 4400 Nyíregyháza, Hungary;
| | - Henriett Butz
- National Tumorbiology Laboratory Budapest, Department of Molecular Genetics, National Institute of Oncology, 1122 Budapest, Hungary; (H.B.); (A.P.)
| | - Attila Patócs
- National Tumorbiology Laboratory Budapest, Department of Molecular Genetics, National Institute of Oncology, 1122 Budapest, Hungary; (H.B.); (A.P.)
| | - István Balogh
- Department of Human Genetics, Faculty of Medicine, University of Debrecen, 4032 Debrecen, Hungary;
- Division of Clinical Genetics, Department of Laboratory Medicine, Faculty of Medicine, University of Debrecen, 4032 Debrecen, Hungary
| | - Katalin Koczok
- Department of Laboratory Medicine, Faculty of Medicine, University of Debrecen, 4032 Debrecen, Hungary; (L.M.); (V.M.); (Z.S.); (O.N.)
| |
Collapse
|
5
|
Mela A, Rdzanek E, Tysarowski A, Sakowicz M, Jaroszyński J, Furtak-Niczyporuk M, Żurek G, Poniatowski ŁA, Jagielska B. The impact of changing the funding model for genetic diagnostics and improved access to personalized medicine in oncology. Expert Rev Pharmacoecon Outcomes Res 2023; 23:43-54. [PMID: 36437684 DOI: 10.1080/14737167.2023.2140139] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
AIM In January 2017, a new funding model for diagnostic genetic testing in cancer was introduced in Poland. OBJECTIVES The aim of this study was to assess the impact of changing the funding model for genetic diagnosis in oncology on improving access to personalized medicine in Poland between 2017 and 2019. METHODS The analysis included data on settlements with the National Health Fund for genetic tests in cancer under a contract of the hospital treatment type and under the contract in the type of separately contracted services between 2017 and 2019. RESULTS The 150,647 diagnostic genetic tests were reported, which were billed to 111,872 patients. The average number of tests per patient was 1.35. One test was billed to 83.5% of patients, 11.2% of patients had two tests billed, and 5.3% had at least three tests billed. The number of services provided under the hospital treatment contract in 2018 doubled compared to the previous year. For separately contracted services, more than threefold increase in genetic testing performed in 2019 compared to 2018 was observed. CONCLUSION our data show that the novel funding model for genetic services introduced in Poland has positive impact on the availability of genetic testing for patients.
Collapse
Affiliation(s)
- Aneta Mela
- Department of Experimental and Clinical Pharmacology, Centre for Preclinical Research and Technology (CePT), Medical University of Warsaw, Warsaw, Poland
| | - Elżbieta Rdzanek
- Department of Experimental and Clinical Pharmacology, Centre for Preclinical Research and Technology (CePT), Medical University of Warsaw, Warsaw, Poland
| | - Andrzej Tysarowski
- Department of Pathology and Laboratory Medicine, Maria Skłodowska-Curie National Research Institute of Oncology, Warsaw, Poland.,Department of Molecular and Translational Oncology, Maria Skłodowska-Curie National Research Institute of Oncology, Warsaw, Poland
| | - Magdalena Sakowicz
- Department of Health Services Billing, Maria Skłodowska-Curie National Research Institute of Oncology, Warsaw, Poland
| | - Janusz Jaroszyński
- Department of Administrative Procedure, Faculty of Law and Administration, Maria Curie-Skłodowska University of Lublin, Lublin, Poland
| | | | - Grzegorz Żurek
- Department of Biostructure, Wrocław University of Health and Sport Sciences, Wrocław, Poland
| | - Łukasz A Poniatowski
- Department of Neurosurgery, Otto-von-Guericke University Magdeburg, Magdeburg, Germany
| | - Beata Jagielska
- President of the Polish Alliance for Personalized Medicine Association; Rafal' Masztak Grochów Hospital Independent Public Healthcare Centre, Warsaw, Poland
| |
Collapse
|
6
|
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.
Collapse
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.
| |
Collapse
|
7
|
Huszno J, Pigłowski W, Mazur M, Pamuła-Piłat J, Zajkowicz A, Kierzkowska AF, Wojciechowska MO. BRCA1/BRCA2 variants of uncertain significance in clinical practice: A case report. Mol Clin Oncol 2021; 15:222. [PMID: 34548921 DOI: 10.3892/mco.2021.2385] [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: 07/13/2020] [Accepted: 05/11/2021] [Indexed: 11/05/2022] Open
Abstract
The influence of BRCA1/2 variants of uncertain significance (VUSs) on the cancer risk and their association with the response to treatment is uncertain. The aim of the present study was to evaluate the role of BRCA VUS in patients with breast cancer. A total of two cases of breast cancer patients with the BRCA VUS were described. The complete coding sequence of BRCA1/2 genes was analyzed from the genomic DNA material by next generation sequencing on the Ion Torrent platform. The presence of c.3454G>A (p.Asp1152Asn) VUS in the BRCA1 gene was reported in a 64-year-old woman with invasive breast carcinoma. The characteristics of the breast tumors were the following: moderately differentiated-intermediate grade (NG-2 G-2), HER2 (+), estrogen receptor (ER) (+++), progesterone receptor (PR) (+++), luminal A subtype and pT2 N1a Mx. The second detected VUS was the c.2374T>C (p.Tyr792His) variant in the BRCA2 gene. This variant was reported in a 33-year-old woman who was diagnosed with right breast cancer (cT2N1M0). The invasive breast carcinoma was characterized as follows: NG-2 G-2, ER (+++), PR (+++), Ki-67 10%, HER2 (+++) and luminal B subtype. The data demonstrated that patients with VUSs should be managed based on their family history of cancer and clinicopathological characteristics. The clinical significance of the VUS in BRCA1/2 may change over time and reclassification of the variant to 'pathogenic' or 'benign' should be undertaken. Patients with VUS should be followed up regularly.
Collapse
Affiliation(s)
- Joanna Huszno
- Genetic Outpatient Clinic, Maria Sklodowska-Curie, National Research Institute of Oncology, Gliwice Branch, 44-100 Gliwice, Poland
| | - Wojciech Pigłowski
- The Department of Genetic and Molecular Diagnostics of Cancer, Maria Sklodowska-Curie, National Research Institute of Oncology, Gliwice Branch, 44-100 Gliwice, Poland.,Department of Tumor Pathology, Maria Sklodowska-Curie, National Research Institute of Oncology, Gliwice Branch, 44-100 Gliwice, Poland
| | - Magdalena Mazur
- The Department of Genetic and Molecular Diagnostics of Cancer, Maria Sklodowska-Curie, National Research Institute of Oncology, Gliwice Branch, 44-100 Gliwice, Poland
| | - Jolanta Pamuła-Piłat
- The Department of Genetic and Molecular Diagnostics of Cancer, Maria Sklodowska-Curie, National Research Institute of Oncology, Gliwice Branch, 44-100 Gliwice, Poland
| | - Artur Zajkowicz
- The Department of Genetic and Molecular Diagnostics of Cancer, Maria Sklodowska-Curie, National Research Institute of Oncology, Gliwice Branch, 44-100 Gliwice, Poland
| | - Anna Fiszer Kierzkowska
- The Department of Genetic and Molecular Diagnostics of Cancer, Maria Sklodowska-Curie, National Research Institute of Oncology, Gliwice Branch, 44-100 Gliwice, Poland
| | - Małgorzata Oczko Wojciechowska
- The Department of Genetic and Molecular Diagnostics of Cancer, Maria Sklodowska-Curie, National Research Institute of Oncology, Gliwice Branch, 44-100 Gliwice, Poland
| |
Collapse
|
8
|
Diepenbroek M, Bayer B, Anslinger K. Pushing the Boundaries: Forensic DNA Phenotyping Challenged by Single-Cell Sequencing. Genes (Basel) 2021; 12:genes12091362. [PMID: 34573344 PMCID: PMC8466929 DOI: 10.3390/genes12091362] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Revised: 08/24/2021] [Accepted: 08/27/2021] [Indexed: 12/26/2022] Open
Abstract
Single-cell sequencing is a fast developing and very promising field; however, it is not commonly used in forensics. The main motivation behind introducing this technology into forensics is to improve mixture deconvolution, especially when a trace consists of the same cell type. Successful studies demonstrate the ability to analyze a mixture by separating single cells and obtaining CE-based STR profiles. This indicates a potential use of the method in other forensic investigations, like forensic DNA phenotyping, in which using mixed traces is not fully recommended. For this study, we collected single-source autopsy blood from which the white cells were first stained and later separated with the DEPArray™ N×T System. Groups of 20, 10, and 5 cells, as well as 20 single cells, were collected and submitted for DNA extraction. Libraries were prepared using the Ion AmpliSeq™ PhenoTrivium Panel, which includes both phenotype (HIrisPlex-S: eye, hair, and skin color) and ancestry-associated SNP-markers. Prior to sequencing, half of the single-cell-based libraries were additionally amplified and purified in order to improve the library concentrations. Ancestry and phenotype analysis resulted in nearly full consensus profiles resulting in correct predictions not only for the cells groups but also for the ten re-amplified single-cell libraries. Our results suggest that sequencing of single cells can be a promising tool used to deconvolute mixed traces submitted for forensic DNA phenotyping.
Collapse
|
9
|
BRCA1/2 Mutation Detection in the Tumor Tissue from Selected Polish Patients with Breast Cancer Using Next Generation Sequencing. Genes (Basel) 2021; 12:genes12040519. [PMID: 33918338 PMCID: PMC8065856 DOI: 10.3390/genes12040519] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Revised: 03/30/2021] [Accepted: 03/30/2021] [Indexed: 12/24/2022] Open
Abstract
(1) Background: Although, in the mutated BRCA detected in the Polish population of patients with breast cancer, there is a large percentage of recurrent pathogenic variants, an increasing need for the assessment of rare BRCA1/2 variants using NGS can be observed. (2) Methods: We studied 75 selected patients with breast cancer (negative for the presence of 5 mutations tested in the Polish population in the prophylactic National Cancer Control Program). DNA extracted from the cancer tissue of these patients was used to prepare a library and to sequence all coding regions of the BRCA1/2 genes. (3) Results: We detected nine pathogenic variants in 8 out of 75 selected patients (10.7%). We identified one somatic and eight germline variants. We also used different bioinformatic NGS software programs to analyze NGS FASTQ files and established that tertiary analysis performed with different tools was more likely to give the same outcome if we analyzed files received from secondary analysis using the same method. (4) Conclusions: Our study emphasizes (i) the importance of an NGS validation process with a bioinformatic procedure included; (ii) the importance of screening both somatic and germline pathogenic variants; (iii) the urgent need to identify additional susceptible genes in order to explain the high percentage of non-BRCA-related hereditary cases of breast cancer.
Collapse
|
10
|
Sokolenko AP, Sokolova TN, Ni VI, Preobrazhenskaya EV, Iyevleva AG, Aleksakhina SN, Romanko AA, Bessonov AA, Gorodnova TV, Anisimova EI, Savonevich EL, Bizin IV, Stepanov IA, Krivorotko PV, Berlev IV, Belyaev AM, Togo AV, Imyanitov EN. Frequency and spectrum of founder and non-founder BRCA1 and BRCA2 mutations in a large series of Russian breast cancer and ovarian cancer patients. Breast Cancer Res Treat 2020; 184:229-235. [PMID: 32776218 DOI: 10.1007/s10549-020-05827-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Accepted: 07/20/2020] [Indexed: 12/17/2022]
Abstract
BACKGROUND The spectrum of BRCA1 and BRCA2 mutations in Slavic countries is characterized by a high prevalence of founder alleles. METHODS We analyzed a large data set of Russian breast cancer (BC) and ovarian cancer (OC) patients, who were subjected to founder mutation tests or full-length BRCA1 and BRCA2 analysis. RESULTS The most commonly applied test, which included four founder mutations (BRCA1: 5382insC, 4153delA, 185delAG; BRCA2: 6174delT), identified BRCA1 or BRCA2 heterozygosity in 399/8533 (4.7%) consecutive BC patients, 230/2317 (9.9%) OC patients, and 30/118 (25.4%) women with a combination of BC and OC. The addition of another four recurrent BRCA1 mutations to the test (BRCA1 C61G, 2080delA, 3819del5, 3875del4) resulted in evident increase in the number of identified mutation carriers (BC: 16/993 (1.6%); OC: 34/1289 (2.6%); BC + OC: 2/39 (5.1%)). Full-length sequencing of the entire BRCA1 and BRCA2 coding region was applied to 785 women, very most of whom demonstrated clinical signs of BRCA-driven disease, but turned out negative for all described above founder alleles. This analysis revealed additional BRCA1 or BRCA2 mutation carriers in 54/282 (19.1%) BC, 50/472 (10.6%) OC, and 13/31 (42%) BC + OC patients. The analysis of frequencies of founder and "rare" BRCA1 and BRCA2 pathogenic alleles across various clinical subgroups (BC vs. OC vs. BC + OC; family history positive vs. negative; young vs. late-onset; none vs. single vs. multiple clinical indicators of BRCA1- or BRCA2-associated disease) revealed that comprehensive BRCA1 and BRCA2 analysis increased more than twice the number of identified mutation carriers in all categories of the examined women. CONCLUSION Full-length BRCA1 and BRCA2 sequencing is strongly advised to Slavic subjects, who have medical indications for BRCA1 and BRCA2 testing but are negative for recurrent BRCA1 and BRCA2 mutations.
Collapse
Affiliation(s)
- Anna P Sokolenko
- Department of Tumor Growth Biology, N.N. Petrov Institute of Oncology, Saint-Petersburg, Russia. .,Department of Medical Genetics, St.-Petersburg Pediatric Medical University, Saint-Petersburg, Russia.
| | - Tatiana N Sokolova
- Department of Tumor Growth Biology, N.N. Petrov Institute of Oncology, Saint-Petersburg, Russia.,Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Federal Research and Clinical Center of Physical and Chemical Medicine, Moscow, Russia
| | - Valeria I Ni
- Department of Tumor Growth Biology, N.N. Petrov Institute of Oncology, Saint-Petersburg, Russia
| | - Elena V Preobrazhenskaya
- Department of Tumor Growth Biology, N.N. Petrov Institute of Oncology, Saint-Petersburg, Russia.,Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Federal Research and Clinical Center of Physical and Chemical Medicine, Moscow, Russia
| | - Aglaya G Iyevleva
- Department of Tumor Growth Biology, N.N. Petrov Institute of Oncology, Saint-Petersburg, Russia.,Department of Medical Genetics, St.-Petersburg Pediatric Medical University, Saint-Petersburg, Russia.,Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Federal Research and Clinical Center of Physical and Chemical Medicine, Moscow, Russia
| | - Svetlana N Aleksakhina
- Department of Tumor Growth Biology, N.N. Petrov Institute of Oncology, Saint-Petersburg, Russia.,Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Federal Research and Clinical Center of Physical and Chemical Medicine, Moscow, Russia
| | - Alexandr A Romanko
- Department of Tumor Growth Biology, N.N. Petrov Institute of Oncology, Saint-Petersburg, Russia.,Department of Medical Genetics, St.-Petersburg Pediatric Medical University, Saint-Petersburg, Russia
| | - Alexandr A Bessonov
- Department of Mammology, N.N. Petrov Institute of Oncology, Saint-Petersburg, Russia
| | - Tatiana V Gorodnova
- Department of Oncogynecology, N.N. Petrov Institute of Oncology, Saint-Petersburg, Russia
| | | | - Elena L Savonevich
- Department of Obstetrics and Gynecology, Grodno State Medical University, Grodno, Belarus
| | - Ilya V Bizin
- Department of Tumor Growth Biology, N.N. Petrov Institute of Oncology, Saint-Petersburg, Russia
| | - Ilya A Stepanov
- Department of Tumor Growth Biology, N.N. Petrov Institute of Oncology, Saint-Petersburg, Russia
| | - Petr V Krivorotko
- Department of Mammology, N.N. Petrov Institute of Oncology, Saint-Petersburg, Russia
| | - Igor V Berlev
- Department of Oncogynecology, N.N. Petrov Institute of Oncology, Saint-Petersburg, Russia
| | - Alexey M Belyaev
- Department of Tumor Growth Biology, N.N. Petrov Institute of Oncology, Saint-Petersburg, Russia.,Department of Oncology, I.I. Mechnikov North-Western Medical University, Saint-Petersburg, Russia
| | - Alexandr V Togo
- Department of Tumor Growth Biology, N.N. Petrov Institute of Oncology, Saint-Petersburg, Russia.,Department of Medical Genetics, St.-Petersburg Pediatric Medical University, Saint-Petersburg, Russia.,Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Federal Research and Clinical Center of Physical and Chemical Medicine, Moscow, Russia
| | - Evgeny N Imyanitov
- Department of Tumor Growth Biology, N.N. Petrov Institute of Oncology, Saint-Petersburg, Russia.,Department of Medical Genetics, St.-Petersburg Pediatric Medical University, Saint-Petersburg, Russia.,Department of Oncology, I.I. Mechnikov North-Western Medical University, Saint-Petersburg, Russia
| |
Collapse
|
11
|
Pirim D, Kaya N, Yıldırım EU, Sag SO, Temel SG. Characterization and in silico analyses of the BRCA1/2 variants identified in individuals with personal and/or family history of BRCA-related cancers. Int J Biol Macromol 2020; 162:1166-1177. [PMID: 32599251 DOI: 10.1016/j.ijbiomac.2020.06.222] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2020] [Revised: 04/05/2020] [Accepted: 06/24/2020] [Indexed: 12/17/2022]
Abstract
Pathogenic variants in the coding regions of the BRCA1/2 lead dysfunctional or nonfunctional BRCA proteins however the contribution of non-coding BRCA1/2 variants to BRCA-related disease risk has not been fully elucidated. Thus, we characterized the functional impact of both coding and non-coding BRCA1/2 variants identified in individuals with personal and/or family history of BRCA-related cancers. The data were produced by resequencing the exons and exon-intron junctions of the BRCA1/2 in 125 individuals and were comprehensively analyzed by using bioinformatics tools and databases. A total of 96 variants (59 coding and 37 non-coding) including 7 novel variants were identified and analyzed for their functional importance. We identified 11 missense variants that potentially affect protein function; 22 variants were likely to alter different types of posttranslational modifications. Also, multiple non-coding BRCA1/2 variants were found to reside in the critical regulatory regions that have the potential to act as eQTLs and affect alternative splicing. The results of our study shed light on the possible contributions of not only coding variants but also non-coding BRCA1/2 variants in BRCRA-related cancers. Further investigation is required to fully understand their potential associations with phenotypes which may ultimately lead their utilization on cancer management as a biomarker.
Collapse
Affiliation(s)
- Dilek Pirim
- Bursa Uludag University, Department of Molecular Biology and Genetics, Bursa, Turkey; Bursa Uludag University, Institute of Health Sciences, Department of Translational Medicine, Bursa, Turkey.
| | - Niyazi Kaya
- Bursa Uludag University, Institute of Natural and Applied Sciences, Department of Molecular Biology and Genetics, Bursa, Turkey
| | - Elif Uz Yıldırım
- Bursa Uludag University, Department of Molecular Biology and Genetics, Bursa, Turkey; Bursa Uludag University, Institute of Health Sciences, Department of Translational Medicine, Bursa, Turkey
| | - Sebnem Ozemri Sag
- Bursa Uludag University, Faculty of Medicine, Department of Medical Genetics, Bursa, Turkey
| | - Sehime Gulsun Temel
- Bursa Uludag University, Faculty of Medicine, Department of Medical Genetics, Bursa, Turkey; Bursa Uludag University, Institute of Health Sciences, Department of Translational Medicine, Bursa, Turkey; Bursa Uludag University, Faculty of Medicine, Department of Histology and Embryology, Bursa, Turkey.
| |
Collapse
|
12
|
Zelli V, Compagnoni C, Cannita K, Capelli R, Capalbo C, Di Vito Nolfi M, Alesse E, Zazzeroni F, Tessitore A. Applications of Next Generation Sequencing to the Analysis of Familial Breast/Ovarian Cancer. High Throughput 2020; 9:ht9010001. [PMID: 31936873 PMCID: PMC7151204 DOI: 10.3390/ht9010001] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Revised: 01/02/2020] [Accepted: 01/07/2020] [Indexed: 12/24/2022] Open
Abstract
Next generation sequencing (NGS) provides a powerful tool in the field of medical genetics, allowing one to perform multi-gene analysis and to sequence entire exomes (WES), transcriptomes or genomes (WGS). The generated high-throughput data are particularly suitable for enhancing the understanding of the genetic bases of complex, multi-gene diseases, such as cancer. Among the various types of tumors, those with a familial predisposition are of great interest for the isolation of novel genes or gene variants, detectable at the germline level and involved in cancer pathogenesis. The identification of novel genetic factors would have great translational value, helping clinicians in defining risk and prevention strategies. In this regard, it is known that the majority of breast/ovarian cases with familial predisposition, lacking variants in the highly penetrant BRCA1 and BRCA2 genes (non-BRCA), remains unexplained, although several less penetrant genes (e.g., ATM, PALB2) have been identified. In this scenario, NGS technologies offer a powerful tool for the discovery of novel factors involved in familial breast/ovarian cancer. In this review, we summarize and discuss the state of the art applications of NGS gene panels, WES and WGS in the context of familial breast/ovarian cancer.
Collapse
Affiliation(s)
- Veronica Zelli
- Department of Biotechnological and Applied Clinical Sciences, University of L’Aquila, Via Vetoio, Coppito 2, 67100 L’Aquila, Italy; (V.Z.); (C.C.); (R.C.); (M.D.V.N.); (E.A.); (F.Z.)
- Center for Molecular Diagnostics and Advanced Therapies, University of L’Aquila, Via Petrini, 67100 L’Aquila, Italy
| | - Chiara Compagnoni
- Department of Biotechnological and Applied Clinical Sciences, University of L’Aquila, Via Vetoio, Coppito 2, 67100 L’Aquila, Italy; (V.Z.); (C.C.); (R.C.); (M.D.V.N.); (E.A.); (F.Z.)
| | - Katia Cannita
- Medical Oncology Unit, St Salvatore Hospital, Via L. Natali 1, 67100 L’Aquila, Italy;
| | - Roberta Capelli
- Department of Biotechnological and Applied Clinical Sciences, University of L’Aquila, Via Vetoio, Coppito 2, 67100 L’Aquila, Italy; (V.Z.); (C.C.); (R.C.); (M.D.V.N.); (E.A.); (F.Z.)
| | - Carlo Capalbo
- Department of Molecular Medicine, University of Rome “La Sapienza”, Viale Regina Elena 324, 00161 Rome, Italy;
| | - Mauro Di Vito Nolfi
- Department of Biotechnological and Applied Clinical Sciences, University of L’Aquila, Via Vetoio, Coppito 2, 67100 L’Aquila, Italy; (V.Z.); (C.C.); (R.C.); (M.D.V.N.); (E.A.); (F.Z.)
| | - Edoardo Alesse
- Department of Biotechnological and Applied Clinical Sciences, University of L’Aquila, Via Vetoio, Coppito 2, 67100 L’Aquila, Italy; (V.Z.); (C.C.); (R.C.); (M.D.V.N.); (E.A.); (F.Z.)
| | - Francesca Zazzeroni
- Department of Biotechnological and Applied Clinical Sciences, University of L’Aquila, Via Vetoio, Coppito 2, 67100 L’Aquila, Italy; (V.Z.); (C.C.); (R.C.); (M.D.V.N.); (E.A.); (F.Z.)
| | - Alessandra Tessitore
- Department of Biotechnological and Applied Clinical Sciences, University of L’Aquila, Via Vetoio, Coppito 2, 67100 L’Aquila, Italy; (V.Z.); (C.C.); (R.C.); (M.D.V.N.); (E.A.); (F.Z.)
- Center for Molecular Diagnostics and Advanced Therapies, University of L’Aquila, Via Petrini, 67100 L’Aquila, Italy
- Correspondence:
| |
Collapse
|
13
|
Multigene Panel Testing Increases the Number of Loci Associated with Gastric Cancer Predisposition. Cancers (Basel) 2019; 11:cancers11091340. [PMID: 31514334 PMCID: PMC6769562 DOI: 10.3390/cancers11091340] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Revised: 09/02/2019] [Accepted: 09/08/2019] [Indexed: 12/24/2022] Open
Abstract
The main gene involved in gastric cancer (GC) predisposition is CDH1, the pathogenic variants of which are associated with diffuse-type gastric cancer (DGC) and lobular breast cancer (LBC). CDH1 only explains a fraction (10–50%) of patients suspected of DGC/LBC genetic predisposition. To identify novel susceptibility genes, thus improving the management of families at risk, we performed a multigene panel testing on selected patients. We searched for germline pathogenic variants in 94 cancer-related genes in 96 GC or LBC Italian patients with early-onset and/or family history of GC. We found CDH1 pathogenic variants in 10.4% of patients. In 11.5% of cases, we identified loss-of-function variants in BRCA1, BRCA2, PALB2, and ATM breast/ovarian cancer susceptibility genes, as well as in MSH2, PMS2, BMPR1A, PRF1, and BLM genes. In 78.1% of patients, we did not find any variants with clear-cut clinical significance; however, 37.3% of these cases harbored rare missense variants predicted to be damaging by bioinformatics tools. Multigene panel testing decreased the number of patients that would have otherwise remained genetically unexplained. Besides CDH1, our results demonstrated that GC pathogenic variants are distributed across a number of susceptibility genes and reinforced the emerging link between gastric and breast cancer predisposition.
Collapse
|
14
|
Moes-Sosnowska J, Rzepecka IK, Chodzynska J, Dansonka-Mieszkowska A, Szafron LM, Balabas A, Lotocka R, Sobiczewski P, Kupryjanczyk J. Clinical importance of FANCD2, BRIP1, BRCA1, BRCA2 and FANCF expression in ovarian carcinomas. Cancer Biol Ther 2019; 20:843-854. [PMID: 30822218 PMCID: PMC6606037 DOI: 10.1080/15384047.2019.1579955] [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] [Indexed: 12/15/2022] Open
Abstract
OBJECTIVE DNA repair pathways are potential targets of molecular therapy in cancer patients. The FANCD2, BRIP1, BRCA1/2, and FANCF genes are involved in homologous recombination DNA repair, which implicates their possible role in cell response to DNA-damaging agents. We evaluated a clinical significance of pre-treatment expression of these genes at mRNA level in 99 primary, advanced-stage ovarian carcinomas from patients, who later received taxane-platinum (TP) or platinum-cyclophosphamide (PC) treatment. METHODS Gene expression was determined with the use of Real-Time PCR. The BRCA2 and BRIP1 gene sequence was investigated with the use of SSCP, dHPLC, and PCR-sequencing. RESULTS Increased FANCD2 expression occurred to be a negative prognostic factor for all patients (PC+TP:HR 3.85, p = 0.0003 for the risk of recurrence; HR 1.96, p = 0.02 for the risk of death), and this association was even stronger in the TP-treated group (HR 6.7, p = 0.0002 and HR 2.33, p = 0.01, respectively). Elevated BRIP1 expression was the only unfavorable molecular factor in the PC-treated patients (HR 8.37, p = 0.02 for the risk of recurrence). Additionally, an increased FANCD2 and BRCA1/2 expression levels were associated with poor ovarian cancer outcome in either TP53-positive or -negative subgroups of the TP-treated patients, however these groups were small. Sequence analysis identified one protein truncating variant (1/99) in BRCA2 and no mutations (0/56) in BRIP1. CONCLUSIONS Our study shows for the first time that FANCD2 overexpression is a strong negative prognostic factor in ovarian cancer, particularly in patients treated with TP regimen. Moreover, increased mRNA level of the BRIP1 is a negative prognostic factor in the PC-treated patients. Next, changes in the BRCA2 and BRIP1 genes are rare and together with other analyzed FA genes considered as homologous recombination deficiency may not affect the expression level of analyzed genes.
Collapse
Affiliation(s)
- Joanna Moes-Sosnowska
- a Department of Immunology , Maria Sklodowska-Curie Institute - Oncology Center , Warsaw , Poland
| | - Iwona K Rzepecka
- b Department of Pathology and Laboratory Diagnostics , Maria Sklodowska-Curie Institute - Oncology Center , Warsaw , Poland
| | - Joanna Chodzynska
- c Laboratory of Bioinformatics and Biostatistics , Maria Sklodowska-Curie Institute - Oncology Center , Warsaw , Poland
| | - Agnieszka Dansonka-Mieszkowska
- b Department of Pathology and Laboratory Diagnostics , Maria Sklodowska-Curie Institute - Oncology Center , Warsaw , Poland
| | - Lukasz M Szafron
- a Department of Immunology , Maria Sklodowska-Curie Institute - Oncology Center , Warsaw , Poland
| | - Aneta Balabas
- d Department of Genetics , Maria Sklodowska-Curie Institute - Oncology Center , Warsaw , Poland
| | - Renata Lotocka
- b Department of Pathology and Laboratory Diagnostics , Maria Sklodowska-Curie Institute - Oncology Center , Warsaw , Poland
| | - Piotr Sobiczewski
- e Department of Gynecologic Oncology , Maria Sklodowska-Curie Institute - Oncology Center , Warsaw , Poland
| | - Jolanta Kupryjanczyk
- b Department of Pathology and Laboratory Diagnostics , Maria Sklodowska-Curie Institute - Oncology Center , Warsaw , Poland
| |
Collapse
|
15
|
Kowalik A, Siołek M, Kopczyński J, Krawiec K, Kalisz J, Zięba S, Kozak-Klonowska B, Wypiórkiewicz E, Furmańczyk J, Nowak-Ozimek E, Chłopek M, Macek P, Smok-Kalwat J, Góźdź S. BRCA1 founder mutations and beyond in the Polish population: A single-institution BRCA1/2 next-generation sequencing study. PLoS One 2018; 13:e0201086. [PMID: 30040829 PMCID: PMC6057642 DOI: 10.1371/journal.pone.0201086] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Accepted: 07/10/2018] [Indexed: 12/22/2022] Open
Abstract
Hereditary mutations in BRCA1/2 genes increase the risk of breast cancer by 60–80% and ovarian cancer by about 20–40% in female carriers. Detection of inherited mutations in asymptomatic carriers allows for the implementation of appropriate preventive measures. BRCA1/2 genotyping is also important for poly(adenosine diphosphate)-ribose polymerase (PARP) inhibitor administration. This work addresses the need for next-generation sequencing (NGS) technology for the detection of BRCA1/2 mutations in Poland where until recently mostly founder mutations have been tested, and whether BRCA diagnostics should be extended beyond the panel of founder mutations in this population. The study comprises 2931 patients who were referred for genetic counseling and tested for founder and recurrent mutations in BRCA1 (5382insC (c.5266dupC; p.Gln1756Profs), c.5370C>T (c.5251C>T; p.R1751*), 300T>G (c.181T>G; p.Cys61Gly), 185delAG (c.68_69delAG; p.Glu23Valfs), and 4153delA (c.4035delA; p.Glu1346Lysfs)) by high-resolution melting/Sanger sequencing. A total of 103 (3.5%) mutations were detected, including 53 (51%) in healthy subjects and 50 (49%) in cancer patients. Then, based on more stringent clinical and pedigree criteria, sequencing of all BRCA1/2 exons was performed in 454 (16%) patients without founder mutations by NGS, which detected 58 mutations (12.8%), 40 (8.8%) of which were pathogenic. In 14 (3.1%) subjects, variants of uncertain significance (VUS) were detected, and in four (0.9%) subjects, the detected mutations were benign. In total, 161 mutations were detected using our two-step algorithm (founder test and NGS), of which 64% were founder mutations, 25% were NGS-detected pathogenic mutations, 9% were VUS, and 2% were benign. In addition, 38 mutations not yet reported in the Polish population were detected. In total, founder mutations accounted for only 64% of all detected mutations, and the remaining mutations (36%) were dispersed across the BRCA1/2 gene sequences. Thus, in Poland, testing for constitutional mutations in BRCA1/2 should be carried out in two stages, where NGS is performed in qualifying subjects if founder mutations are not identified.
Collapse
Affiliation(s)
- Artur Kowalik
- Department of Molecular Diagnostics, Holycross Cancer Centre, Kielce, Poland
- * E-mail:
| | - Monika Siołek
- Genetic Clinic, Holycross Cancer Centre, Kielce, Poland
| | - Janusz Kopczyński
- Department of Surgical Pathology, Holycross Cancer Centre, Kielce, Poland
| | - Kamila Krawiec
- Department of Molecular Diagnostics, Holycross Cancer Centre, Kielce, Poland
| | - Joanna Kalisz
- Department of Molecular Diagnostics, Holycross Cancer Centre, Kielce, Poland
| | - Sebastian Zięba
- Department of Molecular Diagnostics, Holycross Cancer Centre, Kielce, Poland
| | | | | | - Jowita Furmańczyk
- Department of Molecular Diagnostics, Holycross Cancer Centre, Kielce, Poland
| | | | - Małgorzata Chłopek
- Department of Molecular Diagnostics, Holycross Cancer Centre, Kielce, Poland
| | - Paweł Macek
- Department of Cancer Epidemiology and Cancer Control, Holycross Cancer Centre, Kielce, Poland
| | | | - Stanisław Góźdź
- Oncology Clinic, Holycross Cancer Centre, Kielce, Poland
- The Faculty of Medicine and Health Sciences, Jan Kochanowski University in Kielce, Poland
| |
Collapse
|
16
|
Norum J, Grindedal EM, Heramb C, Karsrud I, Ariansen SL, Undlien DE, Schlichting E, Mæhle L. BRCA mutation carrier detection. A model-based cost-effectiveness analysis comparing the traditional family history approach and the testing of all patients with breast cancer. ESMO Open 2018; 3:e000328. [PMID: 29682331 PMCID: PMC5905828 DOI: 10.1136/esmoopen-2018-000328] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2018] [Revised: 02/20/2018] [Accepted: 02/21/2018] [Indexed: 12/29/2022] Open
Abstract
Background Identification of BRCA mutation carriers among patients with breast cancer (BC) involves costs and gains. Testing has been performed according to international guidelines, focusing on family history (FH) of breast and/or ovarian cancer. An alternative is testing all patients with BC employing sequencing of the BRCA genes and Multiplex Ligation Probe Amplification (MLPA). Patients and methods A model-based cost-effectiveness analysis, employing data from Oslo University Hospital, Ullevål (OUH-U) and a decision tree, was done. The societal and the healthcare perspectives were focused and a lifetime perspective employed. The comparators were the traditional FH approach used as standard of care at OUH-U in 2013 and the intervention (testing all patients with BC) performed in 2014 and 2015 at the same hospital. During the latter period, 535 patients with BC were offered BRCA testing with sequencing and MLPA. National 2014 data on mortality rates and costs were implemented, a 3% discount rate used and the costing year was 2015. The incremental cost-effectiveness ratio was calculated in euros (€) per life-year gained (LYG). Results The net healthcare cost (healthcare perspective) was €40 503/LYG. Including all resource use (societal perspective), the cost was €5669/LYG. The univariate sensitivity analysis documented the unit cost of the BRCA test and the number of LYGs the prominent parameters affecting the result. Diagnostic BRCA testing of all patients with BC was superior to the FH approach and cost-effective within the frequently used thresholds (healthcare perspective) in Norway (€60 000–€80 000/LYG).
Collapse
Affiliation(s)
- Jan Norum
- Department of Surgery, Finnmark Hospital, Hammerfest, Norway
| | | | - Cecilie Heramb
- Department of Medical Genetics, Oslo University Hospital and University of Oslo, Oslo, Norway
| | - Inga Karsrud
- Section for Breast and Endocrine Surgery, Department of Cancer, Oslo University Hospital, Oslo, Norway
| | - Sarah Louise Ariansen
- Department of Medical Genetics, Oslo University Hospital and University of Oslo, Oslo, Norway
| | - Dag Erik Undlien
- Section for Breast and Endocrine Surgery, Department of Cancer, Oslo University Hospital, Oslo, Norway
| | - Ellen Schlichting
- Section for Breast and Endocrine Surgery, Department of Cancer, Oslo University Hospital, Oslo, Norway
| | - Lovise Mæhle
- Department of Medical Genetics, Oslo University Hospital and University of Oslo, Oslo, Norway
| |
Collapse
|
17
|
Lugowska I, Teterycz P, Mikula M, Kulecka M, Kluska A, Balabas A, Piatkowska M, Wagrodzki M, Pienkowski A, Rutkowski P, Ostrowski J. IDH1/2 Mutations Predict Shorter Survival in Chondrosarcoma. J Cancer 2018; 9:998-1005. [PMID: 29581779 PMCID: PMC5868167 DOI: 10.7150/jca.22915] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2017] [Accepted: 01/28/2018] [Indexed: 12/11/2022] Open
Abstract
Background. Recent studies have shown that isocitrate dehydrogenase 1/2 (IDH1/2)- activating mutations occur in a variety of cancers, including acute myeloid leukaemia, gliomas, and chondrosarcomas (CHS)s. The effect of IDH1/2 mutation on overall survival (OS) has not been reported in CHS. The aim of our study was to assess the prevalence of known cancer-related gene mutations in CHS, as well as their prognostic role in patient survival. Methods. DNA from FFPE samples of 80 patients (F:M- 1:1.3; mean age: 58 years; range 27-86) with histologically confirmed CHS (G1:29; G2:34; G3:17) was subjected to library preparation with the Ion AmpliSeq Cancer Hotspot Panel v2 and sequenced on the PGM Ion Torrent. Results. Among the clinical features only histological grade influenced OS. Deep sequencing identified 1784 single nucleotide variants. Of them, 426 were considered to be pathogenic or probably pathogenic. Activating IDH1/2 mutations were found in 27 patients (34%) including 17 R132 IDH1 (21%), 10 R172 IDH2 (13%) and 3 R140 IDH2 variants (4%). Three patients had concurrent IDH1 and IDH2 mutations. The R140 IDH2 mutant has not been reported to date in CHS patients. OS for CHS patients with IDH1/2 mutations was significantly lower than in patients without mutations (93% vs 64%; p<0.001). No other genetic feature of the Cancer Hotspot Panel had an impact on OS. Conclusions. In CHS, IDH1/2-mutation status and the histological aggressiveness of the CHS are important predictors for OS. The R140 IDH2 may also be a novel target for the treatment of CHS patients.
Collapse
Affiliation(s)
- Iwona Lugowska
- Department of Soft Tissue/Bone Sarcoma and Melanoma, Maria Sklodowska-Curie Memorial Cancer Center and Institute of Oncology; Roentgena 5, 02-781 Warsaw, Poland.,Early Phase Clinical Trials Unit, Maria Sklodowska-Curie Memorial Cancer Center and Institute of Oncology; Roentgena 5, 02-781 Warsaw, Poland
| | - Pawel Teterycz
- Department of Soft Tissue/Bone Sarcoma and Melanoma, Maria Sklodowska-Curie Memorial Cancer Center and Institute of Oncology; Roentgena 5, 02-781 Warsaw, Poland
| | - Michal Mikula
- Department of Genetics, Maria Sklodowska-Curie Memorial Cancer Center and Institute of Oncology; Roentgena 5, 02-781 Warsaw, Poland
| | - Maria Kulecka
- Department of Gastroenterology, Hepatology and Clinical Oncology, Medical Center for Postgraduate Education, Roentgena 5, 02-781 Warsaw, Poland
| | - Anna Kluska
- Department of Genetics, Maria Sklodowska-Curie Memorial Cancer Center and Institute of Oncology; Roentgena 5, 02-781 Warsaw, Poland
| | - Aneta Balabas
- Department of Genetics, Maria Sklodowska-Curie Memorial Cancer Center and Institute of Oncology; Roentgena 5, 02-781 Warsaw, Poland
| | - Magdalena Piatkowska
- Department of Genetics, Maria Sklodowska-Curie Memorial Cancer Center and Institute of Oncology; Roentgena 5, 02-781 Warsaw, Poland
| | - Michal Wagrodzki
- Department of Pathology, Maria Sklodowska-Curie Memorial Cancer Center and Institute of Oncology; Roentgena 502-781 Warsaw, Poland
| | - Andrzej Pienkowski
- Department of Soft Tissue/Bone Sarcoma and Melanoma, Maria Sklodowska-Curie Memorial Cancer Center and Institute of Oncology; Roentgena 5, 02-781 Warsaw, Poland
| | - Piotr Rutkowski
- Department of Soft Tissue/Bone Sarcoma and Melanoma, Maria Sklodowska-Curie Memorial Cancer Center and Institute of Oncology; Roentgena 5, 02-781 Warsaw, Poland
| | - Jerzy Ostrowski
- Department of Genetics, Maria Sklodowska-Curie Memorial Cancer Center and Institute of Oncology; Roentgena 5, 02-781 Warsaw, Poland.,Department of Gastroenterology, Hepatology and Clinical Oncology, Medical Center for Postgraduate Education, Roentgena 5, 02-781 Warsaw, Poland
| |
Collapse
|
18
|
Double Heterozygosity for BRCA1 Pathogenic Variant and BRCA2 Polymorphic Stop Codon K3326X: A Case Report in a Southern Italian Family. Int J Mol Sci 2018; 19:ijms19010285. [PMID: 29346284 PMCID: PMC5796231 DOI: 10.3390/ijms19010285] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2017] [Revised: 01/15/2018] [Accepted: 01/16/2018] [Indexed: 11/17/2022] Open
Abstract
Here, we describe a patient with bilateral breast cancer and melanoma, and with a concomitant double variant, namely p.Gln563Ter in BRCA1 and p.Lys3326Ter in BRCA2. The BRCA2 p.Lys3326Ter (K3326X) (rs11571833) mutation identified in our patient is a debated substitution of thymidine for adenine which is currently regarded as benign polymorphism in main gene databases. Recent studies, however, describe this variant as associated with breast and ovarian tumors. Based on the observation of the cancer’s earliest age of onset in this subject, our purpose was to reevaluate this variant according to recent papers indicating a role of powerful modifier of the genetic penetrance. Genetic testing was performed in all consenting patient’s relatives, and in the collection of the clinical data particular attention was paid to the age of onset of the neoplasia. Following our observation that the our patient with double heterozygosis had an early age of onset for cancer similar to a few rare cases of double mutation for BRCA1 and BRCA2, we also performed an extensive review of the literature relative to patients carrying a double heterozygosity for both genes. In line with previous studies relative to the rare double heterozygosity in both BRCA1/2 genes, we found the earlier onset of breast cancer in our patient with both BRCA1/2 mutations with respect to other relatives carrying the single BRCA1 mutation. The presence of the second K3326X variant in our case induces a phenotype characterized by early onset of the neoplasia in a manner similar to the other cases of double heterozygosity previously described. Therefore, we suggest that during the genetic counseling, it should be recommendable to evaluate the presence of the K3326X variant in association with other pathogenic mutations.
Collapse
|
19
|
Heramb C, Wangensteen T, Grindedal EM, Ariansen SL, Lothe S, Heimdal KR, Mæhle L. BRCA1 and BRCA2 mutation spectrum - an update on mutation distribution in a large cancer genetics clinic in Norway. Hered Cancer Clin Pract 2018; 16:3. [PMID: 29339979 PMCID: PMC5761139 DOI: 10.1186/s13053-017-0085-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2017] [Accepted: 12/28/2017] [Indexed: 12/13/2022] Open
Abstract
Background Founder mutations in the two breast cancer genes, BRCA1 and BRCA2, have been described in many populations, among these are Ashkenazi-Jewish, Polish, Norwegian and Icelandic. Founder mutation testing in patients with relevant ancestry has been a cost-efficient approach in such populations. Four Norwegian BRCA1 founder mutations were defined by haplotyping in 2001, and accounted for 68% of BRCA1 mutation carriers at the time. After 15 more years of genetic testing, updated knowledge on the mutation spectrum of both BRCA1 and BRCA2 in Norway is needed. In this study, we aim at describing the mutation spectrum and frequencies in the BRCA1/2 carrier population of the largest clinic of hereditary cancer in Norway. Methods A total of 2430 BRCA1 carriers from 669 different families, and 1092 BRCA2 carriers from 312 different families were included in a quality of care study. All variants were evaluated regarding pathogenicity following ACMG/ENIGMA criteria. The variants were assessed in AlaMut and supplementary databases to determine whether they were known to be founder mutations in other populations. Results There were 120 different BRCA1 and 87 different BRCA2 variants among the mutation carriers. Forty-six per cent of the registered BRCA1/2 families (454/981) had a previously reported Norwegian founder mutation. The majority of BRCA1/2 mutations (71%) were rare, each found in only one or two families. Fifteen per cent of BRCA1 families and 25% of BRCA2 families had one of these rare variants. The four well-known Norwegian BRCA1 founder mutations previously confirmed through haplotyping were still the four most frequent mutations in BRCA1 carriers, but the proportion of BRCA1 mutation carriers accounted for by these mutations had fallen from 68 to 52%, and hence the founder effect was weaker than previously described. Conclusions The spectrum of BRCA1 and BRCA2 mutations in the carrier population at Norway’s largest cancer genetics clinic is diverse, and with a weaker founder effect than previously described. As a consequence, retesting the families that previously have been tested with specific tests/founder mutation tests should be a prioritised strategy to find more mutation positive families and possibly prevent cancer in healthy relatives.
Collapse
Affiliation(s)
- Cecilie Heramb
- Department of Medical Genetics, Oslo University Hospital, Oslo, Norway.,University of Oslo, Oslo, Norway.,Norwegian National Advisory Unit on Women's Health, Oslo University Hospital, Oslo, Norway
| | | | | | | | - Sheba Lothe
- Department of Medical Genetics, MSc Oslo University Hospital, Oslo, Norway
| | | | - Lovise Mæhle
- Department of Medical Genetics, Oslo University Hospital, Oslo, Norway
| |
Collapse
|
20
|
Fountzilas G, Psyrri A, Giannoulatou E, Tikas I, Manousou K, Rontogianni D, Ciuleanu E, Ciuleanu T, Resiga L, Zaramboukas T, Papadopoulou K, Bobos M, Chrisafi S, Tsolaki E, Markou K, Giotakis E, Koutras A, Psoma E, Kalogera-Fountzila A, Skondra M, Bamia C, Pectasides D, Kotoula V. Prevalent somaticBRCA1mutations shape clinically relevant genomic patterns of nasopharyngeal carcinoma in Southeast Europe. Int J Cancer 2017; 142:66-80. [DOI: 10.1002/ijc.31023] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2017] [Accepted: 08/01/2017] [Indexed: 12/16/2022]
Affiliation(s)
- George Fountzilas
- Laboratory of Molecular Oncology; Hellenic Foundation for Cancer Research/Aristotle University of Thessaloniki; Thessaloniki Greece
- Faculty of Medicine, School of Health Sciences; Aristotle University of Thessaloniki; Thessaloniki Greece
| | - Amanda Psyrri
- Division of Oncology, Second Department of Internal Medicine; Attikon University Hospital; Athens Greece
| | - Eleni Giannoulatou
- Victor Chang Cardiac Research Institute; Darlinghurst NSW Australia
- The University of New South Wales; Kensington NSW Australia
| | - Ioannis Tikas
- Laboratory of Molecular Oncology; Hellenic Foundation for Cancer Research/Aristotle University of Thessaloniki; Thessaloniki Greece
| | - Kyriaki Manousou
- Section of Biostatistics, Hellenic Cooperative Oncology Group; Data Office; Athens Greece
| | | | | | - Tudor Ciuleanu
- Institute of Oncology Ion Chiricuta and UMF Iuliu Hatieganu; Cluj-Napoca Romania
| | - Liliana Resiga
- Department of Pathology; Ion Chiricuta Cancer Institute; Cluj Romania
| | - Thomas Zaramboukas
- Department of Pathology; School of Health Sciences, Faculty of Medicine, Aristotle University of Thessaloniki; Thessaloniki Greece
| | - Kyriaki Papadopoulou
- Laboratory of Molecular Oncology; Hellenic Foundation for Cancer Research/Aristotle University of Thessaloniki; Thessaloniki Greece
| | - Mattheos Bobos
- Laboratory of Molecular Oncology; Hellenic Foundation for Cancer Research/Aristotle University of Thessaloniki; Thessaloniki Greece
| | - Sofia Chrisafi
- Laboratory of Molecular Oncology; Hellenic Foundation for Cancer Research/Aristotle University of Thessaloniki; Thessaloniki Greece
| | - Eleftheria Tsolaki
- Laboratory of Molecular Oncology; Hellenic Foundation for Cancer Research/Aristotle University of Thessaloniki; Thessaloniki Greece
| | - Konstantinos Markou
- First Department of Otorhinolaryngology; AHEPA Hospital, School of Health Sciences, Faculty of Medicine, Aristotle University of Thessaloniki; Thessaloniki Greece
| | - Evangelos Giotakis
- Department of Otolaryngology Head and Neck Surgery; Hippokration Hospital, National and Kapodistrian University of Athens; Athens Greece
| | - Angelos Koutras
- Division of Oncology, Department of Medicine; University Hospital, University of Patras Medical School; Patras Greece
| | - Elsa Psoma
- Department of Radiology; AHEPA Hospital, School of Health Sciences, Faculty of Medicine, Aristotle University of Thessaloniki; Thessaloniki Greece
| | - Anna Kalogera-Fountzila
- Department of Radiology; AHEPA Hospital, School of Health Sciences, Faculty of Medicine, Aristotle University of Thessaloniki; Thessaloniki Greece
| | - Maria Skondra
- Oncology Section, Second Department of Internal Medicine; Hippokration Hospital; Athens
| | - Christina Bamia
- Department of Hygiene, Epidemiology and Medical Statistics; National and Kapodistrian University of Athens, Medical School; Athens Greece
| | - Dimitrios Pectasides
- Oncology Section, Second Department of Internal Medicine; Hippokration Hospital; Athens
| | - Vassiliki Kotoula
- Laboratory of Molecular Oncology; Hellenic Foundation for Cancer Research/Aristotle University of Thessaloniki; Thessaloniki Greece
- Department of Pathology; School of Health Sciences, Faculty of Medicine, Aristotle University of Thessaloniki; Thessaloniki Greece
| |
Collapse
|
21
|
Abstract
Background Identification of BRCA mutations in breast cancer (BC) patients influences treatment and survival and may be of importance for their relatives. Testing is often restricted to women fulfilling high-risk criteria. However, there is limited knowledge of the sensitivity of such a strategy, and of the clinical aspects of BC caused by BRCA mutations in less selected BC cohorts. The aim of this report was to address these issues by evaluating the results of BRCA testing of BC patients in South-Eastern Norway. Methods 1371 newly diagnosed BC patients were tested with sequencing and Multi Ligation Probe Amplification (MLPA). Prevalence of mutations was calculated, and BC characteristics among carriers and non-carriers compared. Sensitivity and specificity of common guidelines for BRCA testing to identify carriers was analyzed. Number of identified female mutation positive relatives was evaluated. Results A pathogenic BRCA mutation was identified in 3.1%. Carriers differed from non-carriers in terms of age at diagnosis, family history, grade, ER/PR-status, triple negativity (TNBC) and Ki67, but not in HER2 and TNM status. One mutation positive female relative was identified per mutation positive BC patient. Using age of onset below 40 or TNBC as criteria for testing identified 32-34% of carriers. Common guidelines for testing identified 45-90%, and testing all below 60 years identified 90%. Thirty-seven percent of carriers had a family history of cancer that would have qualified for predictive BRCA testing. A Variant of Uncertain Significance (VUS) was identified in 4.9%. Conclusions Mutation positive BC patients differed as a group from mutation negative. However, the commonly used guidelines for testing were insufficient to detect all mutation carriers in the BC cohort. Thirty-seven percent had a family history of cancer that would have qualified for predictive testing before they were diagnosed with BC. Based on our combined observations, we suggest it is time to discuss whether all BC patients should be offered BRCA testing, both to optimize treatment and improve survival for these women, but also to enable identification of healthy mutation carriers within their families. Health services need to be aware of referral possibility for healthy women with cancer in their family. Electronic supplementary material The online version of this article (doi:10.1186/s12885-017-3422-2) contains supplementary material, which is available to authorized users.
Collapse
|
22
|
Hwang SM, Lee KC, Lee MS, Park KU. Comparison of Ion Personal Genome Machine Platforms for the Detection of Variants in BRCA1 and BRCA2. Cancer Res Treat 2017; 50:255-264. [PMID: 28392550 PMCID: PMC5784618 DOI: 10.4143/crt.2017.062] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2017] [Accepted: 04/03/2017] [Indexed: 11/26/2022] Open
Abstract
Purpose Transition to next generation sequencing (NGS) for BRCA1/BRCA2 analysis in clinical laboratories is ongoing but different platforms and/or data analysis pipelines give different results resulting in difficulties in implementation. We have evaluated the Ion Personal Genome Machine (PGM) Platforms (Ion PGM, Ion PGM Dx, Thermo Fisher Scientific) for the analysis of BRCA1/2. Materials and Methods The results of Ion PGM with OTG-snpcaller, a pipeline based on Torrent mapping alignment program and Genome Analysis Toolkit, from 75 clinical samples and 14 reference DNA samples were compared with Sanger sequencing for BRCA1/BRCA2. Ten clinical samples and 14 reference DNA samples were additionally sequenced by Ion PGM Dx with Torrent Suite. Results Fifty types of variants including 18 pathogenic or variants of unknown significance were identified from 75 clinical samples and known variants of the reference samples were confirmed by Sanger sequencing and/or NGS. One false-negative results were present for Ion PGM/OTG-snpcaller for an indel variant misidentified as a single nucleotide variant. However, eight discordant results were present for Ion PGM Dx/Torrent Suite with both false-positive and -negative results. A 40-bp deletion, a 4-bp deletion and a 1-bp deletion variant was not called and a false-positive deletion was identified. Four other variants were misidentified as another variant. Conclusion Ion PGM/OTG-snpcaller showed acceptable performance with good concordance with Sanger sequencing. However, Ion PGM Dx/Torrent Suite showed many discrepant results not suitable for use in a clinical laboratory, requiring further optimization of the data analysis for calling variants.
Collapse
Affiliation(s)
- Sang Mee Hwang
- Department of Laboratory Medicine, Seoul National University Bundang Hospital, Seongnam, Korea.,Department of Laboratory Medicine, Seoul National University College of Medicine, Seoul, Korea
| | - Ki Chan Lee
- Eone-Diagnomics Genome Center, Incheon, Korea
| | | | - Kyoung Un Park
- Department of Laboratory Medicine, Seoul National University Bundang Hospital, Seongnam, Korea.,Department of Laboratory Medicine, Seoul National University College of Medicine, Seoul, Korea
| |
Collapse
|
23
|
PALB2 mutations in BRCA1/2-mutation negative breast and ovarian cancer patients from Poland. BMC Med Genomics 2017; 10:14. [PMID: 28279176 PMCID: PMC5345197 DOI: 10.1186/s12920-017-0251-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2016] [Accepted: 03/03/2017] [Indexed: 12/20/2022] Open
Abstract
Background The PALB2 gene encodes a protein that plays a crucial role in maintaining genomic integrity. Germline inactivating mutations in PALB2 are associated with an increased risk of breast and ovarian cancer. The prevalence and spectrum of recurrent PALB2 germline mutations in breast and ovarian cancer patients from Poland is not clearly defined. Methods PALB2 exons were amplified from 460 BRCA1/2-mutation negative women with familial breast and/or ovarian cancer and early-onset breast cancer using AmpliSeq technology and sequenced on an Ion Torrent PGM sequencer. In addition, eight selected variants were genotyped using TaqMan assays in 807 BRCA1/2-mutation negative breast cancer patients and 1690 healthy women. Results Two recurrent PALB2 mutations, c.172_175delTTGT and c.509_510delGA, were identified, along with one novel mutation, c.347insT. In total, PALB2 pathogenic mutations were detected in 7/460 (1.5%) patients. Furthermore, in breast and/or ovarian cancer patients, several single nucleotide variants (SNVs) were detected in the PALB2 coding region. In an additional group of 807 patients, eight (1%) carriers of two pathogenic mutations, c.172_175delTTGT (0.5%) and c.509_510delGA (0.5%), were identified. The c.509_510delGA mutation was not identified in healthy controls, while c.172_175delTTGT was identified in 4/1690 (0.24%) of control women. Conclusions Germline mutations in the PALB2 gene were observed at a frequency of approximately 1.5% in Polish breast and/or ovarian cancer patients. Our study confirms two recurrent PALB2 mutations; c.172_175delGA and c.509_510delGA.
Collapse
|
24
|
Kobayashi Y, Yang S, Nykamp K, Garcia J, Lincoln SE, Topper SE. Pathogenic variant burden in the ExAC database: an empirical approach to evaluating population data for clinical variant interpretation. Genome Med 2017; 9:13. [PMID: 28166811 PMCID: PMC5295186 DOI: 10.1186/s13073-017-0403-7] [Citation(s) in RCA: 130] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2016] [Accepted: 01/13/2017] [Indexed: 12/25/2022] Open
Abstract
Background The frequency of a variant in the general population is a key criterion used in the clinical interpretation of sequence variants. With certain exceptions, such as founder mutations, the rarity of a variant is a prerequisite for pathogenicity. However, defining the threshold at which a variant should be considered “too common” is challenging and therefore diagnostic laboratories have typically set conservative allele frequency thresholds. Methods Recent publications of large population sequencing data, such as the Exome Aggregation Consortium (ExAC) database, provide an opportunity to characterize with accuracy and precision the frequency distributions of very rare disease-causing alleles. Allele frequencies of pathogenic variants in ClinVar, as well as variants expected to be pathogenic through the nonsense-mediated decay (NMD) pathway, were analyzed to study the burden of pathogenic variants in 79 genes of clinical importance. Results Of 1364 BRCA1 and BRCA2 variants that are well characterized as pathogenic or that are expected to lead to NMD, 1350 variants had an allele frequency of less than 0.0025%. The remaining 14 variants were previously published founder mutations. Importantly, we observed no difference in the distributions of pathogenic variants expected to be lead to NMD compared to those that are not. Therefore, we expanded the analysis to examine the distributions of NMD expected variants in 77 additional genes. These 77 genes were selected to represent a broad set of clinical areas, modes of inheritance, and penetrance. Among these variants, most (97.3%) had an allele frequency of less than 0.01%. Furthermore, pathogenic variants with allele frequencies greater than 0.01% were well characterized in publications and included many founder mutations. Conclusions The observations made in this study suggest that, with certain caveats, a very low allele frequency threshold can be adopted to more accurately interpret sequence variants. Electronic supplementary material The online version of this article (doi:10.1186/s13073-017-0403-7) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Yuya Kobayashi
- Invitae Corporation, 1400 16th St., San Francisco, CA, 94103, USA.
| | - Shan Yang
- Invitae Corporation, 1400 16th St., San Francisco, CA, 94103, USA
| | - Keith Nykamp
- Invitae Corporation, 1400 16th St., San Francisco, CA, 94103, USA
| | - John Garcia
- Invitae Corporation, 1400 16th St., San Francisco, CA, 94103, USA
| | | | - Scott E Topper
- Invitae Corporation, 1400 16th St., San Francisco, CA, 94103, USA
| |
Collapse
|
25
|
Romanowicz H, Strapagiel D, Słomka M, Sobalska-Kwapis M, Kępka E, Siewierska-Górska A, Zadrożny M, Bieńkiewicz J, Smolarz B. New single nucleotide polymorphisms (SNPs) in homologous recombination repair genes detected by microarray analysis in Polish breast cancer patients. Clin Exp Med 2016; 17:541-546. [DOI: 10.1007/s10238-016-0441-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2016] [Accepted: 11/14/2016] [Indexed: 11/29/2022]
|
26
|
Evaluation of an amplicon-based next-generation sequencing panel for detection of BRCA1 and BRCA2 genetic variants. Breast Cancer Res Treat 2016; 158:433-40. [PMID: 27383479 DOI: 10.1007/s10549-016-3891-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2016] [Accepted: 06/27/2016] [Indexed: 01/15/2023]
Abstract
The recent advances in the next-generation sequencing (NGS) technology have enabled fast, accurate, and cost-effective genetic testing. Here, we evaluated the performance of a targeted NGS panel for BRCA1/2 sequencing and confirmed its applicability in routine clinical diagnostics. We tested samples from 88 patients using the TruSeq custom panel (Illumina Inc, USA) and a MiSeq sequencer (Illumina) and compared the results to the outcomes of conventional Sanger sequencing. All 1015 sequence variations identified by Sanger sequencing were detected by NGS, except for one missense variant that might have been missed due to a rare mutation on a primer-binding site. One deletion variation, c.1909 + 12delT of BRCA2, was falsely called in all samples due to a homopolymer error. In addition, seven different single-nucleotide substitutions with low variant frequencies (range: 16.2-33.3 %) were falsely called by NGS. In a separate batch, 10 different false-positive variations were found in five samples. The overall sensitivity and positive predictive value of NGS were estimated to be 99.9 and 87.5 %, respectively. The false-positive results could be excluded by setting quality and alternative allele ratio filters and/or by visual inspection using the IGV software. Targeted NGS panel for BRCA1 and BRCA2 showed an excellent agreement with Sanger sequencing results. We therefore conclude that this NGS panel can be used for routine diagnostic method in a clinical genetic laboratory.
Collapse
|
27
|
Verma M. Genome-wide association studies and epigenome-wide association studies go together in cancer control. Future Oncol 2016; 12:1645-64. [PMID: 27079684 PMCID: PMC5551540 DOI: 10.2217/fon-2015-0035] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2015] [Accepted: 03/22/2016] [Indexed: 02/07/2023] Open
Abstract
Completion of the human genome a decade ago laid the foundation for: using genetic information in assessing risk to identify individuals and populations that are likely to develop cancer, and designing treatments based on a person's genetic profiling (precision medicine). Genome-wide association studies (GWAS) completed during the past few years have identified risk-associated single nucleotide polymorphisms that can be used as screening tools in epidemiologic studies of a variety of tumor types. This led to the conduct of epigenome-wide association studies (EWAS). This article discusses the current status, challenges and research opportunities in GWAS and EWAS. Information gained from GWAS and EWAS has potential applications in cancer control and treatment.
Collapse
Affiliation(s)
- Mukesh Verma
- Methods & Technologies Branch, Epidemiology & Genomics Research Program, Division of Cancer Control & Population Sciences, National Cancer Institute (NCI), NIH, 9609 Medical Center Drive, Suite 4E102, Rockville, MD 20850, USA
| |
Collapse
|
28
|
Mucaki EJ, Caminsky NG, Perri AM, Lu R, Laederach A, Halvorsen M, Knoll JHM, Rogan PK. A unified analytic framework for prioritization of non-coding variants of uncertain significance in heritable breast and ovarian cancer. BMC Med Genomics 2016; 9:19. [PMID: 27067391 PMCID: PMC4828881 DOI: 10.1186/s12920-016-0178-5] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2015] [Accepted: 03/15/2016] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Sequencing of both healthy and disease singletons yields many novel and low frequency variants of uncertain significance (VUS). Complete gene and genome sequencing by next generation sequencing (NGS) significantly increases the number of VUS detected. While prior studies have emphasized protein coding variants, non-coding sequence variants have also been proven to significantly contribute to high penetrance disorders, such as hereditary breast and ovarian cancer (HBOC). We present a strategy for analyzing different functional classes of non-coding variants based on information theory (IT) and prioritizing patients with large intragenic deletions. METHODS We captured and enriched for coding and non-coding variants in genes known to harbor mutations that increase HBOC risk. Custom oligonucleotide baits spanning the complete coding, non-coding, and intergenic regions 10 kb up- and downstream of ATM, BRCA1, BRCA2, CDH1, CHEK2, PALB2, and TP53 were synthesized for solution hybridization enrichment. Unique and divergent repetitive sequences were sequenced in 102 high-risk, anonymized patients without identified mutations in BRCA1/2. Aside from protein coding and copy number changes, IT-based sequence analysis was used to identify and prioritize pathogenic non-coding variants that occurred within sequence elements predicted to be recognized by proteins or protein complexes involved in mRNA splicing, transcription, and untranslated region (UTR) binding and structure. This approach was supplemented by in silico and laboratory analysis of UTR structure. RESULTS 15,311 unique variants were identified, of which 245 occurred in coding regions. With the unified IT-framework, 132 variants were identified and 87 functionally significant VUS were further prioritized. An intragenic 32.1 kb interval in BRCA2 that was likely hemizygous was detected in one patient. We also identified 4 stop-gain variants and 3 reading-frame altering exonic insertions/deletions (indels). CONCLUSIONS We have presented a strategy for complete gene sequence analysis followed by a unified framework for interpreting non-coding variants that may affect gene expression. This approach distills large numbers of variants detected by NGS to a limited set of variants prioritized as potential deleterious changes.
Collapse
Affiliation(s)
- Eliseos J Mucaki
- Department of Biochemistry, Schulich School of Medicine and Dentistry, Western University, London, ON, N6A 2C1, Canada
| | - Natasha G Caminsky
- Department of Biochemistry, Schulich School of Medicine and Dentistry, Western University, London, ON, N6A 2C1, Canada
| | - Ami M Perri
- Department of Biochemistry, Schulich School of Medicine and Dentistry, Western University, London, ON, N6A 2C1, Canada
| | - Ruipeng Lu
- Department of Computer Science, Faculty of Science, Western University, London, N6A 2C1, Canada
| | - Alain Laederach
- Department of Biology, University of North Carolina, Chapel Hill, NC, 27599-3290, USA
| | - Matthew Halvorsen
- Institute for Genomic Medicine, Columbia University Medical Center, New York, NY, 10032, USA
| | - Joan H M Knoll
- Department of Pathology and Laboratory Medicine, Schulich School of Medicine and Dentistry, Western University, London, N6A 2C1, Canada
- Cytognomix Inc., London, Canada
| | - Peter K Rogan
- Department of Biochemistry, Schulich School of Medicine and Dentistry, Western University, London, ON, N6A 2C1, Canada.
- Department of Computer Science, Faculty of Science, Western University, London, N6A 2C1, Canada.
- Cytognomix Inc., London, Canada.
- Department of Oncology, Schulich School of Medicine and Dentistry, Western University, London, N6A 2C1, Canada.
| |
Collapse
|
29
|
Recurrent mutations of BRCA1, BRCA2 and PALB2 in the population of breast and ovarian cancer patients in Southern Poland. Hered Cancer Clin Pract 2016; 14:5. [PMID: 26843898 PMCID: PMC4739084 DOI: 10.1186/s13053-016-0046-5] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2015] [Accepted: 01/28/2016] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND Mutations in the BRCA1, BRCA2 and PALB2 genes are well-established risk factors for the development of breast and/or ovarian cancer. The frequency and spectrum of mutations in these genes has not yet been examined in the population of Southern Poland. METHODS We examined the entire coding sequences of the BRCA1 and BRCA2 genes and genotyped a recurrent mutation of the PALB2 gene (c.509_510delGA) in 121 women with familial and/or early-onset breast or ovarian cancer from Southern Poland. RESULTS A BRCA1 mutation was identified in 11 of 121 patients (9.1 %) and a BRCA2 mutation was identified in 10 of 121 patients (8.3 %). Two founder mutations of BRCA1 accounted for 91 % of all BRCA1 mutation carriers (c.5266dupC was identified in six patients and c.181 T > G was identified in four patients). Three of the seven different BRCA2 mutations were detected in two patients each (c.9371A > T, c.9403delC and c.1310_1313delAAGA). Three mutations have not been previously reported in the Polish population (BRCA1 c.3531delT, BRCA2 c.1310_1313delAAGA and BRCA2 c.9027delT). The recurrent PALB2 mutation c.509_510delGA was identified in two patients (1.7 %). CONCLUSIONS The standard panel of BRCA1 founder mutations is sufficiently sensitive for the identification of BRCA1 mutation carriers in Southern Poland. The BRCA2 mutations c.9371A > T and c.9403delC as well as the PALB2 mutation c.509_510delGA should be included in the testing panel for this population.
Collapse
|
30
|
Dean M, Boland J, Yeager M, Im KM, Garland L, Rodriguez-Herrera M, Perez M, Mitchell J, Roberson D, Jones K, Lee HJ, Eggebeen R, Sawitzke J, Bass S, Zhang X, Robles V, Hollis C, Barajas C, Rath E, Arentz C, Figueroa JA, Nguyen DD, Nahleh Z. Addressing health disparities in Hispanic breast cancer: accurate and inexpensive sequencing of BRCA1 and BRCA2. Gigascience 2015; 4:50. [PMID: 26543556 PMCID: PMC4634732 DOI: 10.1186/s13742-015-0088-z] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2015] [Accepted: 08/13/2015] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND Germline mutations in the BRCA1 and BRCA2 genes account for 20-25 % of inherited breast cancers and about 10 % of all breast cancer cases. Detection of BRCA mutation carriers can lead to therapeutic interventions such as mastectomy, oophorectomy, hormonal prevention therapy, improved screening, and targeted therapies such as PARP-inhibition. We estimate that African Americans and Hispanics are 4-5 times less likely to receive BRCA screening, despite having similar mutation frequencies as non-Jewish Caucasians, who have higher breast cancer mortality. To begin addressing this health disparity, we initiated a nationwide trial of BRCA testing of Latin American women with breast cancer. Patients were recruited through community organizations, clinics, public events, and by mail and Internet. Subjects completed the consent process and questionnaire, and provided a saliva sample by mail or in person. DNA from 120 subjects was used to sequence the entirety of BRCA1 and BRCA2 coding regions and splice sites, and validate pathogenic mutations, with a total material cost of $85/subject. Subjects ranged in age from 23 to 81 years (mean age, 51 years), 6 % had bilateral disease, 57 % were ER/PR+, 23 % HER2+, and 17 % had triple-negative disease. RESULTS A total of seven different predicted deleterious mutations were identified, one newly described and the rest rare. In addition, four variants of unknown effect were found. CONCLUSIONS Application of this strategy on a larger scale could lead to improved cancer care of minority and underserved populations.
Collapse
Affiliation(s)
- Michael Dean
- Laboratory of Experimental Immunology, National Cancer Institute, Frederick, MD 21702 USA
| | - Joseph Boland
- Cancer Genetics Research Laboratory, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Gaithersburg, MD USA
| | - Meredith Yeager
- Cancer Genetics Research Laboratory, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Gaithersburg, MD USA
| | - Kate M. Im
- Laboratory of Experimental Immunology, National Cancer Institute, Frederick, MD 21702 USA
| | - Lisa Garland
- Laboratory of Experimental Immunology, National Cancer Institute, Frederick, MD 21702 USA
| | | | - Mylen Perez
- Laboratory of Experimental Immunology, National Cancer Institute, Frederick, MD 21702 USA
| | - Jason Mitchell
- Cancer Genetics Research Laboratory, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Gaithersburg, MD USA
| | - David Roberson
- Cancer Genetics Research Laboratory, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Gaithersburg, MD USA
| | - Kristine Jones
- Cancer Genetics Research Laboratory, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Gaithersburg, MD USA
| | - Hyo Jung Lee
- Cancer Genetics Research Laboratory, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Gaithersburg, MD USA
| | - Rebecca Eggebeen
- Cancer Genetics Research Laboratory, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Gaithersburg, MD USA
| | - Julie Sawitzke
- Basic Science Program, Leidos Biomedical Research, Inc., Frederick, MD USA
| | - Sara Bass
- Cancer Genetics Research Laboratory, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Gaithersburg, MD USA
| | - Xijun Zhang
- Cancer Genetics Research Laboratory, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Gaithersburg, MD USA
| | | | - Celia Hollis
- Latino Community Development Agency, Oklahoma City, OK USA
| | | | - Edna Rath
- Texas Tech University Health Sciences Center, El Paso, TX USA
| | - Candy Arentz
- Texas Tech University Health Sciences Center, Lubbock, TX USA
| | | | - Diane D. Nguyen
- Texas Tech University Health Sciences Center, Lubbock, TX USA
| | - Zeina Nahleh
- Texas Tech University Health Sciences Center, El Paso, TX USA
| |
Collapse
|
31
|
Minucci A, Scambia G, Santonocito C, Concolino P, Canu G, Mignone F, Saggese I, Guarino D, Costella A, Molinario R, De Bonis M, Ferrandina G, Petrillo M, Scaglione GL, Capoluongo E. Clinical impact on ovarian cancer patients of massive parallel sequencing forBRCAmutation detection: the experience at Gemelli hospital and a literature review. Expert Rev Mol Diagn 2015; 15:1383-403. [DOI: 10.1586/14737159.2015.1081059] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
|