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Takao M, Yamaguchi T, Eguchi H, Suzuki O, Mori Y, Chika N, Yamada T, Okazaki Y, Tomita N, Nomizu T, Momma T, Takayama T, Tanakaya K, Akagi K, Tanabe N, Ishida H. Predictive modeling for the germline pathogenic variant of the APC gene in patients with adenomatous polyposis: proposing a new APC score. Surg Today 2024:10.1007/s00595-024-02894-y. [PMID: 38970662 DOI: 10.1007/s00595-024-02894-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2024] [Accepted: 06/23/2024] [Indexed: 07/08/2024]
Abstract
BACKGROUND The precise diagnosis and medical management of patients with suspected familial adenomatous polyposis should be based on genetic testing, which may not always be available. Therefore, establishing a new model for predicting the likelihood of a germline pathogenic variant (GPV) of APC based on its clinical manifestations could prove to be useful in clinical practice. METHODS The presence of GPVs of APC gene was investigated in 162 patients with adenomatous polyposis (≥ 10 polyps) using a multigene panel or single-gene testing. To generate a predictive model for GPV of the APC gene, a logistic regression analysis was performed using the clinicopathological variables available at the time of the diagnosis of adenomatous polyposis. RESULTS Ninety (55.6%) patients had GPV of the APC gene. According to a multivariate logistic regression analysis, age < 40 years, polyps ≥ 100, fundic gland polyposis, and a family history of colorectal polyposis were found to be independent predictors of the GPV of APC and were used to establish a formula for predicting the GPV of APC using the four predictors. The prediction model had an area under the curve of 0.91 (0.86-0.96) according to a receiver operating characteristic analysis. CONCLUSION The model for predicting the GPV of APC will help patients with adenomatous polyposis and physicians make decisions about genetic testing.
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Affiliation(s)
- Misato Takao
- Department of Surgery, Tokyo Metropolitan Cancer and Infectious Diseases Center, Komagome Hospital, Tokyo, Japan
| | - Tatsuro Yamaguchi
- Department of Digestive Tract and General Surgery, Saitama Medical Center, Saitama Medical University, Saitama, Japan.
- Department of Clinical Genetics, Tokyo Metropolitan Cancer and Infectious Diseases Center, Komagome Hospital, 3-18-22 Honkomagome, Bunkyo-Ku, Tokyo, 113-8677, Japan.
| | - Hidetaka Eguchi
- Diagnostics and Therapeutics of Intractable Diseases and Intractable Disease Research Center, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Okihide Suzuki
- Department of Digestive Tract and General Surgery, Saitama Medical Center, Saitama Medical University, Saitama, Japan
| | - Yoshiko Mori
- Department of Digestive Tract and General Surgery, Saitama Medical Center, Saitama Medical University, Saitama, Japan
| | - Noriyasu Chika
- Department of Digestive Tract and General Surgery, Saitama Medical Center, Saitama Medical University, Saitama, Japan
| | - Takeshi Yamada
- Department of Gastrointestinal and Hepato-Biliary-Pancreatic Surgery, Nippon Medical School, Tokyo, Japan
| | - Yasushi Okazaki
- Diagnostics and Therapeutics of Intractable Diseases and Intractable Disease Research Center, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Naohiro Tomita
- Division of Lower GI Surgery, Department of Surgery, Hyogo College of Medicine, Hyogo, Japan
| | - Tadashi Nomizu
- Department of Surgery, Hoshi General Hospital, Fukushima, Japan
| | - Tomoyuki Momma
- Department of Gastrointestinal Tract Surgery, Fukushima Medical University, Fukushima, Japan
| | - Tetsuji Takayama
- Department of Gastroenterology and Oncology, Tokushima University Graduate School of Biomedical Sciences, Tokushima, Japan
| | - Kohji Tanakaya
- Department of Surgery, NHO Iwakuni Clinical Center, Yamaguchi, Japan
| | - Kiwamu Akagi
- Division of Molecular Diagnosis and Cancer Prevention, Saitama Cancer Center, Saitama, Japan
| | - Noriko Tanabe
- Department of Genomic Medicine, Saitama Medical Center, Saitama Medical University, Saitama, Japan
| | - Hideyuki Ishida
- Department of Digestive Tract and General Surgery, Saitama Medical Center, Saitama Medical University, Saitama, Japan
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Karstensen JG, Hansen TVO, Burisch J, Djursby M, Højen H, Madsen MB, Jespersen N, Jelsig AM. Re-evaluating the genotypes of patients with adenomatous polyposis of unknown etiology: a nationwide study. Eur J Hum Genet 2024; 32:588-592. [PMID: 38467732 PMCID: PMC11061120 DOI: 10.1038/s41431-024-01585-z] [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: 10/08/2023] [Revised: 02/18/2024] [Accepted: 02/28/2024] [Indexed: 03/13/2024] Open
Abstract
In the Danish Polyposis Register, patients with over 100 cumulative colorectal adenomas of unknown genetic etiology, named in this study colorectal polyposis (CP), is registered and treated as familial adenomatous polyposis (FAP). In this study, we performed genetic analyses, including whole genome sequencing (WGS), of all Danish patients registered with CP and estimated the detection rate of pathogenic variants (PV). We identified 231 families in the Polyposis Register, 31 of which had CP. A polyposis-associated gene panel was performed and, if negative, patients were offered WGS and screening for mosaicism in blood and/or adenomas. Next-generation sequencing (NGS) was carried out for 27 of the families (four declined). PVs were detected in 11 families, and WGS revealed three additional structural variants in APC. Mosaicism of a PV in APC was detected in two families. As the variant detection rate of eligible families was 60%, 93% of families in the register now have a known genetic etiology.
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Affiliation(s)
- John Gásdal Karstensen
- Danish Polyposis Register, Gastro Unit, Copenhagen University Hospital - Amager and Hvidovre, Hvidovre, Denmark.
- Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark.
| | - Thomas V Overeem Hansen
- Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
- Department of Clinical Genetics, Copenhagen University Hospital - Rigshospitalet, Copenhagen, Denmark
| | - Johan Burisch
- Danish Polyposis Register, Gastro Unit, Copenhagen University Hospital - Amager and Hvidovre, Hvidovre, Denmark
- Gastrounit, Medical Division, Copenhagen University Hospital - Amager and Hvidovre, Hvidovre, Denmark
| | - Malene Djursby
- Department of Clinical Genetics, Copenhagen University Hospital - Rigshospitalet, Copenhagen, Denmark
| | - Helle Højen
- Danish Polyposis Register, Gastro Unit, Copenhagen University Hospital - Amager and Hvidovre, Hvidovre, Denmark
| | - Majbritt Busk Madsen
- Center for Genomic Medicine, Copenhagen University Hospital - Rigshospitalet, Copenhagen, Denmark
| | - Niels Jespersen
- Danish Polyposis Register, Gastro Unit, Copenhagen University Hospital - Amager and Hvidovre, Hvidovre, Denmark
| | - Anne Marie Jelsig
- Department of Clinical Genetics, Copenhagen University Hospital - Rigshospitalet, Copenhagen, Denmark
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3
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Poylin VY, Shaffer VO, Felder SI, Goldstein LE, Goldberg JE, Kalady MF, Lightner AL, Feingold DL, Paquette IM. The American Society of Colon and Rectal Surgeons Clinical Practice Guidelines for the Management of Inherited Adenomatous Polyposis Syndromes. Dis Colon Rectum 2024; 67:213-227. [PMID: 37682806 DOI: 10.1097/dcr.0000000000003072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 09/10/2023]
Affiliation(s)
- Vitaliy Y Poylin
- Division of Gastrointestinal and Oncologic Surgery, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Virginia O Shaffer
- Department of Surgery, Emory University College of Medicine, Atlanta, Georgia
| | - Seth I Felder
- Department of Surgery, Moffit Cancer Center, Tampa, Florida
| | - Lindsey E Goldstein
- Division of General Surgery, North Florida/South Georgia Veteran's Health System, Gainesville, Florida
| | - Joel E Goldberg
- Division of General and Gastrointestinal Surgery, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Matthew F Kalady
- Division of Colon and Rectal Surgery, Ohio State University, Columbus, Ohio
| | - Amy L Lightner
- Department of Colorectal Surgery, Scripps Clinic, San Diego, California
| | - Daniel L Feingold
- Division of Colorectal Surgery, Rutgers University, New Brunswick, New Jersey
| | - Ian M Paquette
- Division of Colon and Rectal Surgery, University of Cincinnati, Cincinnati, Ohio
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4
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Valle L, Monahan KJ. Genetic predisposition to gastrointestinal polyposis: syndromes, tumour features, genetic testing, and clinical management. Lancet Gastroenterol Hepatol 2024; 9:68-82. [PMID: 37931640 DOI: 10.1016/s2468-1253(23)00240-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Revised: 07/19/2023] [Accepted: 07/20/2023] [Indexed: 11/08/2023]
Abstract
Gastrointestinal tract polyposis is characterised by the presence of multiple polyps, particularly in the colorectum, and encompasses both cancer predisposition genetic syndromes and non-syndromic clinical manifestations. The sources of the heterogeneity observed in polyposis syndromes relate to genetic cause, mode of inheritance, polyp burden and histological type, and spectrum and frequency of extracolonic manifestations. These features determine the clinical management of carriers, including strategies for cancer prevention and early detection, and oncological treatments. Despite substantial progress in identifying the genetic causes of polyposis, a large proportion of cases remain genetically unexplained. Although some of these cases might be due to lifestyle, environmental factors, or cancer treatments, it is likely that additional polyposis predisposition genes will be identified. This Review provides an overview of the known syndromes and genes, genetic testing, and clinical management of patients with polyposis, and recent advances and challenges in the field of gastrointestinal polyposis.
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Affiliation(s)
- Laura Valle
- Hereditary Cancer Programme, Catalan Institute of Oncology, Oncobell Programme, IDIBELL, Hospitalet de Llobregat, Barcelona, Spain; Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain.
| | - Kevin J Monahan
- The St Mark's Centre for Familial Intestinal Cancer Lynch Syndrome & Family Cancer Clinic & Polyposis Registry, St Mark's Hospital, London, UK; Imperial College, London, UK.
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5
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Jelsig AM, van Overeem Hansen T, Gede LB, Qvist N, Christensen LL, Lautrup CK, Ljungmann K, Christensen LT, Rønlund K, Tørring PM, Bertelsen B, Sunde L, Karstensen JG. Whole genome sequencing and disease pattern in patients with juvenile polyposis syndrome: a nationwide study. Fam Cancer 2023; 22:429-436. [PMID: 37354305 PMCID: PMC10542306 DOI: 10.1007/s10689-023-00338-z] [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: 04/26/2023] [Accepted: 05/23/2023] [Indexed: 06/26/2023]
Abstract
Juvenile polyposis syndrome (JPS) is a hereditary hamartomatous polyposis syndrome characterized by gastrointestinal juvenile polyps and increased risk of gastrointestinal cancer. Germline pathogenic variants are detected in SMAD4 or BMPR1A, however in a significant number of patients with JPS, the etiology is unknown. From Danish registers, and genetic department and laboratories, we identified all patients in Denmark with a clinical diagnosis of JPS and/or a pathogenic variant in BMPR1A or SMAD4. In patients where no variant had been detected, we performed genetic analysis, including whole genome sequencing. We collected clinical information on all patients to investigate the phenotypic spectrum. Sixty-six patients (mean age 40 years) were included of whom the pathogenic variant was unknown in seven patients. We detected a pathogenic variant in SMAD4 or PTEN in additional three patients and thus ≈ 95% of patients had a pathogenic germline variant. Endoscopic information was available in fifty-two patients (79%) and of these 31 (60%) fulfilled the clinical criteria of JPS. In 41 patients (79%), other types of polyps than juvenile had been removed. Our results suggest that almost all patients with a clinical diagnosis of JPS has a pathogenic variant in mainly BMPR1A, SMAD4, and more rarely PTEN. However, not all patients with a pathogenic variant fulfil the clinical criteria of JPS. We also demonstrated a wide clinical spectrum, and that the histopathology of removed polyps varied.
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Affiliation(s)
- Anne Marie Jelsig
- Department of Clinical Genetics, University Hospital of Copenhagen, Rigshospitalet, Copenhagen, Denmark.
| | - Thomas van Overeem Hansen
- Department of Clinical Genetics, University Hospital of Copenhagen, Rigshospitalet, Copenhagen, Denmark
- Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Lene Bjerring Gede
- Department of Clinical Genetics, University Hospital of Copenhagen, Rigshospitalet, Copenhagen, Denmark
| | - Niels Qvist
- Research Unit for Surgery, Odense University Hospital, Odense, Denmark
- University of Southern Denmark, Odense, Denmark
| | | | | | - Ken Ljungmann
- Department of Surgery, Aarhus University Hospital, Aarhus, Denmark
| | | | - Karina Rønlund
- Department of Clinical Genetics, University Hospital of Southern Denmark, Vejle Hospital, Vejle, Denmark
| | | | - Birgitte Bertelsen
- Center for Genomic Medicine, University Hospital of Copenhagen, Rigshospitalet, Copenhagen, Denmark
| | - Lone Sunde
- Department of Clinical Genetics, Aalborg University Hospital, Aalborg, Denmark
- Department of Clinical Medicine, Aalborg University, Aalborg, Denmark
| | - John Gásdal Karstensen
- Danish Polyposis Registry, Gastrounit, Copenhagen University Hospital - Amager and Hvidovre, Hvidovre, Denmark
- Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
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6
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Ikeda H, Yamaguchi S, Ishi Y, Wakabayashi K, Shimizu A, Kanno-Okada H, Endo T, Ota M, Okamoto M, Motegi H, Iwasaki N, Fujimura M. Supratentorial multifocal gliomas associated with Ollier disease harboring IDH1 R132H mutation: A case report. Neuropathology 2023; 43:413-420. [PMID: 36942363 DOI: 10.1111/neup.12902] [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: 09/21/2022] [Revised: 02/24/2023] [Accepted: 02/26/2023] [Indexed: 03/23/2023]
Abstract
Somatic mosaicism of isocitrate dehydrogenase 1/2 (IDH1/2) mutation is a cause of Ollier disease (OD), characterized by multiple enchondromatosis. A 35-year-old woman who was diagnosed with OD at age 24 underwent resection surgery for multifocal tumors located at the right and left frontal lobes that were discovered incidentally. No apparent spatial connection was observed on preoperative magnetic resonance imaging. Pathological examinations revealed tumor cells with a perinuclear halo in the left frontal lobe tumor, whereas astrocytic tumor cells were observed in the right frontal lobe tumor. Based on positive IDH1 R132H immunostaining and the result of 1p/19q fluorescent in situ hybridization, pathological diagnoses were IDH mutant and 1p/19q-codeleted oligodendroglioma in the right frontal lobe tumor and IDH mutant astrocytoma in the left frontal lobe tumor, respectively. The DNA sequencing revealed IDH1 R132H mutation in the peripheral blood sample and frontal lobe tumors. This case suggested that in patients with OD, astrocytoma and oligodendroglioma can co-occur within the same individual simultaneously, and IDH1 R132H mutation was associated with supratentorial development of gliomas.
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Affiliation(s)
- Hiroshi Ikeda
- Department of Neurosurgery, Hokkaido University School of Medicine, Sapporo, Japan
| | - Shigeru Yamaguchi
- Department of Neurosurgery, Hokkaido University School of Medicine, Sapporo, Japan
| | - Yukitomo Ishi
- Department of Neurosurgery, Hokkaido University School of Medicine, Sapporo, Japan
| | | | - Ai Shimizu
- Surgical Pathology, Hokkaido University Hospital, Sapporo, Japan
| | | | - Takeshi Endo
- Department of Orthopedic Surgery, Hokkaido University School of Medicine, Sapporo, Japan
| | - Mitsutoshi Ota
- Department of Orthopedic Surgery, Hokkaido University School of Medicine, Sapporo, Japan
| | - Michinari Okamoto
- Department of Neurosurgery, Hokkaido University School of Medicine, Sapporo, Japan
| | - Hiroaki Motegi
- Department of Neurosurgery, Hokkaido University School of Medicine, Sapporo, Japan
| | - Norimasa Iwasaki
- Department of Orthopedic Surgery, Hokkaido University School of Medicine, Sapporo, Japan
| | - Miki Fujimura
- Department of Neurosurgery, Hokkaido University School of Medicine, Sapporo, Japan
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7
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Jinda W, Moungthard H, Limwongse C, Pithukpakorn M, Saelee P, Pokkasup N, Khunpukdee S, Sukthaworn S, Jumpasri J. Identification of Genomic Alterations in Thai Patients With Colorectal Cancer Using Next-Generation Sequencing-Based Multigene Cancer Panel. Cureus 2023; 15:e39067. [PMID: 37323311 PMCID: PMC10267666 DOI: 10.7759/cureus.39067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/15/2023] [Indexed: 06/17/2023] Open
Abstract
Introduction Colorectal cancer (CRC) is one of the leading causes of death and illness in the general population. Although the incidence of CRC is steadily decreasing worldwide, it is being diagnosed more in individuals under 50 years of age. Multiple disease-causing variants have been reported to be involved in the development of CRC. This study aimed to investigate the molecular and clinical characteristics of Thai patients with CRC. Methods NGS-based multigene cancer panel testing was performed on 21 unrelated patients. Target enrichment was performed using a custom-designed Ion AmpliSeq on-demand panel. Thirty-six genes associated with CRC and other cancer were analyzed for variant detection. Results Sixteen variants (five nonsense, eight missense, two deletions, and one duplication) in nine genes were identified in 12 patients. Eight (66.7%) patients harboring disease-causing deleterious variants in genes APC, ATM, BRCA2, MSH2, and MUTYH. One of the eight patients also carried additional heterozygous variants in genes ATM, BMPR1A, and MUTYH. In addition, four patients carried variants of uncertain significance in genes APC, MLH1, MSH2, STK11, and TP53. Among all detected genes, APC was the most frequent causative gene observed in CRC patients, which is consistent with previous reports. Conclusion This study demonstrated the comprehensive molecular and clinical characterization of CRC patients. These findings showed the benefits of using multigene cancer panel sequencing for pathogenic gene detection and showed the prevalence of genetic aberrations in Thai patients with CRC.
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Affiliation(s)
- Worapoj Jinda
- Division of Research and Technology Assessment, National Cancer Institute, Bangkok, THA
| | - Hathaiwan Moungthard
- Division of Gastrointestinal and Liver Clinic, National Cancer Institute, Bangkok, THA
| | - Chanin Limwongse
- Division of Medical Genetics, Department of Medicine, Faculty of Medicine, Siriraj Hospital, Mahidol University, Bangkok, THA
| | - Manop Pithukpakorn
- Division of Medical Genetics, Department of Medicine, Faculty of Medicine, Siriraj Hospital, Mahidol University, Bangkok, THA
| | - Pensri Saelee
- Division of Research and Technology Assessment, National Cancer Institute, Bangkok, THA
| | - Nareerat Pokkasup
- Division of Gastrointestinal and Liver Clinic, National Cancer Institute, Bangkok, THA
| | - Saipan Khunpukdee
- Division of Gastrointestinal and Liver Clinic, National Cancer Institute, Bangkok, THA
| | | | - Jaruphan Jumpasri
- Division of Policy and Medical Strategy Development, National Cancer Institute, Bangkok, THA
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8
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Catch them if you are aware: PTEN postzygotic mosaicism in clinically suspicious patients with PTEN Hamartoma Tumour Syndrome and literature review. Eur J Med Genet 2022; 65:104533. [DOI: 10.1016/j.ejmg.2022.104533] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Revised: 05/19/2022] [Accepted: 05/26/2022] [Indexed: 12/12/2022]
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9
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Long JM, Powers JM, Katona BW. Evaluation of Classic, Attenuated, and Oligopolyposis of the Colon. Gastrointest Endosc Clin N Am 2022; 32:95-112. [PMID: 34798989 PMCID: PMC8607742 DOI: 10.1016/j.giec.2021.08.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
The goal of this review is to provide an overview of evaluating patients with adenomatous polyposis of the colon, including elements such as generating a differential diagnosis, referral considerations for genetic testing, genetic testing options, and expected outcomes from genetic testing in these individuals. In more recent years, adenomatous colonic polyposis has evolved beyond the more robustly characterized familial adenomatous polyposis (FAP) and MUTYH-associated polyposis (MAP) now encompassing more newly described genes and associated syndromes. Technological innovation, from whole-exome sequencing to multigene panel testing, has dramatically increased the amount of genotypic and phenotypic data amassed in adenomatous polyposis cohorts, which has contributed greatly to informing diagnosis and clinical management of affected individuals and their families.
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Affiliation(s)
- Jessica M. Long
- Division of Hematology/Oncology, Department of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Jacquelyn M. Powers
- Division of Hematology/Oncology, Department of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Bryson W. Katona
- Division of Gastroenterology and Hepatology, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
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10
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Jelsig AM, Byrjalsen A, Busk Madsen M, Kuhlmann TP, van Overeem Hansen T, Wadt KAW, Karstensen JG. Novel Genetic Causes of Gastrointestinal Polyposis Syndromes. Appl Clin Genet 2021; 14:455-466. [PMID: 34866929 PMCID: PMC8637176 DOI: 10.2147/tacg.s295157] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Accepted: 11/10/2021] [Indexed: 12/12/2022] Open
Abstract
Hereditary polyposis syndromes are characterized by a large number and/or histopathologically specific polyps in the gastrointestinal tract and a high risk of both colorectal cancer and extracolonic cancer at an early age. While the genes responsible for some of the syndromes, eg, APC in familial adenomatous polyposis and STK11 in Peutz-Jeghers syndrome, have been known for decades, novel genetic causes have recently been detected that have shed light on the broader clinical spectrum of syndromes. Genetic diagnoses are important because they can facilitate a personalized surveillance program. Furthermore, at-risk members of the patient's family can be tested and enrolled in surveillance as needed. In some cases, prenatal diagnostics should be offered. In this paper, we describe the development in germline genetics of the hereditary polyposis syndromes over the last 10-12 years, their clinical characteristics, as well as how to implement genetic analyses in the diagnostic pipeline.
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Affiliation(s)
- Anne Marie Jelsig
- Department of Clinical Genetics, University Hospital of Copenhagen, Copenhagen, Denmark
| | - Anna Byrjalsen
- Department of Clinical Genetics, University Hospital of Copenhagen, Copenhagen, Denmark
| | - Majbritt Busk Madsen
- Center for Genomic Medicine, University Hospital of Copenhagen, Copenhagen, Denmark
| | - Tine Plato Kuhlmann
- Department of Pathology, University Hospital of Copenhagen, Herlev Hospital, Herlev, Denmark
| | | | - Karin A W Wadt
- Department of Clinical Genetics, University Hospital of Copenhagen, Copenhagen, Denmark.,Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
| | - John Gásdal Karstensen
- Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark.,Danish Polyposis Registry, Gastro Unit, Copenhagen University Hospital - Amager and Hvidovre, Copenhagen, Denmark
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11
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Perne C, Peters S, Cartolano M, Horpaopan S, Grimm C, Altmüller J, Sommer AK, Hillmer AM, Thiele H, Odenthal M, Möslein G, Adam R, Sivalingam S, Kirfel J, Schweiger MR, Peifer M, Spier I, Aretz S. Variant profiling of colorectal adenomas from three patients of two families with MSH3-related adenomatous polyposis. PLoS One 2021; 16:e0259185. [PMID: 34843512 PMCID: PMC8629245 DOI: 10.1371/journal.pone.0259185] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Accepted: 10/14/2021] [Indexed: 12/12/2022] Open
Abstract
The spectrum of somatic genetic variation in colorectal adenomas caused by biallelic pathogenic germline variants in the MSH3 gene, was comprehensively analysed to characterise mutational signatures and identify potential driver genes and pathways of MSH3-related tumourigenesis. Three patients from two families with MSH3-associated polyposis were included. Whole exome sequencing of nine adenomas and matched normal tissue was performed. The amount of somatic variants in the MSH3-deficient adenomas and the pattern of single nucleotide variants (SNVs) was similar to sporadic adenomas, whereas the fraction of small insertions/deletions (indels) (21-42% of all small variants) was significantly higher. Interestingly, pathogenic somatic APC variants were found in all but one adenoma. The vast majority (12/13) of these were di-, tetra-, or penta-base pair (bp) deletions. The fraction of APC indels was significantly higher than that reported in patients with familial adenomatous polyposis (FAP) (p < 0.01) or in sporadic adenomas (p < 0.0001). In MSH3-deficient adenomas, the occurrence of APC indels in a repetitive sequence context was significantly higher than in FAP patients (p < 0.01). In addition, the MSH3-deficient adenomas harboured one to five (recurrent) somatic variants in 13 established or candidate driver genes for early colorectal carcinogenesis, including ACVR2A and ARID genes. Our data suggest that MSH3-related colorectal carcinogenesis seems to follow the classical APC-driven pathway. In line with the specific function of MSH3 in the mismatch repair (MMR) system, we identified a characteristic APC mutational pattern in MSH3-deficient adenomas, and confirmed further driver genes for colorectal tumourigenesis.
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Affiliation(s)
- Claudia Perne
- Institute of Human Genetics, Medical Faculty, University of Bonn, Bonn, Germany
- Center for Hereditary Tumor Syndromes, University Hospital Bonn, Bonn, Germany
| | - Sophia Peters
- Institute of Human Genetics, Medical Faculty, University of Bonn, Bonn, Germany
| | - Maria Cartolano
- Department of Translational Genomics, Center of Integrated Oncology Cologne-Bonn, Medical Faculty, University of Cologne, Cologne, Germany
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany
| | - Sukanya Horpaopan
- Department of Anatomy, Faculty of Medical Science, Naresuan University, Phitsanulok, Thailand
| | - Christina Grimm
- Institute for Translational Epigenetics, Medical Faculty and University Clinic Cologne, University of Cologne, Cologne, Germany
| | - Janine Altmüller
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany
- Cologne Center for Genomics (CCG), Faculty of Medicine, University of Cologne, University Hospital Cologne, Cologne, Germany
- Berlin Institute of Health at Charité, Core Facility Genomics, Berlin, Germany
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
| | - Anna K. Sommer
- Institute of Human Genetics, Medical Faculty, University of Bonn, Bonn, Germany
| | - Axel M. Hillmer
- Institute of Pathology, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
| | - Holger Thiele
- Cologne Center for Genomics (CCG), Faculty of Medicine, University of Cologne, University Hospital Cologne, Cologne, Germany
| | - Margarete Odenthal
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany
- Institute of Pathology, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
| | - Gabriela Möslein
- Zentrum für Hereditäre Tumore, BETHESDA Khs. Duisburg, Duisburg, Germany
| | - Ronja Adam
- Cancer Center Amsterdam, Amsterdam University Medical Centers, Amsterdam, The Netherlands
| | - Sugirthan Sivalingam
- Core Unit for Bioinformatics Data Analysis, Medical Faculty, University of Bonn, Bonn, Germany
- Institute for Genomic Statistics and Bioinformatics, Medical Faculty, University of Bonn, Bonn, Germany
- Institute for Medical Biometry, Informatics and Epidemiology, Medical Faculty, University of Bonn, Bonn, Germany
| | - Jutta Kirfel
- Institute of Pathology, University of Lübeck, Lübeck, Germany
| | - Michal R. Schweiger
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany
- Institute for Translational Epigenetics, Medical Faculty and University Clinic Cologne, University of Cologne, Cologne, Germany
| | - Martin Peifer
- Department of Translational Genomics, Center of Integrated Oncology Cologne-Bonn, Medical Faculty, University of Cologne, Cologne, Germany
| | - Isabel Spier
- Institute of Human Genetics, Medical Faculty, University of Bonn, Bonn, Germany
- Center for Hereditary Tumor Syndromes, University Hospital Bonn, Bonn, Germany
| | - Stefan Aretz
- Institute of Human Genetics, Medical Faculty, University of Bonn, Bonn, Germany
- Center for Hereditary Tumor Syndromes, University Hospital Bonn, Bonn, Germany
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12
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Olkinuora AP, Peltomäki PT, Aaltonen LA, Rajamäki K. From APC to the genetics of hereditary and familial colon cancer syndromes. Hum Mol Genet 2021; 30:R206-R224. [PMID: 34329396 PMCID: PMC8490010 DOI: 10.1093/hmg/ddab208] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Revised: 07/01/2021] [Accepted: 07/05/2021] [Indexed: 11/12/2022] Open
Abstract
Hereditary colorectal cancer (CRC) syndromes attributable to high penetrance mutations represent 9-26% of young-onset CRC cases. The clinical significance of many of these mutations is understood well enough to be used in diagnostics and as an aid in patient care. However, despite the advances made in the field, a significant proportion of familial and early-onset cases remains molecularly uncharacterized and extensive work is still needed to fully understand the genetic nature of CRC susceptibility. With the emergence of next-generation sequencing and associated methods, several predisposition loci have been unraveled, but validation is incomplete. Individuals with cancer-predisposing mutations are currently enrolled in life-long surveillance, but with the development of new treatments, such as cancer vaccinations, this might change in the not so distant future for at least some individuals. For individuals without a known cause for their disease susceptibility, prevention and therapy options are less precise. Herein, we review the progress achieved in the last three decades with a focus on how CRC predisposition genes were discovered. Furthermore, we discuss the clinical implications of these discoveries and anticipate what to expect in the next decade.
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Affiliation(s)
- Alisa P Olkinuora
- Department of Medical and Clinical Genetics, Medicum, University of Helsinki, 00014 Helsinki, Finland
- iCAN Digital Precision Cancer Medicine Flagship, University of Helsinki, 00014 Helsinki, Finland
| | - Päivi T Peltomäki
- Department of Medical and Clinical Genetics, Medicum, University of Helsinki, 00014 Helsinki, Finland
- iCAN Digital Precision Cancer Medicine Flagship, University of Helsinki, 00014 Helsinki, Finland
| | - Lauri A Aaltonen
- Department of Medical and Clinical Genetics, Medicum, University of Helsinki, 00014 Helsinki, Finland
- iCAN Digital Precision Cancer Medicine Flagship, University of Helsinki, 00014 Helsinki, Finland
- Applied Tumor Genomics Research Program, Research Programs Unit, University of Helsinki, 00014 Helsinki, Finland
| | - Kristiina Rajamäki
- Department of Medical and Clinical Genetics, Medicum, University of Helsinki, 00014 Helsinki, Finland
- Applied Tumor Genomics Research Program, Research Programs Unit, University of Helsinki, 00014 Helsinki, Finland
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13
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Rofes P, González S, Navarro M, Moreno-Cabrera JM, Solanes A, Darder E, Carrasco E, Iglesias S, Salinas M, Gómez C, Velasco À, Tuset N, Varela M, Llort G, Ramon Y Cajal T, Grau È, Dueñas N, de la Ossa Merlano N, Matías-Guiu X, Rivera B, Balmaña J, Pineda M, Brunet J, Capellá G, Del Valle J, Lázaro C. Paired Somatic-Germline Testing of 15 Polyposis and Colorectal Cancer-Predisposing Genes Highlights the Role of APC Mosaicism in de Novo Familial Adenomatous Polyposis. J Mol Diagn 2021; 23:1452-1459. [PMID: 34454113 DOI: 10.1016/j.jmoldx.2021.07.024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Revised: 07/02/2021] [Accepted: 07/21/2021] [Indexed: 11/28/2022] Open
Abstract
Familial adenomatous polyposis (FAP) is an autosomal dominant syndrome responsible for 1% of colorectal cancers (CRCs). Up to 90% of classic FAPs are caused by inactivating mutations in APC, and mosaicism has been previously reported in 20% of de novo cases, usually linked to milder phenotypic manifestations. This study aimed to explore the prevalence of mosaicism in 11 unsolved cases of classic FAP and to evaluate the diagnostic yield of somatic testing. Paired samples of colorectal polyps, tumors, and/or mucosa were analyzed using a custom next-generation sequencing panel targeting 15 polyposis and CRC-predisposing genes. Whenever possible, the extension of mosaicism to blood or sperm was also examined. Of 11 patients with classic adenomatous polyposis, a mosaic pathogenic variant in APC was identified in 7 (64%). No other altered genes were identified. In two of seven patients (29%), mosaicism was found restricted to colonic tissues, whereas in five of seven patients (71%), it was extended to the blood. Germline affectation was confirmed in one patient. We report the first analysis at a somatic level of 15 genes associated with CRC susceptibility, which highlights the role of APC mosaicism in classic FAP etiology. The results further reinforce the importance of testing target tissues when blood test results are negative.
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Affiliation(s)
- Paula Rofes
- Hereditary Cancer Program, Program in Molecular Mechanisms and Experimental Therapy in Oncology (Oncobell), Bellvitge Institute for Biomedical Research (IDIBELL), Catalan Institute of Oncology, l'Hospitalet del Llobregat, Spain; Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
| | - Sara González
- Hereditary Cancer Program, Program in Molecular Mechanisms and Experimental Therapy in Oncology (Oncobell), Bellvitge Institute for Biomedical Research (IDIBELL), Catalan Institute of Oncology, l'Hospitalet del Llobregat, Spain; Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
| | - Matilde Navarro
- Hereditary Cancer Program, Program in Molecular Mechanisms and Experimental Therapy in Oncology (Oncobell), Bellvitge Institute for Biomedical Research (IDIBELL), Catalan Institute of Oncology, l'Hospitalet del Llobregat, Spain; Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain; Hereditary Cancer Program, Program for Predictive and Personalized Medicine of Cancer-Germans Trias i Pujol Research Institute (PMPPC-IGTP), Badalona, Spain
| | - José Marcos Moreno-Cabrera
- Hereditary Cancer Program, Program in Molecular Mechanisms and Experimental Therapy in Oncology (Oncobell), Bellvitge Institute for Biomedical Research (IDIBELL), Catalan Institute of Oncology, l'Hospitalet del Llobregat, Spain; Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain; Hereditary Cancer Program, Program for Predictive and Personalized Medicine of Cancer-Germans Trias i Pujol Research Institute (PMPPC-IGTP), Badalona, Spain
| | - Ares Solanes
- Hereditary Cancer Program, Program in Molecular Mechanisms and Experimental Therapy in Oncology (Oncobell), Bellvitge Institute for Biomedical Research (IDIBELL), Catalan Institute of Oncology, l'Hospitalet del Llobregat, Spain; Hereditary Cancer Program, Program for Predictive and Personalized Medicine of Cancer-Germans Trias i Pujol Research Institute (PMPPC-IGTP), Badalona, Spain
| | - Esther Darder
- Hereditary Cancer Program, Catalan Institute of Oncology, Girona Institute for Biomedical Research (IDIBGi), Girona, Spain
| | - Estela Carrasco
- Hereditary Cancer Genetics Group, Vall d'Hebron Institute of Oncology (VHIO), Vall d'Hebron Barcelona Hospital Campus, Barcelona, Spain
| | - Sílvia Iglesias
- Hereditary Cancer Program, Program in Molecular Mechanisms and Experimental Therapy in Oncology (Oncobell), Bellvitge Institute for Biomedical Research (IDIBELL), Catalan Institute of Oncology, l'Hospitalet del Llobregat, Spain
| | - Mónica Salinas
- Hereditary Cancer Program, Program in Molecular Mechanisms and Experimental Therapy in Oncology (Oncobell), Bellvitge Institute for Biomedical Research (IDIBELL), Catalan Institute of Oncology, l'Hospitalet del Llobregat, Spain
| | - Carolina Gómez
- Hereditary Cancer Program, Program in Molecular Mechanisms and Experimental Therapy in Oncology (Oncobell), Bellvitge Institute for Biomedical Research (IDIBELL), Catalan Institute of Oncology, l'Hospitalet del Llobregat, Spain
| | - Àngela Velasco
- Hereditary Cancer Program, Catalan Institute of Oncology, Girona Institute for Biomedical Research (IDIBGi), Girona, Spain
| | - Noemí Tuset
- Medical Oncology Department, Arnau de Vilanova University Hospital, Lleida, Spain
| | - Mar Varela
- Department of Pathology, Bellvitge University Hospital, Catalan Institute of Oncology, l'Hospitalet del Llobregat, Spain
| | - Gemma Llort
- Medical Oncology Department, Parc Taulí University Hospital, Sabadell, Spain
| | | | - Èlia Grau
- Hereditary Cancer Program, Program in Molecular Mechanisms and Experimental Therapy in Oncology (Oncobell), Bellvitge Institute for Biomedical Research (IDIBELL), Catalan Institute of Oncology, l'Hospitalet del Llobregat, Spain; Hereditary Cancer Program, Program for Predictive and Personalized Medicine of Cancer-Germans Trias i Pujol Research Institute (PMPPC-IGTP), Badalona, Spain
| | - Núria Dueñas
- Hereditary Cancer Program, Program in Molecular Mechanisms and Experimental Therapy in Oncology (Oncobell), Bellvitge Institute for Biomedical Research (IDIBELL), Catalan Institute of Oncology, l'Hospitalet del Llobregat, Spain; Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
| | - Napoleón de la Ossa Merlano
- Department of Pathology, General University Hospital of Catalonia, QuironSalud Group, Sant Cugat del Vallès, Spain
| | - Xavier Matías-Guiu
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain; Department of Pathology, Bellvitge University Hospital, IDIBELL, University of Barcelona, Barcelona, Spain; Department of Pathology, Arnau de Vilanova University Hospital, Lleida Institute for Biomedical Research (IRBLleida), University of Lleida, Lleida, Spain
| | - Bárbara Rivera
- Hereditary Cancer Program, Program in Molecular Mechanisms and Experimental Therapy in Oncology (Oncobell), Bellvitge Institute for Biomedical Research (IDIBELL), Catalan Institute of Oncology, l'Hospitalet del Llobregat, Spain; Gerald Bronfman Department of Oncology, McGill University, Montreal, Quebec, Canada
| | - Judith Balmaña
- Hereditary Cancer Genetics Group, Vall d'Hebron Institute of Oncology (VHIO), Vall d'Hebron Barcelona Hospital Campus, Barcelona, Spain
| | - Marta Pineda
- Hereditary Cancer Program, Program in Molecular Mechanisms and Experimental Therapy in Oncology (Oncobell), Bellvitge Institute for Biomedical Research (IDIBELL), Catalan Institute of Oncology, l'Hospitalet del Llobregat, Spain; Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
| | - Joan Brunet
- Hereditary Cancer Program, Program in Molecular Mechanisms and Experimental Therapy in Oncology (Oncobell), Bellvitge Institute for Biomedical Research (IDIBELL), Catalan Institute of Oncology, l'Hospitalet del Llobregat, Spain; Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain; Hereditary Cancer Program, Catalan Institute of Oncology, Girona Institute for Biomedical Research (IDIBGi), Girona, Spain
| | - Gabriel Capellá
- Hereditary Cancer Program, Program in Molecular Mechanisms and Experimental Therapy in Oncology (Oncobell), Bellvitge Institute for Biomedical Research (IDIBELL), Catalan Institute of Oncology, l'Hospitalet del Llobregat, Spain; Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
| | - Jesús Del Valle
- Hereditary Cancer Program, Program in Molecular Mechanisms and Experimental Therapy in Oncology (Oncobell), Bellvitge Institute for Biomedical Research (IDIBELL), Catalan Institute of Oncology, l'Hospitalet del Llobregat, Spain; Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
| | - Conxi Lázaro
- Hereditary Cancer Program, Program in Molecular Mechanisms and Experimental Therapy in Oncology (Oncobell), Bellvitge Institute for Biomedical Research (IDIBELL), Catalan Institute of Oncology, l'Hospitalet del Llobregat, Spain; Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain.
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14
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Takao M, Yamaguchi T, Eguchi H, Yamada T, Okazaki Y, Tomita N, Nomizu T, Momma T, Takayama T, Tanakaya K, Akagi K, Ishida H. APC germline variant analysis in the adenomatous polyposis phenotype in Japanese patients. Int J Clin Oncol 2021; 26:1661-1670. [PMID: 34106356 DOI: 10.1007/s10147-021-01946-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Accepted: 05/25/2021] [Indexed: 11/24/2022]
Abstract
BACKGROUND Familial adenomatous polyposis (FAP), an autosomal dominant disorder characterized by multiple colonic polyps, is caused by a germline pathogenic variant of the APC gene. However, this variant is not detected in up to 30% of patients with the adenomatous polyposis phenotype. METHODS We performed next-generation sequencing (NGS) to identify the causative genes in FAP patients with 10 or more polyps. For patients in whom the APC germline variant was not able to be identified, we screened for APC mosaicism using high-coverage NGS of APC with DNA from leucocytes and/or frozen tissue. RESULTS The pathogenic APC germline variant was found in 93.3%, 71.6%, and 17.1% of patients with profuse-type polyposis, sparse-type polyposis, and oligo-polyposis, respectively. The APC germline variant detection rate in patients with FAP-related diseases was 69.7% for fundic gland polyposis, 79.7% for duodenal adenoma, 94.7% for desmoid tumor, and 71.4% for thyroid cancer, with increasing numbers of extracolonic lesions associated with an increasing APC germline variant detection rate. A mosaic test detected nine patients with APC mosaicism. A comparison of APC-associated polyposis with APC mosaicism showed that patients with APC mosaicism had a low frequency of duodenal adenoma and a family history of colonic polyposis. CONCLUSIONS We determined the detection rate of the APC germline variant by phenotype and identified APC mosaicism. Genetic testing of FAP patients is important because it can help with surgical decision-making, monitoring, and genetic counseling. Furthermore, genetic testing by NGS proved to be an effective method of detecting APC germline variants.
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Affiliation(s)
- Misato Takao
- Department of Surgery, Tokyo Metropolitan Cancer and Infectious Diseases Center, Komagome Hospital, 3-18-22, Honkomagome, Bunkyo-ku, Tokyo, 113-8677, Japan.,Department of Digestive Tract and General Surgery, Saitama Medical Center, Saitama Medical University, Saitama, Japan
| | - Tatsuro Yamaguchi
- Department of Surgery, Tokyo Metropolitan Cancer and Infectious Diseases Center, Komagome Hospital, 3-18-22, Honkomagome, Bunkyo-ku, Tokyo, 113-8677, Japan. .,Department of Digestive Tract and General Surgery, Saitama Medical Center, Saitama Medical University, Saitama, Japan. .,Department of Clinical Genetics, Tokyo Metropolitan Cancer and Infectious Diseases Center, Komagome Hospital, Tokyo, Japan.
| | - Hidetaka Eguchi
- Diagnostics and Therapeutics of Intractable Diseases and Intractable Disease Research Center, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Takeshi Yamada
- Department of Gastrointestinal and Hepato-Biliary-Pancreatic Surgery, Nippon Medical School, Tokyo, Japan
| | - Yasushi Okazaki
- Diagnostics and Therapeutics of Intractable Diseases and Intractable Disease Research Center, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Naohiro Tomita
- Division of Lower GI Surgery, Department of Surgery, Hyogo College of Medicine, Nishinomiya, Japan
| | - Tadashi Nomizu
- Department of Surgery, Hoshi General Hospital, Koriyama, Japan
| | - Tomoyuki Momma
- Department of Gastrointestinal Tract Surgery, Fukushima Medical University, Fukushima, Japan
| | - Tetsuji Takayama
- Department of Gastroenterology and Oncology, Institute of Biomedical Sciences, Tokushima University Graduate School, Tokushima, Japan
| | - Kohji Tanakaya
- Department of Surgery, Iwakuni Clinical Center, Iwakuni, Japan
| | - Kiwamu Akagi
- Division of Molecular Diagnosis and Cancer Prevention, Saitama Cancer Center, Saitama, Japan
| | - Hideyuki Ishida
- Department of Digestive Tract and General Surgery, Saitama Medical Center, Saitama Medical University, Saitama, Japan
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15
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Urso EDL, Ponz de Leon M, Vitellaro M, Piozzi GN, Bao QR, Martayan A, Remo A, Stigliano V, Oliani C, Lucci Cordisco E, Pucciarelli S, Ranzani GN, Viel A. Definition and management of colorectal polyposis not associated with APC/MUTYH germline pathogenic variants: AIFEG consensus statement. Dig Liver Dis 2021; 53:409-417. [PMID: 33504457 DOI: 10.1016/j.dld.2020.11.018] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Revised: 11/16/2020] [Accepted: 11/18/2020] [Indexed: 02/06/2023]
Abstract
An expert consensus panel convened by the Italian Association for Inherited and Familial Gastrointestinal Tumors (Associazione Italiana per lo Studio della Familiarità ed Ereditarietà dei Tumori Gastrointestinali, AIFEG) reviewed the literature and agreed on a number of position statements regarding the definition and management of polyposis coli without an identified pathogenic mutation on the APC or MUTYH genes, defined in the document as NAMP (non-APC/MUTYH polyposis).
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Affiliation(s)
- Emanuele Damiano Luca Urso
- Clinica Chirurgica I, Department of Surgical, Oncological and Gastroenterological Sciences (DiSCOG), University Hospital of Padua, Italy
| | - Maurizio Ponz de Leon
- Department of Internal Medicine, University of Modena and Reggio Emilia. Retired, Italy
| | - Marco Vitellaro
- Unit of Hereditary Digestive Tract Tumors, Department of Surgery, Fondazione IRCCS Istituto Nazionale Tumori, Milan, Italy; Colorectal Surgery Unit, Department of Surgery, Fondazione IRCCS Istituto Nazionale Tumori, Milan, Italy.
| | - Guglielmo Niccolò Piozzi
- Colorectal Surgery Unit, Department of Surgery, Fondazione IRCCS Istituto Nazionale Tumori, Milan, Italy
| | - Quoc Riccardo Bao
- Clinica Chirurgica I, Department of Surgical, Oncological and Gastroenterological Sciences (DiSCOG), University Hospital of Padua, Italy
| | - Aline Martayan
- Clinical Pathology Unit, IRCCS Regina Elena National Cancer Institute, Rome, Italy
| | - Andrea Remo
- Pathology Unit, Services Department, ULSS9 Scaligera, Verona, Italy
| | - Vittoria Stigliano
- Division of Gastroenterology and Digestive Endoscopy, IRCCS Regina Elena National Cancer Institute, Rome, Italy
| | | | | | - Salvatore Pucciarelli
- Clinica Chirurgica I, Department of Surgical, Oncological and Gastroenterological Sciences (DiSCOG), University Hospital of Padua, Italy
| | | | - Alessandra Viel
- Functional Oncogenomics and Genetics Unit, IRCCS Centro di Riferimento Oncologico di Aviano (CRO), Aviano, Italy
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16
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Use of sanger and next-generation sequencing to screen for mosaic and intronic APC variants in unexplained colorectal polyposis patients. Fam Cancer 2021; 21:79-83. [PMID: 33683519 PMCID: PMC8799582 DOI: 10.1007/s10689-021-00236-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Accepted: 02/16/2021] [Indexed: 12/12/2022]
Abstract
In addition to classic germline APC gene variants, APC mosaicism and deep intronic germline APC variants have also been reported to be causes of adenomatous polyposis. In this study, we investigated 80 unexplained colorectal polyposis patients without germline pathogenic variants in known polyposis predisposing genes to detect mosaic and deep intronic APC variants. All patients developed more than 50 colorectal polyps, with adenomas being predominantly observed. To detect APC mosaicism, we performed next-generation sequencing (NGS) in leukocyte DNA. Furthermore, using Sanger sequencing, the cohort was screened for the following previously reported deep intronic pathogenic germline APC variants: c.1408 + 731C > T, p.(Gly471Serfs*55), c.1408 + 735A > T, p.(Gly471Serfs*55), c.1408 + 729A > G, p.(Gly471Serfs*55) and c.532-941G > A, p.(Phe178Argfs*22). We did not detect mosaic or intronic APC variants in the screened unexplained colorectal polyposis patients. The results of this study indicate that the deep intronic APC variants investigated in this study are not a cause of colorectal polyposis in this Dutch population. In addition, NGS did not detect any further mosaic variants in our cohort.
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17
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[Gastrointestinal polyposis syndromes]. Internist (Berl) 2020; 62:133-144. [PMID: 33237439 DOI: 10.1007/s00108-020-00903-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
BACKGROUND Gastrointestinal polyposis syndromes are the second most common cause of hereditary colorectal carcinomas after Lynch syndrome (hereditary non-polyposis colon cancer, HNPCC). The detection of a causal germline mutation in an affected family member serves for differential diagnosis, assessment of the recurrence risk and predictive testing of healthy individuals at risk. OBJECTIVES The present article aims to provide an overview of the differential diagnosis of different gastrointestinal polyposis syndromes based on the endoscopic findings, polyp histology, extraintestinal phenotype and molecular genetic diagnostics. MATERIALS AND METHODS The present article is based on a literature search on gastrointestinal polyposis syndromes. RESULTS In addition to familial adenomatous polyposis (FAP), there are further subtypes of adenomatous polyposis that can often only be distinguished by the detection of a causative germline mutation and are sometimes associated with different extracolonic manifestations. In hamartomatous polyposis syndromes, the clinical overlaps often cause differential diagnostic problems. Serratated polyposis syndrome is possibly the most frequent polyposis syndrome, although its cause is currently largely unexplained. CONCLUSIONS Early detection and correct classification of polyposis is crucial for adequate prevention and therapy. Access to multidisciplinary expert centres is useful for the care of families.
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18
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te Paske IBAW, Ligtenberg MJL, Hoogerbrugge N, de Voer RM. Candidate Gene Discovery in Hereditary Colorectal Cancer and Polyposis Syndromes-Considerations for Future Studies. Int J Mol Sci 2020; 21:ijms21228757. [PMID: 33228212 PMCID: PMC7699508 DOI: 10.3390/ijms21228757] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Revised: 11/17/2020] [Accepted: 11/18/2020] [Indexed: 12/15/2022] Open
Abstract
To discover novel high-penetrant risk loci for hereditary colorectal cancer (hCRC) and polyposis syndromes many whole-exome and whole-genome sequencing (WES/WGS) studies have been performed. Remarkably, these studies resulted in only a few novel high-penetrant risk genes. Given this observation, the possibility and strategy to identify high-penetrant risk genes for hCRC and polyposis needs reconsideration. Therefore, we reviewed the study design of WES/WGS-based hCRC and polyposis gene discovery studies (n = 37) and provide recommendations to optimize discovery and validation strategies. The group of genetically unresolved patients is phenotypically heterogeneous, and likely composed of distinct molecular subtypes. This knowledge advocates for the screening of a homogeneous, stringently preselected discovery cohort and obtaining multi-level evidence for variant pathogenicity. This evidence can be collected by characterizing the molecular landscape of tumors from individuals with the same affected gene or by functional validation in cell-based models. Together, the combined approach of a phenotype-driven, tumor-based candidate gene search might elucidate the potential contribution of novel genetic predispositions in genetically unresolved hCRC and polyposis.
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Affiliation(s)
- Iris B. A. W. te Paske
- Department of Human Genetics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands; (I.B.A.W.t.P.); (M.J.L.L.); (N.H.)
| | - Marjolijn J. L. Ligtenberg
- Department of Human Genetics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands; (I.B.A.W.t.P.); (M.J.L.L.); (N.H.)
- Department of Pathology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
| | - Nicoline Hoogerbrugge
- Department of Human Genetics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands; (I.B.A.W.t.P.); (M.J.L.L.); (N.H.)
| | - Richarda M. de Voer
- Department of Human Genetics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands; (I.B.A.W.t.P.); (M.J.L.L.); (N.H.)
- Correspondence: ; Tel.: +31-24-36-14107
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19
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Jansen AML, Goel A. Mosaicism in Patients With Colorectal Cancer or Polyposis Syndromes: A Systematic Review. Clin Gastroenterol Hepatol 2020; 18:1949-1960. [PMID: 32147591 PMCID: PMC7725418 DOI: 10.1016/j.cgh.2020.02.049] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Revised: 02/09/2020] [Accepted: 02/14/2020] [Indexed: 02/07/2023]
Abstract
BACKGROUND & AIMS Somatic mosaicism, in which variants arise post-zygotically and are therefore not present in all cells in the body, may be an underestimated cause of colorectal cancer (CRC) and polyposis syndromes. We performed a systematic review to provide a comprehensive overview of somatic mosaicism in patients with CRC and polyposis syndromes. METHODS We searched PubMed through March 2018 to identify reports of mosaicism in patients with CRC or polyposis syndromes. We divided the final set of studies into 3 subgroups describing APC mosaicism, mosaicism in other CRC susceptibility genes, and epigenetic mosaicism. RESULTS Of the 232 articles identified in our systematic search, 46 met the criteria for further analysis. Of these, 35 studies described mosaic variants or epimutations in patients with CRC or polyposis syndromes. Nineteen studies described APC mosaicism, comprising a total of 57 patients. Six described mosaicism in genes associated with familial CRC syndromes, such as Lynch and Cowden syndromes. Ten studies described epigenetic mosaicism, sometimes resulting from a germline variant (such as deletion of EPCAM). CONCLUSIONS We found that somatic mosaicism is underdiagnosed but critical for determining the clinical management of patients with de novo polyposis who possibly carry mosaic APC variants, and present a decision tree for the clinical management of these patients. Mosaicism in genes associated with susceptibility to CRC contributes to development of other familial CRC syndromes. Heritable epigenetic mosaicism is likely underestimated and could have a dominant pattern of inheritance. However, the inheritance of primary mosaic epimutations, without an underlying genetic cause, is complex and not fully understood.
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Affiliation(s)
- Anne Maria Lucia Jansen
- Center for Gastrointestinal Research, Center for Translational Genomics and Oncology, Baylor Scott & White Research Institute and Charles A. Sammons Cancer Center, Dallas, Texas
| | - Ajay Goel
- Center for Gastrointestinal Research, Center for Translational Genomics and Oncology, Baylor Scott & White Research Institute and Charles A. Sammons Cancer Center, Dallas, Texas; Department of Molecular Diagnostics and Experimental Therapeutics, Beckman Research Institute of City of Hope, Duarte, California.
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20
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Guillerm E, Svrcek M, Bardier-Dupas A, Basset N, Coulet F, Colas C. Molecular tumor testing in patients with Lynch-like syndrome reveals a de novo mosaic variant of a mismatch repair gene transmitted to offspring. Eur J Hum Genet 2020; 28:1624-1628. [PMID: 32678338 DOI: 10.1038/s41431-020-0689-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2018] [Revised: 02/19/2020] [Accepted: 06/18/2020] [Indexed: 11/09/2022] Open
Abstract
In Lynch-like syndrome, patients have tumors with microsatellite instability but no germline pathogenic variant in mismatch repair genes or somatic methylation of the MLH1 promoter. Identification of the mechanism that causes these tumors is crucial for guiding screening of the patients and their relatives. Double somatic hits are the usual explanation for these cases; however, we have previously reported a de novo mosaic pathogenic variant in a patient with Lynch-like syndrome. Using tumoral NGS analysis of a series of 16 patients with Lynch-like syndrome, we found six patients with double somatic hits, including one patient with mosaicism of a de novo pathogenic variant in MSH2. This variant was transmitted to the patient's offspring, which has significant implications for genetic counseling.
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Affiliation(s)
- Erell Guillerm
- Department of Genetics, Hôpital Universitaire Pitié Salpêtrière (Assistance Publique-Hôpitaux de Paris), Paris VI University, Paris, France. .,INSERM, UMRS 938-Centre de Recherche Saint-Antoine, Equipe 'Instabilité des Microsatellites et Cancers', Equipe labellisée par la Ligue Nationale contre le Cancer, Paris, France. .,France Université Pierre et Marie Curie, Paris, France.
| | - Magali Svrcek
- INSERM, UMRS 938-Centre de Recherche Saint-Antoine, Equipe 'Instabilité des Microsatellites et Cancers', Equipe labellisée par la Ligue Nationale contre le Cancer, Paris, France.,France Université Pierre et Marie Curie, Paris, France.,Department of Pathology, Hôpital Saint Antoine (Assistance Publique-Hôpitaux de Paris), Paris VI University, Paris, France
| | - Armelle Bardier-Dupas
- Department of Pathology, Hôpital Universitaire Pitié Salpêtrière (Assistance Publique-Hôpitaux de Paris), Paris VI University, Paris, France
| | - Noémie Basset
- Department of Genetics, Hôpital Universitaire Pitié Salpêtrière (Assistance Publique-Hôpitaux de Paris), Paris VI University, Paris, France.,INSERM, UMRS 938-Centre de Recherche Saint-Antoine, Equipe 'Instabilité des Microsatellites et Cancers', Equipe labellisée par la Ligue Nationale contre le Cancer, Paris, France.,France Université Pierre et Marie Curie, Paris, France
| | - Florence Coulet
- Department of Genetics, Hôpital Universitaire Pitié Salpêtrière (Assistance Publique-Hôpitaux de Paris), Paris VI University, Paris, France.,INSERM, UMRS 938-Centre de Recherche Saint-Antoine, Equipe 'Instabilité des Microsatellites et Cancers', Equipe labellisée par la Ligue Nationale contre le Cancer, Paris, France.,France Université Pierre et Marie Curie, Paris, France
| | - Chrystelle Colas
- Department of Genetics, Hôpital Universitaire Pitié Salpêtrière (Assistance Publique-Hôpitaux de Paris), Paris VI University, Paris, France.,INSERM, UMRS 938-Centre de Recherche Saint-Antoine, Equipe 'Instabilité des Microsatellites et Cancers', Equipe labellisée par la Ligue Nationale contre le Cancer, Paris, France.,France Université Pierre et Marie Curie, Paris, France.,Department of Genetics, Curie Institute, Paris, France
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21
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Constitutional mosaicism for a BRCA2 mutation as a cause of early-onset breast cancer. Fam Cancer 2020; 19:307-310. [PMID: 32468491 PMCID: PMC7497290 DOI: 10.1007/s10689-020-00186-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Accepted: 05/18/2020] [Indexed: 11/02/2022]
Abstract
Germline mutations in the BRCA1 and BRCA2 genes cause hereditary breast and ovarian cancer syndrome (HBOC). Mutations in these genes are usually inherited, and reports of de novo BRCA1/2 mutations are rare. To date, only one patient with low-level BRCA1 mutation mosaicism has been published. We report on a breast cancer patient with constitutional somatic mosaicism of a BRCA2 mutation. BRCA2 mutation c.9294C>G, p.(Tyr3098Ter) was detected in 20% of reads in DNA extracted from peripheral blood using next-generation sequencing (NGS). The BRCA2 mutation was subsequently observed at similar levels in normal breast tissue, adipose tissue, normal right fallopian tube tissue and ovaries of the patient, suggesting that this mutation occurred early in embryonic development. This is the first case to report constitutional mosaicism for a BRCA2 mutation and shows that BRCA2 mosaicism can underlie early-onset breast cancer. NGS for BRCA1/2 should be considered for patients whose tumors harbor a BRCA1/2 mutation and for individuals suggestive of genetic predisposition but without a family history of HBO.
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22
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Monahan KJ, Bradshaw N, Dolwani S, Desouza B, Dunlop MG, East JE, Ilyas M, Kaur A, Lalloo F, Latchford A, Rutter MD, Tomlinson I, Thomas HJW, Hill J. Guidelines for the management of hereditary colorectal cancer from the British Society of Gastroenterology (BSG)/Association of Coloproctology of Great Britain and Ireland (ACPGBI)/United Kingdom Cancer Genetics Group (UKCGG). Gut 2020; 69:411-444. [PMID: 31780574 PMCID: PMC7034349 DOI: 10.1136/gutjnl-2019-319915] [Citation(s) in RCA: 232] [Impact Index Per Article: 58.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/20/2019] [Revised: 10/25/2019] [Accepted: 11/05/2019] [Indexed: 12/12/2022]
Abstract
Heritable factors account for approximately 35% of colorectal cancer (CRC) risk, and almost 30% of the population in the UK have a family history of CRC. The quantification of an individual's lifetime risk of gastrointestinal cancer may incorporate clinical and molecular data, and depends on accurate phenotypic assessment and genetic diagnosis. In turn this may facilitate targeted risk-reducing interventions, including endoscopic surveillance, preventative surgery and chemoprophylaxis, which provide opportunities for cancer prevention. This guideline is an update from the 2010 British Society of Gastroenterology/Association of Coloproctology of Great Britain and Ireland (BSG/ACPGBI) guidelines for colorectal screening and surveillance in moderate and high-risk groups; however, this guideline is concerned specifically with people who have increased lifetime risk of CRC due to hereditary factors, including those with Lynch syndrome, polyposis or a family history of CRC. On this occasion we invited the UK Cancer Genetics Group (UKCGG), a subgroup within the British Society of Genetic Medicine (BSGM), as a partner to BSG and ACPGBI in the multidisciplinary guideline development process. We also invited external review through the Delphi process by members of the public as well as the steering committees of the European Hereditary Tumour Group (EHTG) and the European Society of Gastrointestinal Endoscopy (ESGE). A systematic review of 10 189 publications was undertaken to develop 67 evidence and expert opinion-based recommendations for the management of hereditary CRC risk. Ten research recommendations are also prioritised to inform clinical management of people at hereditary CRC risk.
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Affiliation(s)
- Kevin J Monahan
- Family Cancer Clinic, St Mark's Hospital, London, UK
- Faculty of Medicine, Imperial College, London, UK
| | - Nicola Bradshaw
- Clinical Genetics, West of Scotland Genetics Services, Glasgow, Glasgow, UK
| | - Sunil Dolwani
- Gastroenterology, Cardiff and Vale NHS Trust, Cardiff, UK
| | - Bianca Desouza
- Clinical Genetics, Guy's and St Thomas' NHS Foundation Trust, London, UK
| | | | - James E East
- Translational Gastroenterology Unit, John Radcliffe Hospital, Oxford, UK
- Oxford NIHR Biomedical Research Centre, University of Oxford, Oxford, UK
| | - Mohammad Ilyas
- Faculty of Medicine & Health Sciences, Nottingham University, Nottingham, UK
| | - Asha Kaur
- Head of Policy and Campaigns, Bowel Cancer UK, London, UK
| | - Fiona Lalloo
- Genetic Medicine, Central Manchester University Hospitals Foundation Trust, Manchester, UK
| | | | - Matthew D Rutter
- Gastroenterology, University Hospital of North Tees, Stockton-on-Tees, UK
- Northern Institute for Cancer Research, Newcastle University, Newcastle upon Tyne, UK
| | - Ian Tomlinson
- Nuffield Department of Clinical Medicine, Wellcome Trust Centre for Human Genetics, Birmingham, UK
- Cancer Research Centre, University of Edinburgh, Edinburgh, UK
| | - Huw J W Thomas
- Family Cancer Clinic, St Mark's Hospital, London, UK
- Faculty of Medicine, Imperial College, London, UK
| | - James Hill
- Genetic Medicine, Central Manchester University Hospitals Foundation Trust, Manchester, UK
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23
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Rubinstein JC, Khan SA, Christison-Lagay ER, Cha C. APC mutational patterns in gastric adenocarcinoma are enriched for missense variants with associated decreased survival. Genes Chromosomes Cancer 2020; 59:64-68. [PMID: 31353684 DOI: 10.1002/gcc.22792] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Revised: 07/16/2019] [Accepted: 07/22/2019] [Indexed: 01/24/2023] Open
Abstract
Adenomatous polyposis coli (APC) mutations are causally associated with familial adenomatous polyposis (FAP) and are recurrent somatic events across numerous tumor types, including gastric adenocarcinoma. Severity of disease in FAP correlates with specific APC mutations, but the impact of given mutations on phenotype in gastric cancer is not well studied. Sequencing data from the Genomic Data Commons (GDC) demonstrate an APC mutational pattern in gastric cancer that differs dramatically from that seen in colon cancer. Exome sequencing data from APC-mutant colon and gastric adenocarcinomas in GDC was filtered for single nucleotide variants (SNVs) using MuTect2 Variant Aggregation and Masking pipeline, Somatic Aggregation Workflow. APC mutations were found in 57/441 gastric (12.9%) and 309/433 colon adenocarcinomas (71.4%). There was a significant difference in the proportion of stopgain, frameshift, and missense mutations between tumor types(P < .00001). Colon tumors were predominated by frameshift and stopgains, comprising 47.7% and 35.7%, respectively. In contrast, 47.1% of gastric mutations were missense. Gastric tumors harboring missense mutations showed decreased overall survival relative to other mutational subtypes(P = .008). In the gastric samples, 25.9% of frameshift and stopgain mutations are in the 3' portion of the gene, compared to 1.4% of colon samples. APC mutations demonstrate different distributions in gastric and colon adenocarcinoma, with a shift toward missense variants in gastric tumors and worse survival in gastric tumors harboring them. As different mutations confer variable degrees of protein dysfunction and resultant clinical manifestation, expanded investigation of specific mutational patterns will prove integral to future-risk stratification strategies.
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Affiliation(s)
- Jill C Rubinstein
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Sajid A Khan
- Department of Surgery, Yale School of Medicine, New Haven, Connecticut
| | | | - Charles Cha
- Department of Surgery, Yale School of Medicine, New Haven, Connecticut
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24
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Lorca V, Garre P. Current status of the genetic susceptibility in attenuated adenomatous polyposis. World J Gastrointest Oncol 2019; 11:1101-1114. [PMID: 31908716 PMCID: PMC6937445 DOI: 10.4251/wjgo.v11.i12.1101] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Revised: 08/18/2019] [Accepted: 10/14/2019] [Indexed: 02/05/2023] Open
Abstract
Adenomatous polyposis (AP) is classified according to cumulative adenoma number in classical AP (CAP) and attenuated AP (AAP). Genetic susceptibility is the major risk factor in CAP due to mutations in the known high predisposition genes APC and MUTYH. However, the contribution of genetic susceptibility to AAP is lower and less understood. New predisposition genes have been recently proposed, and some of them have been validated, but their scarcity hinders accurate risk estimations and prevalence calculations. AAP is a heterogeneous condition in terms of severity, clinical features and heritability. Therefore, clinicians do not have strong discriminating criteria for the recommendation of the genetic study of known predisposition genes, and the detection rate is low. Elucidation and knowledge of new AAP high predisposition genes are of great importance to offer accurate genetic counseling to the patient and family members. This review aims to update the genetic knowledge of AAP, and to expound the difficulties involved in the genetic analysis of a highly heterogeneous condition such as AAP.
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Affiliation(s)
- Víctor Lorca
- Laboratorio de Oncología Molecular, Grupo de Investigación Clínica y Traslacional en Oncología, Hospital Clínico San Carlos, Madrid 28040, Spain
| | - Pilar Garre
- Laboratorio de Oncología Molecular, Servicio de Oncología, Hospital Clínico San Carlos, Madrid 28040, Spain
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25
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Kim B, Won D, Jang M, Kim H, Choi JR, Kim TI, Lee ST. Next-generation sequencing with comprehensive bioinformatics analysis facilitates somatic mosaic APC gene mutation detection in patients with familial adenomatous polyposis. BMC Med Genomics 2019; 12:103. [PMID: 31269945 PMCID: PMC6610853 DOI: 10.1186/s12920-019-0553-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2019] [Accepted: 06/19/2019] [Indexed: 02/06/2023] Open
Abstract
Background Familial adenomatous polyposis (FAP) is an autosomal dominant colorectal tumor characterized by numerous adenomatous colonic polyps that often lead to colon cancer. Although most patients with FAP harbored germline mutations in APC gene, it was recently recognized that patients with clinical FAP, but without detectable pathogenic mutations, could be associated with somatic mosaic APC mutation. Methods We reanalyzed the nest-generation sequencing (NGS) gene panel testing results of patients who were diagnosed with FAP, but did not have APC mutations, at Yonsei Cancer Prevention Center between July 2016 and March 2018. We tested several variant calling algorithms to identify low level mosaic variants. In one patient with a low frequency APC mutation, NGS analysis was performed together with endoscopic biopsy. Variant calling tools HaplotypeCaller, MuTect2, VarScan2, and Pindel were used. We also used 3′-Modified Oligonucleotides (MEMO)-PCR or conventional PCR for confirmation. Results Among 28 patients with clinical suspicion of FAP but no detectable pathogenic variants of colonic polyposis associated genes, somatic mosaic pathogenic variants were identified in seven patients. The variant allele frequency ranged from 0.3 to 7.7%. These variants were mostly detected through variant caller MuTect2 and Pindel, and were further confirmed using mutant enrichment with MEMO-PCR. Conclusions The NGS with an adequate combination of bioinformatics tools is effective to detect low level somatic variants in a single assay. Because mosaic APC mutations are more frequent than previously thought, the presence of mosaic mutations must be considered when analyzing genetic tests of patients with FAP. Electronic supplementary material The online version of this article (10.1186/s12920-019-0553-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Borahm Kim
- Department of Laboratory Medicine, Yonsei University College of Medicine, 50 Yonsei-ro, Seodaemun-gu, Seoul, 03722, Republic of Korea
| | - Dongju Won
- Department of Laboratory Medicine, Yonsei University College of Medicine, 50 Yonsei-ro, Seodaemun-gu, Seoul, 03722, Republic of Korea
| | - Mi Jang
- Department of Pathology, Yonsei University College of Medicine, Seoul, Korea
| | - Hoguen Kim
- Department of Pathology, Yonsei University College of Medicine, Seoul, Korea
| | - Jong Rak Choi
- Department of Laboratory Medicine, Yonsei University College of Medicine, 50 Yonsei-ro, Seodaemun-gu, Seoul, 03722, Republic of Korea
| | - Tae Il Kim
- Department of Internal Medicine and Institute of Gastroenterology, Brain Korea 21 PLUS Project for Medical Sciences Yonsei Cancer Prevention Center, Yonsei University College of Medicine, 50 Yonsei-ro, Seodaemun-gu, Seoul, 03722, Republic of Korea.
| | - Seung-Tae Lee
- Department of Laboratory Medicine, Yonsei University College of Medicine, 50 Yonsei-ro, Seodaemun-gu, Seoul, 03722, Republic of Korea.
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26
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Development, technical validation, and clinical application of a multigene panel for hereditary gastrointestinal cancer and polyposis. TUMORI JOURNAL 2019; 105:338-352. [DOI: 10.1177/0300891619847085] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Introduction: Recent advances in technology and research are rapidly changing the diagnostic approach to hereditary gastrointestinal cancer (HGIC) syndromes. Although the practice of clinical genetics is currently transitioning from targeted criteria-based testing to multigene panels, important challenges remain to be addressed. The aim of this study was to develop and technically validate the performance of a multigene panel for HGIC. Methods: CGT-colon-G14 is an amplicon-based panel designed to detect single nucleotide variants and small insertions/deletions in 14 well-established or presumed high-penetrance genes involved in HGIC. The assay parameters tested were sensitivity, specificity, accuracy, and inter-run and intra-run reproducibility. Performance and clinical impact were determined using 48 samples of patients with suspected HGIC/polyposis previously tested with the targeted approach. Results: The CGT-colon-G14 panel showed 99.99% accuracy and 100% inter- and intra-run reproducibility. Moreover, panel testing detected 1 actionable pathogenic variant and 16 variants with uncertain clinical impact that were missed by the conventional approach because they were located in genes not previously analyzed. Conclusion: Introduction of the CGT-colon-G14 panel into the clinic could provide a higher diagnostic yield than a step-wise approach; however, results may not always be straightforward without the implementation of new genetic counseling models.
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27
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Abstract
Familial adenomatous polyposis (FAP) is usually caused by germline mutations in the adenomatous polyposis coli (APC) gene. The classic form is characterized by hundreds to thousands of adenomas in the colorectum and early onset colorectal cancer (CRC) if left untreated. FAP is also associated with multiple extra-colonic manifestations such as gastroduodenal polyps, osteomas, epidermoid cysts, fibromas and desmoids. Most desmoid tumours in FAP patients occur intra-abdominally. Approximately 15–20% of the APC mutations are de novo mutations. Somatic mosaicism has been reported in some sporadic cases of polyposis but is probably an underestimated cause of the disease. This case report presents the detection of a mosaic APC mutation in a 26-year-old woman who as a child had been diagnosed with desmoid type fibromatosis. FAP was suggested when she presented with extensive extra abdominal fibromatosis. Our findings indicate that APC mutations may be suspected in patients presenting with a desmoid regardless of its location. If there is clinical evidence that the patient has FAP, adenomas and colonic mucosa in addition to leukocyte DNA should be included in the screening, preferably using methods that are more sensitive than Sanger sequencing.
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28
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Bowles KR, Mancini-DiNardo D, Coffee B, Cox HC, Qian Y, Elias M, Singh N, Judkins T, Leclair B, Roa BB. Hereditary cancer testing challenges: assembling the analytical pieces to solve the patient clinical puzzle. Future Oncol 2018; 15:65-79. [PMID: 30113232 DOI: 10.2217/fon-2018-0476] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Expanded genetic test utilization to guide cancer management has driven the development of larger gene panels and greater diversity in the patient population pursuing testing, resulting in increased identification of atypical or technically challenging genetic findings. To ensure appropriate patient care, it is critical that genetic tests adequately identify and characterize these findings. We describe genetic testing challenges frequently encountered by our laboratory and the methodologies we employ to improve test accuracy for the identification and characterization of atypical genetic findings. While these findings may be individually rare, 15,745 (9%) individuals tested by our laboratory for hereditary cancer risk had an atypical genetic finding, highlighting the importance of employing highly accurate and comprehensive methods in clinical genetic testing.
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Affiliation(s)
- Karla R Bowles
- Myriad Genetic Laboratories, Inc., 320 Wakara Way, Salt Lake City, UT 84108, USA
| | | | - Bradford Coffee
- Myriad Genetic Laboratories, Inc., 320 Wakara Way, Salt Lake City, UT 84108, USA
| | - Hannah C Cox
- Myriad Genetic Laboratories, Inc., 320 Wakara Way, Salt Lake City, UT 84108, USA
| | - Yaping Qian
- Myriad Genetic Laboratories, Inc., 320 Wakara Way, Salt Lake City, UT 84108, USA
| | - Maria Elias
- Myriad Genetic Laboratories, Inc., 320 Wakara Way, Salt Lake City, UT 84108, USA
| | - Nanda Singh
- Myriad Genetic Laboratories, Inc., 320 Wakara Way, Salt Lake City, UT 84108, USA
| | - Thaddeus Judkins
- Myriad Genetic Laboratories, Inc., 320 Wakara Way, Salt Lake City, UT 84108, USA
| | - Benoît Leclair
- Myriad Genetic Laboratories, Inc., 320 Wakara Way, Salt Lake City, UT 84108, USA
| | - Benjamin B Roa
- Myriad Genetic Laboratories, Inc., 320 Wakara Way, Salt Lake City, UT 84108, USA
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29
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Optimization of the diagnosis of inherited colorectal cancer using NGS and capture of exonic and intronic sequences of panel genes. Eur J Hum Genet 2018; 26:1597-1602. [PMID: 29967336 DOI: 10.1038/s41431-018-0207-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2017] [Revised: 05/28/2018] [Accepted: 06/05/2018] [Indexed: 11/08/2022] Open
Abstract
We have developed and validated for the diagnosis of inherited colorectal cancer (CRC) a massive parallel sequencing strategy based on: (i) fast capture of exonic and intronic sequences from ten genes involved in Mendelian forms of CRC (MLH1, MSH2, MSH6, PMS2, APC, MUTYH, STK11, SMAD4, BMPR1A and PTEN); (ii) sequencing on MiSeq and NextSeq 500 Illumina platforms; (iii) a bioinformatic pipeline that includes BWA-Picard-GATK (Broad Institute) and CASAVA (Illumina) in parallel for mapping and variant calling, Alamut Batch (Interactive BioSoftware) for annotation, CANOES for CNV detection and finally, chimeric reads analysis for the detection of other types of structural variants (SVs). Analysis of 1644 new index cases allowed the identification of 323 patients with class 4 or 5 variants, corresponding to a 20% disease-causing variant detection rate. This rate reached 37% in patients with Lynch syndrome, suspected on the basis of tumour analyses. Thanks to this strategy, we detected overlapping phenotypes (e.g., MUTYH biallelic mutations mimicking Lynch syndrome), mosaic alterations and complex SVs such as a genomic deletion involving the last BMPR1A exons and PTEN, an Alu insertion within MSH2 exon 8 and a mosaic deletion of STK11 exons 3-10. This strategy allows, in a single step, detection of all types of CRC gene alterations including SVs and provides a high disease-causing variant detection rate, thus optimizing the diagnosis of inherited CRC.
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30
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RNA analysis of cancer predisposing genes in formalin-fixed paraffin-embedded tissue determines aberrant splicing. Eur J Hum Genet 2018; 26:1143-1150. [PMID: 29706640 DOI: 10.1038/s41431-018-0153-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2017] [Revised: 03/20/2018] [Accepted: 03/30/2018] [Indexed: 02/01/2023] Open
Abstract
High-throughput sequencing efforts in molecular tumour diagnostics detect increasing numbers of novel variants, including variants predicted to affect splicing. In silico prediction tools can reliably predict the effect of variant disrupting canonical splice sites; however, experimental validation is required to confirm aberrant splicing. Here, we present RNA analysis performed for 13 canonical splice site variants predicted or known to result in splicing in the cancer predisposition genes MLH1, MSH2, MSH6, APC and BRCA1. Total nucleic acid was successfully isolated for 10 variants from eight formalin-fixed paraffin-embedded (FFPE) tumour tissues and two B-cell lines. Aberrant splicing was confirmed in all six variants known to result in splicing. Of one known variant in the B-cell line, aberrant splicing could only be detected after formalin fixation, which indicated that formalin fixation could possibly inhibit RNA degradation. Aberrant splicing was concluded in three of four predicted splice variants of uncertain significance, supporting their pathogenic effect. With this assay, somatic splice variants can be easily and rapidly analysed, enabling retrospective analysis to support the pathogenicity of variants predicted to result in splicing when only FFPE material is available.
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31
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Ciavarella M, Miccoli S, Prossomariti A, Pippucci T, Bonora E, Buscherini F, Palombo F, Zuntini R, Balbi T, Ceccarelli C, Bazzoli F, Ricciardiello L, Turchetti D, Piazzi G. Somatic APC mosaicism and oligogenic inheritance in genetically unsolved colorectal adenomatous polyposis patients. Eur J Hum Genet 2018; 26:387-395. [PMID: 29367705 PMCID: PMC5839046 DOI: 10.1038/s41431-017-0086-y] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2017] [Revised: 10/26/2017] [Accepted: 11/13/2017] [Indexed: 12/27/2022] Open
Abstract
Germline variants in the APC gene cause familial adenomatous polyposis. Inherited variants in MutYH, POLE, POLD1, NTHL1, and MSH3 genes and somatic APC mosaicism have been reported as alternative causes of polyposis. However, ~30-50% of cases of polyposis remain genetically unsolved. Thus, the aim of this study was to investigate the genetic causes of unexplained adenomatous polyposis. Eight sporadic cases with >20 adenomatous polyps by 35 years of age or >50 adenomatous polyps by 55 years of age, and no causative germline variants in APC and/or MutYH, were enrolled from a cohort of 56 subjects with adenomatous colorectal polyposis. APC gene mosaicism was investigated on DNA from colonic adenomas by Sanger sequencing or Whole Exome Sequencing (WES). Mosaicism extension to other tissues (peripheral blood, saliva, hair follicles) was evaluated using Sanger sequencing and/or digital PCR. APC second hit was investigated in adenomas from mosaic patients. WES was performed on DNA from peripheral blood to identify additional polyposis candidate variants. We identified APC mosaicism in 50% of patients. In three cases mosaicism was restricted to the colon, while in one it also extended to the duodenum and saliva. One patient without APC mosaicism, carrying an APC in-frame deletion of uncertain significance, was found to harbor rare germline variants in OGG1, POLQ, and EXO1 genes. In conclusion, our restrictive selection criteria improved the detection of mosaic APC patients. In addition, we showed for the first time that an oligogenic inheritance of rare variants might have a cooperative role in sporadic colorectal polyposis onset.
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Affiliation(s)
- Michele Ciavarella
- Medical Genetics Unit, S.Orsola-Malpighi Hospital, University of Bologna, Bologna, Italy
| | - Sara Miccoli
- Medical Genetics Unit, S.Orsola-Malpighi Hospital, University of Bologna, Bologna, Italy
- Center for Studies on Hereditary Cancer, Department of Medical and Surgical Sciences, University of Bologna, Bologna, Italy
| | - Anna Prossomariti
- Department of Medical and Surgical Sciences, University of Bologna, Bologna, Italy
- Center for Applied Biomedical Research (CRBA), S.Orsola-Malpighi Hospital, University of Bologna, Bologna, Italy
| | - Tommaso Pippucci
- Medical Genetics Unit, S.Orsola-Malpighi Hospital, University of Bologna, Bologna, Italy
| | - Elena Bonora
- Medical Genetics Unit, S.Orsola-Malpighi Hospital, University of Bologna, Bologna, Italy
- Center for Studies on Hereditary Cancer, Department of Medical and Surgical Sciences, University of Bologna, Bologna, Italy
| | - Francesco Buscherini
- Medical Genetics Unit, S.Orsola-Malpighi Hospital, University of Bologna, Bologna, Italy
| | - Flavia Palombo
- Medical Genetics Unit, S.Orsola-Malpighi Hospital, University of Bologna, Bologna, Italy
| | - Roberta Zuntini
- Medical Genetics Unit, S.Orsola-Malpighi Hospital, University of Bologna, Bologna, Italy
- Center for Studies on Hereditary Cancer, Department of Medical and Surgical Sciences, University of Bologna, Bologna, Italy
| | - Tiziana Balbi
- Pathology Unit, S. Orsola-Malpighi Hospital, University of Bologna, Bologna, Italy
| | - Claudio Ceccarelli
- Department of Experimental, Diagnostic and Specialty Medicine, University of Bologna, Bologna, Italy
| | - Franco Bazzoli
- Department of Medical and Surgical Sciences, University of Bologna, Bologna, Italy
| | - Luigi Ricciardiello
- Center for Studies on Hereditary Cancer, Department of Medical and Surgical Sciences, University of Bologna, Bologna, Italy.
- Department of Medical and Surgical Sciences, University of Bologna, Bologna, Italy.
- Center for Applied Biomedical Research (CRBA), S.Orsola-Malpighi Hospital, University of Bologna, Bologna, Italy.
| | - Daniela Turchetti
- Medical Genetics Unit, S.Orsola-Malpighi Hospital, University of Bologna, Bologna, Italy.
- Center for Studies on Hereditary Cancer, Department of Medical and Surgical Sciences, University of Bologna, Bologna, Italy.
| | - Giulia Piazzi
- Center for Studies on Hereditary Cancer, Department of Medical and Surgical Sciences, University of Bologna, Bologna, Italy.
- Department of Medical and Surgical Sciences, University of Bologna, Bologna, Italy.
- Center for Applied Biomedical Research (CRBA), S.Orsola-Malpighi Hospital, University of Bologna, Bologna, Italy.
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32
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Abstract
Colorectal adenomatous polyposis syndromes encompass a diverse group of disorders with varying modes of inheritance and penetrance. Children may present with overt disease or within screening programs for families at high risk. We provide an overview of the array of pediatric polyposis syndromes, current screening recommendations, and surgical indications and technical considerations. Optimal disease management for these pediatric patients is still evolving and has implications for screening, surveillance, pediatric surgical management, and transition of care gastroenterologic neoplasia physicians and surgeons.
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Affiliation(s)
- Aodhnait S Fahy
- Division of Pediatric Surgery, Department of Surgery, Mayo Clinic, Rochester, Minnesota
| | - Christopher R Moir
- Division of Pediatric Surgery, Department of Surgery, Mayo Clinic, Rochester, Minnesota
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33
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Renaux-Petel M, Charbonnier F, Théry JC, Fermey P, Lienard G, Bou J, Coutant S, Vezain M, Kasper E, Fourneaux S, Manase S, Blanluet M, Leheup B, Mansuy L, Champigneulle J, Chappé C, Longy M, Sévenet N, Paillerets BBD, Guerrini-Rousseau L, Brugières L, Caron O, Sabourin JC, Tournier I, Baert-Desurmont S, Frébourg T, Bougeard G. Contribution of de novo and mosaic TP53 mutations to Li-Fraumeni syndrome. J Med Genet 2017; 55:173-180. [DOI: 10.1136/jmedgenet-2017-104976] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2017] [Revised: 09/28/2017] [Accepted: 10/09/2017] [Indexed: 01/06/2023]
Abstract
BackgroundDevelopment of tumours such as adrenocortical carcinomas (ACC), choroid plexus tumours (CPT) or female breast cancers before age 31 or multiple primary cancers belonging to the Li-Fraumeni (LFS) spectrum is, independently of the familial history, highly suggestive of a germline TP53 mutation. The aim of this study was to determine the contribution of de novo and mosaic mutations to LFS.Methods and resultsAmong 328 unrelated patients harbouring a germline TP53 mutation identified by Sanger sequencing and/or QMPSF, we could show that the mutations had occurred de novo in 40 cases, without detectable parental age effect. Sanger sequencing revealed two mosaic mutations in a child with ACC and in an unaffected father of a child with medulloblastoma. Re-analysis of blood DNA by next-generation sequencing, performed at a depth above 500X, from 108 patients suggestive of LFS without detectable TP53 mutations, allowed us to identify 6 additional cases of mosaic TP53 mutations, in 2/49 children with ACC, 2/21 children with CPT, in 1/31 women with breast cancer before age 31 and in a patient who developed an osteosarcoma at age 12, a breast carcinoma and a breast sarcoma at age 35.ConclusionsThis study performed on a large series of TP53 mutation carriers allows estimating the contribution to LFS of de novo mutations to at least 14% (48/336) and suggests that approximately one-fifth of these de novo mutations occur during embryonic development. Considering the medical impact of TP53 mutation identification, medical laboratories in charge of TP53 testing should ensure the detection of mosaic mutations.
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34
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The American Society of Colon and Rectal Surgeons Clinical Practice Guidelines for the Management of Inherited Polyposis Syndromes. Dis Colon Rectum 2017; 60:881-894. [PMID: 28796726 PMCID: PMC5701653 DOI: 10.1097/dcr.0000000000000912] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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35
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Basso G, Bianchi P, Malesci A, Laghi L. Hereditary or sporadic polyposis syndromes. Best Pract Res Clin Gastroenterol 2017; 31:409-417. [PMID: 28842050 DOI: 10.1016/j.bpg.2017.05.011] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/18/2017] [Accepted: 05/31/2017] [Indexed: 01/31/2023]
Abstract
Polyposis syndromes are encountered in endoscopy practice, and are considered rare entities, accounting for ≤1% of colorectal cancer. Polyposis can occur within inherited syndromes or as "sporadic" cases of unknown etiology. Their proper characterization is relevant for patient management, and should nowadays drive appropriate genetic tests which have a key role in clinical practice for driving surveillance and colorectal cancer prevention, enlarged to relatives. Polyposis classification is based upon polyp number and histology, familial and personal history. This review will explore the polyposis nosology and their genetic determinants in the emerging scenario of Next Generation Sequencing which allow testing multiples genes in parallel. This capability will likely continue to increase the range of polyposis predisposing genes, contributing to define new clinical entities.
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Affiliation(s)
- Gianluca Basso
- Laboratory of Molecular Gastroenterology, Department of Gastroenterology, Humanitas Clinical and Research Center, Via Manzoni 56, 20089 Rozzano (Milan), Italy
| | - Paolo Bianchi
- Laboratory of Molecular Gastroenterology, Department of Gastroenterology, Humanitas Clinical and Research Center, Via Manzoni 56, 20089 Rozzano (Milan), Italy
| | - Alberto Malesci
- Department of Biotechnologies and Translational Medicine, University of Milan, Via Vanvitelli 32, 20133 Milan, Italy; Department of Gastroenterology, Humanitas Clinical and Research Center, Via Manzoni 56, 20089 Rozzano (Milan), Italy
| | - Luigi Laghi
- Laboratory of Molecular Gastroenterology, Department of Gastroenterology, Humanitas Clinical and Research Center, Via Manzoni 56, 20089 Rozzano (Milan), Italy; Department of Gastroenterology, Humanitas Clinical and Research Center, Via Manzoni 56, 20089 Rozzano (Milan), Italy; Hereditary Cancer Genetics Clinic, Humanitas Cancer Center, Humanitas Clinical and Research Center, Via Manzoni 56, 20089 Rozzano (Milan), Italy.
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36
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Talseth-Palmer BA. The genetic basis of colonic adenomatous polyposis syndromes. Hered Cancer Clin Pract 2017; 15:5. [PMID: 28331556 PMCID: PMC5353802 DOI: 10.1186/s13053-017-0065-x] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2016] [Accepted: 03/07/2017] [Indexed: 02/08/2023] Open
Abstract
Colorectal cancer (CRC) is one of the most common forms of cancer worldwide and familial adenomatous polyposis (FAP) accounts for approximately 1% of all CRCs. Adenomatous polyposis syndromes can be divided into; familial adenomatous polyposis (FAP) – classic FAP and attenuated familial adenomatous polyposis (AFAP), MUTYH-associated polyposis (MAP), NTHL1-associated polyposis (NAP) and polymerase proofreading-associated polyposis (PPAP). The polyposis syndromes genetics and clinical manifestation of disease varies and cases with clinical diagnosis of FAP might molecularly show a different diagnosis. This review examines different aspects of the adenomatous polyposis syndromes genetics and clinical manifestation of disease; in addition the genotype-phenotype and modifier alleles of FAP will be discussed. New technology has made it possible to diagnose some of the APC mutation negative patients into their respective syndromes. There still remain many molecularly undiagnosed adenomatous polyposis patients indicating that there remain causative genes to be discovered and with today’s technology these are expected to be identified in the near future. The knowledge about the role of modifier alleles in FAP will contribute to improved pre-symptomatic diagnosis and treatment. New novel mutations will continually be discovered in genes already associated with disease and new genes will be discovered that are associated with adenomatous polyposis. The search for modifier alleles in FAP should be made a priority.
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Affiliation(s)
- Bente A Talseth-Palmer
- Department of Laboratory Medicine, Children's and Women's Health, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology, Trondheim, 7491 Norway.,Clinic for Medicine, Møre og Romsdal Hospital Trust, Molde, Norway.,School of Biomedical Sciences and Pharmacy, Faculty of Health and Medicine, University of Newcastle, Newcastle, NSW Australia.,Hunter Medical Research Institute, Newcastle, NSW Australia.,Clinic for Medicine, Library, Molde Hospital, Parkvegen 84, Molde, 6407 Norway
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37
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Jansen AML, Crobach S, Geurts-Giele WRR, van den Akker BEWM, Garcia MV, Ruano D, Nielsen M, Tops CMJ, Wijnen JT, Hes FJ, van Wezel T, Dinjens WNM, Morreau H. Distinct Patterns of Somatic Mosaicism in the APC Gene in Neoplasms From Patients With Unexplained Adenomatous Polyposis. Gastroenterology 2017; 152:546-549.e3. [PMID: 27816598 DOI: 10.1053/j.gastro.2016.10.040] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/26/2016] [Revised: 10/21/2016] [Accepted: 10/23/2016] [Indexed: 12/02/2022]
Abstract
We investigated the presence and patterns of mosaicism in the APC gene in patients with colon neoplasms not associated with any other genetic variants; we performed deep sequence analysis of APC in at least 2 adenomas or carcinomas per patient. We identified mosaic variants in APC in adenomas from 9 of the 18 patients with 21 to approximately 100 adenomas. Mosaic variants of APC were variably detected in leukocyte DNA and/or non-neoplastic intestinal mucosa of these patients. In a comprehensive sequence analysis of 1 patient, we found no evidence for mosaicism in APC in non-neoplastic intestinal mucosa. One patient was found to carry a mosaic c.4666dupA APC variant in only 10 of 16 adenomas, indicating the importance of screening 2 or more adenomas for genetic variants.
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Affiliation(s)
- Anne M L Jansen
- Department of Pathology, Leiden University Medical Centre, Leiden, The Netherlands; Department of Human Genetics, Leiden University Medical Centre, Leiden, The Netherlands
| | - Stijn Crobach
- Department of Pathology, Leiden University Medical Centre, Leiden, The Netherlands
| | - Willemina R R Geurts-Giele
- Department of Pathology, Erasmus MC Cancer Institute, University Medical Centre Rotterdam, The Netherlands
| | | | | | - Dina Ruano
- Department of Pathology, Leiden University Medical Centre, Leiden, The Netherlands
| | - Maartje Nielsen
- Department of Clinical Genetics, Leiden University Medical Centre, Leiden, The Netherlands
| | - Carli M J Tops
- Department of Clinical Genetics, Leiden University Medical Centre, Leiden, The Netherlands
| | - Juul T Wijnen
- Department of Human Genetics, Leiden University Medical Centre, Leiden, The Netherlands; Department of Clinical Genetics, Leiden University Medical Centre, Leiden, The Netherlands
| | - Frederik J Hes
- Department of Clinical Genetics, Leiden University Medical Centre, Leiden, The Netherlands
| | - Tom van Wezel
- Department of Pathology, Leiden University Medical Centre, Leiden, The Netherlands
| | - Winand N M Dinjens
- Department of Pathology, Erasmus MC Cancer Institute, University Medical Centre Rotterdam, The Netherlands
| | - Hans Morreau
- Department of Pathology, Leiden University Medical Centre, Leiden, The Netherlands.
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38
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Spier I, Kerick M, Drichel D, Horpaopan S, Altmüller J, Laner A, Holzapfel S, Peters S, Adam R, Zhao B, Becker T, Lifton RP, Holinski-Feder E, Perner S, Thiele H, Nöthen MM, Hoffmann P, Timmermann B, Schweiger MR, Aretz S. Exome sequencing identifies potential novel candidate genes in patients with unexplained colorectal adenomatous polyposis. Fam Cancer 2016; 15:281-8. [PMID: 26780541 DOI: 10.1007/s10689-016-9870-z] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
In up to 30% of patients with colorectal adenomatous polyposis, no germline mutation in the known genes APC, causing familial adenomatous polyposis, MUTYH, causing MUTYH-associated polyposis, and POLE or POLD1, causing Polymerase-Proofreading-associated polyposis can be identified, although a hereditary etiology is likely. To uncover new causative genes, exome sequencing was performed using DNA from leukocytes and a total of 12 colorectal adenomas from seven unrelated patients with unexplained sporadic adenomatous polyposis. For data analysis and variant filtering, an established bioinformatics pipeline including in-house tools was applied. Variants were filtered for rare truncating point mutations and copy-number variants assuming a dominant, recessive, or tumor suppressor model of inheritance. Subsequently, targeted sequence analysis of the most promising candidate genes was performed in a validation cohort of 191 unrelated patients. All relevant variants were validated by Sanger sequencing. The analysis of exome sequencing data resulted in the identification of rare loss-of-function germline mutations in three promising candidate genes (DSC2, PIEZO1, ZSWIM7). In the validation cohort, further variants predicted to be pathogenic were identified in DSC2 and PIEZO1. According to the somatic mutation spectra, the adenomas in this patient cohort follow the classical pathways of colorectal tumorigenesis. The present study identified three candidate genes which might represent rare causes for a predisposition to colorectal adenoma formation. Especially PIEZO1 (FAM38A) and ZSWIM7 (SWS1) warrant further exploration. To evaluate the clinical relevance of these genes, investigation of larger patient cohorts and functional studies are required.
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Affiliation(s)
- Isabel Spier
- Institute of Human Genetics, University of Bonn, Sigmund-Freud-Str. 25, 53127, Bonn, Germany. .,Center for Hereditary Tumor Syndromes, University of Bonn, Bonn, Germany.
| | - Martin Kerick
- Department of Vertebrate Genomics, Max Planck Institute for Molecular Genetics, Berlin, Germany.,Cologne Center for Genomics (CCG), University of Cologne, Cologne, Germany
| | - Dmitriy Drichel
- German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany
| | - Sukanya Horpaopan
- Institute of Human Genetics, University of Bonn, Sigmund-Freud-Str. 25, 53127, Bonn, Germany.,Department of Anatomy, Faculty of Medical Science, Naresuan University, Phitsanulok, Thailand
| | - Janine Altmüller
- Cologne Center for Genomics (CCG), University of Cologne, Cologne, Germany.,Institute of Human Genetics, University of Cologne, Cologne, Germany
| | - Andreas Laner
- Medizinische Klinik und Poliklinik IV, Campus Innenstadt, Klinikum der Universität München, Munich, Germany.,Medizinisch Genetisches Zentrum, Munich, Germany
| | - Stefanie Holzapfel
- Institute of Human Genetics, University of Bonn, Sigmund-Freud-Str. 25, 53127, Bonn, Germany.,Center for Hereditary Tumor Syndromes, University of Bonn, Bonn, Germany
| | - Sophia Peters
- Institute of Human Genetics, University of Bonn, Sigmund-Freud-Str. 25, 53127, Bonn, Germany
| | - Ronja Adam
- Institute of Human Genetics, University of Bonn, Sigmund-Freud-Str. 25, 53127, Bonn, Germany.,Center for Hereditary Tumor Syndromes, University of Bonn, Bonn, Germany
| | - Bixiao Zhao
- Departments of Genetics, Howard Hughes Medical Institute, Yale University School of Medicine, New Haven, CT, USA
| | - Tim Becker
- German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany.,Institute of Medical Biometry, Informatics, and Epidemiology, University of Bonn, Bonn, Germany
| | - Richard P Lifton
- Departments of Genetics, Howard Hughes Medical Institute, Yale University School of Medicine, New Haven, CT, USA
| | - Elke Holinski-Feder
- Medizinische Klinik und Poliklinik IV, Campus Innenstadt, Klinikum der Universität München, Munich, Germany.,Medizinisch Genetisches Zentrum, Munich, Germany
| | - Sven Perner
- Section for Prostate Cancer Research, Center for Integrated Oncology Cologne/Bonn, Institute of Pathology, University Hospital of Bonn, Bonn, Germany.,Pathology Network of the University Hospital of Luebeck and Leibniz Research Center Borstel, Borstel, Germany
| | - Holger Thiele
- Cologne Center for Genomics (CCG), University of Cologne, Cologne, Germany
| | - Markus M Nöthen
- Institute of Human Genetics, University of Bonn, Sigmund-Freud-Str. 25, 53127, Bonn, Germany.,Department of Genomics, Life and Brain Center, University of Bonn, Bonn, Germany
| | - Per Hoffmann
- Institute of Human Genetics, University of Bonn, Sigmund-Freud-Str. 25, 53127, Bonn, Germany.,Department of Genomics, Life and Brain Center, University of Bonn, Bonn, Germany.,Division of Medical Genetics, University Hospital Basel, Basel, Switzerland.,Department of Biomedicine, University of Basel, Basel, Switzerland
| | - Bernd Timmermann
- Next Generation Sequencing Group, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Michal R Schweiger
- Department of Vertebrate Genomics, Max Planck Institute for Molecular Genetics, Berlin, Germany.,Cologne Center for Genomics (CCG), University of Cologne, Cologne, Germany
| | - Stefan Aretz
- Institute of Human Genetics, University of Bonn, Sigmund-Freud-Str. 25, 53127, Bonn, Germany.,Center for Hereditary Tumor Syndromes, University of Bonn, Bonn, Germany
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39
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Adam R, Spier I, Zhao B, Kloth M, Marquez J, Hinrichsen I, Kirfel J, Tafazzoli A, Horpaopan S, Uhlhaas S, Stienen D, Friedrichs N, Altmüller J, Laner A, Holzapfel S, Peters S, Kayser K, Thiele H, Holinski-Feder E, Marra G, Kristiansen G, Nöthen MM, Büttner R, Möslein G, Betz RC, Brieger A, Lifton RP, Aretz S. Exome Sequencing Identifies Biallelic MSH3 Germline Mutations as a Recessive Subtype of Colorectal Adenomatous Polyposis. Am J Hum Genet 2016; 99:337-51. [PMID: 27476653 DOI: 10.1016/j.ajhg.2016.06.015] [Citation(s) in RCA: 161] [Impact Index Per Article: 20.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2016] [Accepted: 06/14/2016] [Indexed: 12/20/2022] Open
Abstract
In ∼30% of families affected by colorectal adenomatous polyposis, no germline mutations have been identified in the previously implicated genes APC, MUTYH, POLE, POLD1, and NTHL1, although a hereditary etiology is likely. To uncover further genes with high-penetrance causative mutations, we performed exome sequencing of leukocyte DNA from 102 unrelated individuals with unexplained adenomatous polyposis. We identified two unrelated individuals with differing compound-heterozygous loss-of-function (LoF) germline mutations in the mismatch-repair gene MSH3. The impact of the MSH3 mutations (c.1148delA, c.2319-1G>A, c.2760delC, and c.3001-2A>C) was indicated at the RNA and protein levels. Analysis of the diseased individuals' tumor tissue demonstrated high microsatellite instability of di- and tetranucleotides (EMAST), and immunohistochemical staining illustrated a complete loss of nuclear MSH3 in normal and tumor tissue, confirming the LoF effect and causal relevance of the mutations. The pedigrees, genotypes, and frequency of MSH3 mutations in the general population are consistent with an autosomal-recessive mode of inheritance. Both index persons have an affected sibling carrying the same mutations. The tumor spectrum in these four persons comprised colorectal and duodenal adenomas, colorectal cancer, gastric cancer, and an early-onset astrocytoma. Additionally, we detected one unrelated individual with biallelic PMS2 germline mutations, representing constitutional mismatch-repair deficiency. Potentially causative variants in 14 more candidate genes identified in 26 other individuals require further workup. In the present study, we identified biallelic germline MSH3 mutations in individuals with a suspected hereditary tumor syndrome. Our data suggest that MSH3 mutations represent an additional recessive subtype of colorectal adenomatous polyposis.
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Affiliation(s)
- Ronja Adam
- Institute of Human Genetics, University of Bonn, 53127 Bonn, Germany; Center for Hereditary Tumor Syndromes, University of Bonn, 53127 Bonn, Germany
| | - Isabel Spier
- Institute of Human Genetics, University of Bonn, 53127 Bonn, Germany; Center for Hereditary Tumor Syndromes, University of Bonn, 53127 Bonn, Germany
| | - Bixiao Zhao
- Department of Genetics, Howard Hughes Medical Institute, Yale University School of Medicine, New Haven, CT 06520-8005, USA
| | - Michael Kloth
- Institute of Pathology, University of Cologne, 50937 Cologne, Germany
| | - Jonathan Marquez
- Department of Genetics, Howard Hughes Medical Institute, Yale University School of Medicine, New Haven, CT 06520-8005, USA
| | - Inga Hinrichsen
- Medical Clinic 1, Biomedical Research Laboratory, Goethe-University Frankfurt, 60590 Frankfurt, Germany
| | - Jutta Kirfel
- Institute of Pathology, University of Bonn, 53127 Bonn, Germany
| | - Aylar Tafazzoli
- Institute of Human Genetics, University of Bonn, 53127 Bonn, Germany; Department of Genomics, Life & Brain Center, University of Bonn, 53127 Bonn, Germany
| | - Sukanya Horpaopan
- Institute of Human Genetics, University of Bonn, 53127 Bonn, Germany; Department of Anatomy, Faculty of Medical Science, Naresuan University, Phitsanulok, Chiang Mai 50200, Thailand
| | - Siegfried Uhlhaas
- Institute of Human Genetics, University of Bonn, 53127 Bonn, Germany
| | - Dietlinde Stienen
- Institute of Human Genetics, University of Bonn, 53127 Bonn, Germany
| | | | - Janine Altmüller
- Cologne Center for Genomics, University of Cologne, 50937 Cologne, Germany; Institute of Human Genetics, University of Cologne, 50937 Cologne, Germany
| | - Andreas Laner
- Medizinische Klinik und Poliklinik IV, Ludwig-Maximilians-University, 80336 Munich, Germany; Medical Genetics Center, 80335 Munich, Germany
| | - Stefanie Holzapfel
- Institute of Human Genetics, University of Bonn, 53127 Bonn, Germany; Center for Hereditary Tumor Syndromes, University of Bonn, 53127 Bonn, Germany
| | - Sophia Peters
- Institute of Human Genetics, University of Bonn, 53127 Bonn, Germany
| | - Katrin Kayser
- Institute of Human Genetics, University of Bonn, 53127 Bonn, Germany
| | - Holger Thiele
- Cologne Center for Genomics, University of Cologne, 50937 Cologne, Germany
| | - Elke Holinski-Feder
- Medizinische Klinik und Poliklinik IV, Ludwig-Maximilians-University, 80336 Munich, Germany; Medical Genetics Center, 80335 Munich, Germany
| | - Giancarlo Marra
- Institute of Molecular Cancer Research, University of Zurich, CH-8057 Zurich, Switzerland
| | | | - Markus M Nöthen
- Institute of Human Genetics, University of Bonn, 53127 Bonn, Germany; Department of Genomics, Life & Brain Center, University of Bonn, 53127 Bonn, Germany
| | - Reinhard Büttner
- Institute of Pathology, University of Cologne, 50937 Cologne, Germany
| | - Gabriela Möslein
- HELIOS Klinikum Wuppertal, University of Witten/Herdecke, 42283 Wuppertal, Germany
| | - Regina C Betz
- Institute of Human Genetics, University of Bonn, 53127 Bonn, Germany; Department of Genomics, Life & Brain Center, University of Bonn, 53127 Bonn, Germany
| | - Angela Brieger
- Medical Clinic 1, Biomedical Research Laboratory, Goethe-University Frankfurt, 60590 Frankfurt, Germany
| | - Richard P Lifton
- Department of Genetics, Howard Hughes Medical Institute, Yale University School of Medicine, New Haven, CT 06520-8005, USA
| | - Stefan Aretz
- Institute of Human Genetics, University of Bonn, 53127 Bonn, Germany; Center for Hereditary Tumor Syndromes, University of Bonn, 53127 Bonn, Germany.
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40
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Xue Y, Wilcox WR. Changing paradigm of cancer therapy: precision medicine by next-generation sequencing. Cancer Biol Med 2016; 13:12-8. [PMID: 27144059 PMCID: PMC4850120 DOI: 10.28092/j.issn.2095-3941.2016.0003] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Precision medicine aims to identify the right drug, for the right patient, at the right dose, at the right time, which is particularly important in cancer therapy. Problems such as the variability of treatment response and resistance to medication have been long-standing challenges in oncology, especially for development of new medications. Solid tumors, unlike hematologic malignancies or brain tumors, are remarkably diverse in their cellular origins and developmental timing. The ability of next-generation sequencing (NGS) to analyze the comprehensive landscape of genetic alterations brings promises to diseases that have a highly complex and heterogeneous genetic composition such as cancer. Here we provide an overview of how NGS is able to facilitate precision medicine and change the paradigm of cancer therapy, especially for solid tumors, through technical advancements, molecular diagnosis, response monitoring and clinical trials.
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Affiliation(s)
- Yuan Xue
- Fulgent Diagnostics, Temple City, CA 91780, USA
| | - William R Wilcox
- Department of Human Genetics, Emory University, Atlanta, GA 30322, USA
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41
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Liu Q, Li X, Li S, Qu S, Wang Y, Tang Q, Ma H, Luo Y. Three novel mutations of APC gene in Chinese patients with familial adenomatous polyposis. Tumour Biol 2016; 37:11421-7. [PMID: 27000756 PMCID: PMC4999466 DOI: 10.1007/s13277-016-4986-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2015] [Accepted: 02/10/2016] [Indexed: 12/30/2022] Open
Abstract
Familial adenomatous polyposis (FAP) is an autosomal dominant disorder characterized by the development of hundreds to thousands of colonic adenomas and an increased risk of colorectal cancer. Adenomatous polyposis coli (APC), encoding a large multidomain protein involved in antagonizing the Wnt signaling pathway, has been identified as the main causative gene responsible for FAP. In this study, we identified three novel mutations as well as two recurrent mutations in the APC in five Chinese FAP families by sequencing. Immunohistochemical analysis revealed that among these mutations, a nonsense mutation (c.2510C>G) and two small deletions (c.2016_2047del, c.3180_3184del) led to the truncation of the APC protein and the cytoplasmic and nuclear accumulation of β-catenin in the colorectal samples from affected individuals, respectively. Our study expands the database on mutations of APC and provides evidence to understand the function of APC in FAP.
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Affiliation(s)
- Qi Liu
- The Research Center for Medical Genomics, MOH Key Laboratory of Cell Biology and Key Laboratory of Medical Cell Biology, Ministry of Education, China Medical University, Shenyang, 110122, China
| | - Xiaoxia Li
- Department of Gastrointestinal Surgery, Fourth Affiliated Hospital of China Medical University, Shenyang, 110032, China
| | - Sen Li
- The Research Center for Medical Genomics, MOH Key Laboratory of Cell Biology and Key Laboratory of Medical Cell Biology, Ministry of Education, China Medical University, Shenyang, 110122, China
| | - Shengqiang Qu
- The Research Center for Medical Genomics, MOH Key Laboratory of Cell Biology and Key Laboratory of Medical Cell Biology, Ministry of Education, China Medical University, Shenyang, 110122, China
| | - Yu Wang
- The Research Center for Medical Genomics, MOH Key Laboratory of Cell Biology and Key Laboratory of Medical Cell Biology, Ministry of Education, China Medical University, Shenyang, 110122, China
| | - Qingzhu Tang
- The Research Center for Medical Genomics, MOH Key Laboratory of Cell Biology and Key Laboratory of Medical Cell Biology, Ministry of Education, China Medical University, Shenyang, 110122, China
| | - Hongwei Ma
- Department of Developing Pediatrics, Shengjing Hospital, China Medical University, Shenyang, 110004, China
| | - Yang Luo
- The Research Center for Medical Genomics, MOH Key Laboratory of Cell Biology and Key Laboratory of Medical Cell Biology, Ministry of Education, China Medical University, Shenyang, 110122, China.
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