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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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Tanabe H, Ijiri M, Takahashi K, Sasagawa H, Kamanaka T, Kuroda S, Sato H, Sarashina T, Mizukami Y, Makita Y, Okumura T. Genomic insights into familial adenomatous polyposis: unraveling a rare case with whole APC gene deletion and intellectual disability. Hum Genome Var 2024; 11:13. [PMID: 38548799 PMCID: PMC10978947 DOI: 10.1038/s41439-024-00270-3] [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] [Received: 12/17/2023] [Revised: 01/05/2024] [Accepted: 01/09/2024] [Indexed: 04/01/2024] Open
Abstract
A young patient diagnosed with advanced colon cancer and liver metastasis was found to have familial adenomatous polyposis (FAP) through comprehensive genomic analysis. Whole-genome array comparative genomic hybridization (aCGH) revealed germline deletions at chromosome 5q22.1-22.2 encompassing the entire APC gene. The patient and her son exhibited mild intellectual disability without developmental delay. This case highlights the need for further exploration of the characteristics associated with whole APC deletions. aCGH is a valuable tool for studying FAP and provides a detailed analysis of large deletions.
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Affiliation(s)
- Hiroki Tanabe
- Oncology Center, Asahikawa Medical University Hospital, Asahikawa, Japan.
- Genetic Oncology Department, Asahikawa Medical University Hospital, Asahikawa, Japan.
- Department of Genetic Counseling, Asahikawa Medical University Hospital, Asahikawa, Japan.
| | - Masami Ijiri
- Department of Gastroenterology, Japanese Red Cross Asahikawa Hospital, Asahikawa, Japan
| | - Kenji Takahashi
- Genetic Oncology Department, Asahikawa Medical University Hospital, Asahikawa, Japan
- Department of Internal Medicine, Asahikawa Medical University, Asahikawa, Japan
| | - Honoka Sasagawa
- Department of Genetic Counseling, Asahikawa Medical University Hospital, Asahikawa, Japan
| | - Tomomi Kamanaka
- Oncology Center, Asahikawa Medical University Hospital, Asahikawa, Japan
| | - Shohei Kuroda
- Department of Gastroenterology, Japanese Red Cross Asahikawa Hospital, Asahikawa, Japan
| | - Hiroki Sato
- Department of Internal Medicine, Asahikawa Medical University, Asahikawa, Japan
| | - Takeo Sarashina
- Oncology Center, Asahikawa Medical University Hospital, Asahikawa, Japan
| | - Yusuke Mizukami
- Genetic Oncology Department, Asahikawa Medical University Hospital, Asahikawa, Japan
- Department of Internal Medicine, Asahikawa Medical University, Asahikawa, Japan
| | - Yoshio Makita
- Department of Genetic Counseling, Asahikawa Medical University Hospital, Asahikawa, Japan
| | - Toshikatsu Okumura
- Department of Internal Medicine, Asahikawa Medical University, Asahikawa, Japan
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3
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Oda S, Ushiama M, Nakamura W, Gotoh M, Tanabe N, Watanabe T, Odaka Y, Aoyagi K, Sakamoto H, Nakajima T, Sugano K, Yoshida T, Shiraishi Y, Hirata M. A complex rearrangement between APC and TP63 associated with familial adenomatous polyposis identified by multimodal genomic analysis: a case report. Front Oncol 2023; 13:1205847. [PMID: 37601671 PMCID: PMC10434623 DOI: 10.3389/fonc.2023.1205847] [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] [Received: 04/14/2023] [Accepted: 07/11/2023] [Indexed: 08/22/2023] Open
Abstract
Genetic testing of the APC gene by sequencing analysis and MLPA is available across commercial laboratories for the definitive genetic diagnosis of familial adenomatous polyposis (FAP). However, some genetic alterations are difficult to detect using conventional analyses. Here, we report a case of a complex genomic APC-TP63 rearrangement, which was identified in a patient with FAP by a series of genomic analyses, including multigene panel testing, chromosomal analyses, and long-read sequencing. A woman in her thirties was diagnosed with FAP due to multiple polyps in her colon and underwent total colectomy. Subsequent examination revealed fundic gland polyposis. No family history suggesting FAP was noted except for a first-degree relative with desmoid fibromatosis. The conventional APC gene testing was performed by her former doctor, but no pathogenic variant was detected, except for 2 variants of unknown significance. The patient was referred to our hospital for further genetic analysis. After obtaining informed consent in genetic counseling, we conducted a multigene panel analysis. As insertion of a part of the TP63 sequence was detected within exon16 of APC, further analyses, including chromosomal analysis and long-read sequencing, were performed and a complex translocation between chromosomes 3 and 5 containing several breakpoints in TP63 and APC was identified. No phenotype associated with TP63 pathogenic variants, such as split-hand/foot malformation (SHFM) or ectrodactyly, ectodermal dysplasia, or cleft lip/palate syndrome (EEC) was identified in the patient or her relatives. Multimodal genomic analyses should be considered in cases where no pathogenic germline variants are detected by conventional genetic testing despite an evident medical or family history of hereditary cancer syndromes.
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Affiliation(s)
- Satoyo Oda
- Department of Genetic Medicine and Services, National Cancer Center Hospital, Tokyo, Japan
- Department of Clinical Laboratories, National Cancer Center Hospital, Tokyo, Japan
| | - Mineko Ushiama
- Department of Genetic Medicine and Services, National Cancer Center Hospital, Tokyo, Japan
- Department of Clinical Genomics, National Cancer Center Research Institute, Tokyo, Japan
| | - Wataru Nakamura
- Division of Genome Analysis Platform Development, National Cancer Center Research Institute, Tokyo, Japan
| | - Masahiro Gotoh
- Department of Genetic Medicine and Services, National Cancer Center Hospital, Tokyo, Japan
- Department of Clinical Genomics, National Cancer Center Research Institute, Tokyo, Japan
| | - Noriko Tanabe
- Department of Genetic Medicine and Services, National Cancer Center Hospital, Tokyo, Japan
| | - Tomoko Watanabe
- Department of Genetic Medicine and Services, National Cancer Center Hospital, Tokyo, Japan
| | - Yoko Odaka
- Department of Clinical Genomics, National Cancer Center Research Institute, Tokyo, Japan
| | - Kazuhiko Aoyagi
- Department of Clinical Genomics, National Cancer Center Research Institute, Tokyo, Japan
| | - Hiromi Sakamoto
- Department of Genetic Medicine and Services, National Cancer Center Hospital, Tokyo, Japan
- Department of Clinical Genomics, National Cancer Center Research Institute, Tokyo, Japan
| | - Takeshi Nakajima
- Department Medical Ethics/Medical Genetics, Kyoto University Graduate School of Medicine, Kyoto, Japan
- Department of Clinical Genetics, Cancer Institute Hospital, Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Kokichi Sugano
- Department of Genetic Medicine and Services, National Cancer Center Hospital, Tokyo, Japan
- Department of Genetic Medicine, Kyoundo Hospital, Sasaki Foundation, Tokyo, Japan
| | - Teruhiko Yoshida
- Department of Genetic Medicine and Services, National Cancer Center Hospital, Tokyo, Japan
- Department of Clinical Genomics, National Cancer Center Research Institute, Tokyo, Japan
| | - Yuichi Shiraishi
- Division of Genome Analysis Platform Development, National Cancer Center Research Institute, Tokyo, Japan
| | - Makoto Hirata
- Department of Genetic Medicine and Services, National Cancer Center Hospital, Tokyo, Japan
- Division of Molecular Pathology, National Cancer Center Research Institute, Tokyo, Japan
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Delea M, Massara LS, Espeche LD, Bidondo MP, Barbero P, Oliveri J, Brun P, Fabro M, Galain M, Fernández CS, Taboas M, Bruque CD, Kolomenski JE, Izquierdo A, Berenstein A, Cosentino V, Martinoli C, Vilas M, Rittler M, Mendez R, Furforo L, Liascovich R, Groisman B, Rozental S, Dain L. Genetic Analysis Algorithm for the Study of Patients with Multiple Congenital Anomalies and Isolated Congenital Heart Disease. Genes (Basel) 2022; 13:1172. [PMID: 35885957 PMCID: PMC9317700 DOI: 10.3390/genes13071172] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 06/16/2022] [Accepted: 06/27/2022] [Indexed: 11/20/2022] Open
Abstract
Congenital anomalies (CA) affect 3-5% of newborns, representing the second-leading cause of infant mortality in Argentina. Multiple congenital anomalies (MCA) have a prevalence of 2.26/1000 births in newborns, while congenital heart diseases (CHD) are the most frequent CA with a prevalence of 4.06/1000 births. The aim of this study was to identify the genetic causes in Argentinian patients with MCA and isolated CHD. We recruited 366 patients (172 with MCA and 194 with isolated CHD) born between June 2015 and August 2019 at public hospitals. DNA from peripheral blood was obtained from all patients, while karyotyping was performed in patients with MCA. Samples from patients presenting conotruncal CHD or DiGeorge phenotype (n = 137) were studied using MLPA. Ninety-three samples were studied by array-CGH and 18 by targeted or exome next-generation sequencing (NGS). A total of 240 patients were successfully studied using at least one technique. Cytogenetic abnormalities were observed in 13 patients, while 18 had clinically relevant imbalances detected by array-CGH. After MLPA, 26 patients presented 22q11 deletions or duplications and one presented a TBX1 gene deletion. Following NGS analysis, 12 patients presented pathogenic or likely pathogenic genetic variants, five of them, found in KAT6B, SHH, MYH11, MYH7 and EP300 genes, are novel. Using an algorithm that combines molecular techniques with clinical and genetic assessment, we determined the genetic contribution in 27.5% of the analyzed patients.
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Affiliation(s)
- Marisol Delea
- Centro Nacional de Genética Médica “Dr. Eduardo Castilla”- ANLIS “Dr. Carlos G. Malbrán”, Avda. Las Heras 2670, Buenos Aires 1425, Argentina; (M.D.); (L.D.E.); (M.P.B.); (P.B.); (M.T.); (C.D.B.); (R.M.); (R.L.); (B.G.); (S.R.)
| | - Lucia S. Massara
- Hospital de Alta Complejidad en Red El Cruce—SAMIC. Av. Calchaquí 5401, Florencio Varela 1888, Argentina; (L.S.M.); (J.O.); (P.B.)
| | - Lucia D. Espeche
- Centro Nacional de Genética Médica “Dr. Eduardo Castilla”- ANLIS “Dr. Carlos G. Malbrán”, Avda. Las Heras 2670, Buenos Aires 1425, Argentina; (M.D.); (L.D.E.); (M.P.B.); (P.B.); (M.T.); (C.D.B.); (R.M.); (R.L.); (B.G.); (S.R.)
| | - María Paz Bidondo
- Centro Nacional de Genética Médica “Dr. Eduardo Castilla”- ANLIS “Dr. Carlos G. Malbrán”, Avda. Las Heras 2670, Buenos Aires 1425, Argentina; (M.D.); (L.D.E.); (M.P.B.); (P.B.); (M.T.); (C.D.B.); (R.M.); (R.L.); (B.G.); (S.R.)
- Unidad Académica de Histologia, Embriologia, Biologia Celular y Genética, Facultad de Medicina UBA, Paraguay 2155, Buenos Aires 1121, Argentina
| | - Pablo Barbero
- Centro Nacional de Genética Médica “Dr. Eduardo Castilla”- ANLIS “Dr. Carlos G. Malbrán”, Avda. Las Heras 2670, Buenos Aires 1425, Argentina; (M.D.); (L.D.E.); (M.P.B.); (P.B.); (M.T.); (C.D.B.); (R.M.); (R.L.); (B.G.); (S.R.)
| | - Jaen Oliveri
- Hospital de Alta Complejidad en Red El Cruce—SAMIC. Av. Calchaquí 5401, Florencio Varela 1888, Argentina; (L.S.M.); (J.O.); (P.B.)
| | - Paloma Brun
- Hospital de Alta Complejidad en Red El Cruce—SAMIC. Av. Calchaquí 5401, Florencio Varela 1888, Argentina; (L.S.M.); (J.O.); (P.B.)
| | - Mónica Fabro
- Novagen, Viamonte 1430, Buenos Aires 1055, Argentina; (M.F.); (M.G.); (C.S.F.)
| | - Micaela Galain
- Novagen, Viamonte 1430, Buenos Aires 1055, Argentina; (M.F.); (M.G.); (C.S.F.)
| | | | - Melisa Taboas
- Centro Nacional de Genética Médica “Dr. Eduardo Castilla”- ANLIS “Dr. Carlos G. Malbrán”, Avda. Las Heras 2670, Buenos Aires 1425, Argentina; (M.D.); (L.D.E.); (M.P.B.); (P.B.); (M.T.); (C.D.B.); (R.M.); (R.L.); (B.G.); (S.R.)
| | - Carlos D. Bruque
- Centro Nacional de Genética Médica “Dr. Eduardo Castilla”- ANLIS “Dr. Carlos G. Malbrán”, Avda. Las Heras 2670, Buenos Aires 1425, Argentina; (M.D.); (L.D.E.); (M.P.B.); (P.B.); (M.T.); (C.D.B.); (R.M.); (R.L.); (B.G.); (S.R.)
| | - Jorge E. Kolomenski
- Departamento de Fisiología, Biología Molecular y Celular, Instituto de Biociencias, Biotecnología y Biología Traslacional (iB3), Facultad de Ciencias Exactas y Naturales-UBA, Intendente Güiraldes 2160, Buenos Aires 1428, Argentina;
| | - Agustín Izquierdo
- Centro de Investigaciones Endocrinológicas “Dr. César Bergadá”. Gallo 1330, Buenos Aires 1425, Argentina;
| | - Ariel Berenstein
- Instituto Multidisciplinario de Investigaciones en Patologías Pediátricas, Gallo 1330, Buenos Aires 1425, Argentina;
| | - Viviana Cosentino
- Hospital Interzonal General de Agudos Luisa Cravenna de Gandulfo, Balcarce 351, Lomas de Zamora 1832, Argentina;
| | - Celeste Martinoli
- Hospital Sor Maria Ludovica, Calle 14 1631, La Plata 1904, Argentina;
| | - Mariana Vilas
- Hospital Materno Infantil Ramón Sardá, Esteban de Luca 2151, Buenos Aires 1246, Argentina; (M.V.); (M.R.); (L.F.)
| | - Mónica Rittler
- Hospital Materno Infantil Ramón Sardá, Esteban de Luca 2151, Buenos Aires 1246, Argentina; (M.V.); (M.R.); (L.F.)
| | - Rodrigo Mendez
- Centro Nacional de Genética Médica “Dr. Eduardo Castilla”- ANLIS “Dr. Carlos G. Malbrán”, Avda. Las Heras 2670, Buenos Aires 1425, Argentina; (M.D.); (L.D.E.); (M.P.B.); (P.B.); (M.T.); (C.D.B.); (R.M.); (R.L.); (B.G.); (S.R.)
| | - Lilian Furforo
- Hospital Materno Infantil Ramón Sardá, Esteban de Luca 2151, Buenos Aires 1246, Argentina; (M.V.); (M.R.); (L.F.)
| | - Rosa Liascovich
- Centro Nacional de Genética Médica “Dr. Eduardo Castilla”- ANLIS “Dr. Carlos G. Malbrán”, Avda. Las Heras 2670, Buenos Aires 1425, Argentina; (M.D.); (L.D.E.); (M.P.B.); (P.B.); (M.T.); (C.D.B.); (R.M.); (R.L.); (B.G.); (S.R.)
| | - Boris Groisman
- Centro Nacional de Genética Médica “Dr. Eduardo Castilla”- ANLIS “Dr. Carlos G. Malbrán”, Avda. Las Heras 2670, Buenos Aires 1425, Argentina; (M.D.); (L.D.E.); (M.P.B.); (P.B.); (M.T.); (C.D.B.); (R.M.); (R.L.); (B.G.); (S.R.)
| | - Sandra Rozental
- Centro Nacional de Genética Médica “Dr. Eduardo Castilla”- ANLIS “Dr. Carlos G. Malbrán”, Avda. Las Heras 2670, Buenos Aires 1425, Argentina; (M.D.); (L.D.E.); (M.P.B.); (P.B.); (M.T.); (C.D.B.); (R.M.); (R.L.); (B.G.); (S.R.)
| | - Liliana Dain
- Centro Nacional de Genética Médica “Dr. Eduardo Castilla”- ANLIS “Dr. Carlos G. Malbrán”, Avda. Las Heras 2670, Buenos Aires 1425, Argentina; (M.D.); (L.D.E.); (M.P.B.); (P.B.); (M.T.); (C.D.B.); (R.M.); (R.L.); (B.G.); (S.R.)
- Departamento de Fisiología, Biología Molecular y Celular, Instituto de Biociencias, Biotecnología y Biología Traslacional (iB3), Facultad de Ciencias Exactas y Naturales-UBA, Intendente Güiraldes 2160, Buenos Aires 1428, Argentina;
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Rosina E, Rinaldi B, Silipigni R, Bergamaschi L, Gattuso G, Signoroni S, Guerneri S, Carnevali A, Marchisio PG, Milani D. Incidental finding of APC deletion in a child: double trouble or double chance? - a case report. Ital J Pediatr 2021; 47:31. [PMID: 33588901 PMCID: PMC7885235 DOI: 10.1186/s13052-021-00969-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Accepted: 01/11/2021] [Indexed: 01/08/2023] Open
Abstract
Background 22q11.2 deletion syndrome is one of the most common genomic disorders, characterized by the variable presence of facial dysmorphisms, congenital cardiac defects, velopharyngeal insufficiency/cleft palate, thymic hypoplasia/aplasia, immunodeficiency, parathyroid hypoplasia, developmental delay, learning disabilities, psychiatric disorders, renal, ocular, and skeletal malformations, hearing loss and laryngeal abnormalities. Chromosomal microarray (CMA) hybridization is one of the most performed diagnostic tests but as a genome wide analysis, it can point out relevant incidental copy number variations. Case presentation We report the case of a 2-year-old boy that came to our attention for mild psychomotor delay, poor growth, and minor facial anomalies. Considering a diagnosis of 22q11.2 deletion syndrome, we performed CMA that not only confirmed our diagnosis, but also pointed out an additional de novo 5q21.3q22.2 microdeletion, encompassing APC gene. As a result of the genetic testing we enrolled the patient in a tailored surveillance protocol that enabled the early detection of a hepatoblastoma. The child underwent surgical and chemotherapic treatments with complete cancer eradication. Conclusions The concurrent finding of an expected result and an additional deletion of APC gene represents an example of a relevant issue about the health and ethical management of secondary findings revealed by genome-wide tests. Furthermore, this report highlights the need to develop dedicated surveillance guidelines for children with APC-related polyposis and raise the question whether to suspect and screen for APC-related conditions in cases of sporadic hepatoblastomas.
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Affiliation(s)
- Erica Rosina
- Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Pediatric Highly Intensive Care Unit, Via della Commenda, 9, 20122, Milan, Italy
| | - Berardo Rinaldi
- Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Pediatric Highly Intensive Care Unit, Via della Commenda, 9, 20122, Milan, Italy.
| | - Rosamaria Silipigni
- Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Laboratory of Medical Genetics, Milan, Italy
| | - Luca Bergamaschi
- Pediatric Oncology Unit, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Giovanna Gattuso
- Pediatric Oncology Unit, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Stefano Signoroni
- Pediatric Oncology Unit, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Silvana Guerneri
- Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Laboratory of Medical Genetics, Milan, Italy
| | - Alessandra Carnevali
- Department of Radiology, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Paola Giovanna Marchisio
- Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Pediatric Highly Intensive Care Unit, Via della Commenda, 9, 20122, Milan, Italy.,Department of Pathophysiology and Transplantation, University of Milan, Milan, Italy
| | - Donatella Milani
- Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Pediatric Highly Intensive Care Unit, Via della Commenda, 9, 20122, Milan, Italy
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Pouya F, Mojtabanezhad Shariatpanahi A, Ghaffarzadegan K, Tabatabaee Yazdi SA, Golmohammadzadeh H, Soltani G, Aminian Toosi K, Kerachian MA. A novel large germ line deletion in adenomatous polyposis coli (APC) gene associated with familial adenomatous polyposis. Mol Genet Genomic Med 2018; 6:1031-1040. [PMID: 30259713 PMCID: PMC6305644 DOI: 10.1002/mgg3.479] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2018] [Revised: 08/28/2018] [Accepted: 08/29/2018] [Indexed: 12/12/2022] Open
Abstract
Background Familial adenomatous polyposis (FAP) is a familial colorectal cancer predisposition syndrome characterized by the development of numerous colorectal polyps, which is inherited in an autosomal dominant manner. FAP is caused by germ line mutations in adenomatous polyposis coli (APC) gene. Here, we described the identification of a causative APC gene deletion associated with FAP in an Iranian family. Methods Diagnosis of FAP was based on clinical findings, family history, and medical records (colonoscopy and histopathological data) after the patients were referred to Reza Radiotherapy and Oncology Center, Iran, for colonoscopy. Blood samples were collected, and genomic DNA was extracted. APC mutation screening was conducted by target next‐generation sequencing and quantitative real‐time PCR. Results A novel heterozygous large deletion mutation, c.(135+1_136–1)_(*2113+1_*2114–1) spanning exon 3 to 16 [EX3_16 DEL] of APC gene (GenBank Accession# MG712911), was detected in a proband and all her affected relatives in five generations, which was absent in unaffected family members and normal controls. Conclusions This novel deletion is the first report, describing the largest deletion of APC gene. Our novel finding contributes to a more comprehensive database of germ line mutations of APC gene that could be used in medical practice for the molecular diagnosis, risk assessment susceptibility of the disease for the FAP patients.
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Affiliation(s)
- Farzaneh Pouya
- Department of Medical Genetics, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | | | - Kamran Ghaffarzadegan
- Razavi Cancer Research Center, Razavi Hospital, Imam Reza International University, Mashhad, Iran
| | | | - Hamed Golmohammadzadeh
- Endoscopic and Minimally Invasive Surgery Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Ghodratollah Soltani
- Cancer Genetics Research Unit, Reza Radiotherapy and Oncology Center, Mashhad, Iran
| | - Kian Aminian Toosi
- Cancer Genetics Research Unit, Reza Radiotherapy and Oncology Center, Mashhad, Iran.,Department of Biology, Islamic Azad University Mashhad Branch, Mashhad, Iran
| | - Mohammad Amin Kerachian
- Department of Medical Genetics, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran.,Cancer Genetics Research Unit, Reza Radiotherapy and Oncology Center, Mashhad, Iran.,Cancer Genetics Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
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7
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Szafranski P, Kośmider E, Liu Q, Karolak JA, Currie L, Parkash S, Kahler SG, Roeder E, Littlejohn RO, DeNapoli TS, Shardonofsky FR, Henderson C, Powers G, Poisson V, Bérubé D, Oligny L, Michaud JL, Janssens S, De Coen K, Van Dorpe J, Dheedene A, Harting MT, Weaver MD, Khan AM, Tatevian N, Wambach J, Gibbs KA, Popek E, Gambin A, Stankiewicz P. LINE- and Alu-containing genomic instability hotspot at 16q24.1 associated with recurrent and nonrecurrent CNV deletions causative for ACDMPV. Hum Mutat 2018; 39:1916-1925. [PMID: 30084155 DOI: 10.1002/humu.23608] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2018] [Revised: 08/01/2018] [Accepted: 08/02/2018] [Indexed: 01/20/2023]
Abstract
Transposable elements modify human genome by inserting into new loci or by mediating homology-, microhomology-, or homeology-driven DNA recombination or repair, resulting in genomic structural variation. Alveolar capillary dysplasia with misalignment of pulmonary veins (ACDMPV) is a rare lethal neonatal developmental lung disorder caused by point mutations or copy-number variant (CNV) deletions of FOXF1 or its distant tissue-specific enhancer. Eighty-five percent of 45 ACDMPV-causative CNV deletions, of which junctions have been sequenced, had at least one of their two breakpoints located in a retrotransposon, with more than half of them being Alu elements. We describe a novel ∼35 kb-large genomic instability hotspot at 16q24.1, involving two evolutionarily young LINE-1 (L1) elements, L1PA2 and L1PA3, flanking AluY, two AluSx, AluSx1, and AluJr elements. The occurrence of L1s at this location coincided with the branching out of the Homo-Pan-Gorilla clade, and was preceded by the insertion of AluSx, AluSx1, and AluJr. Our data show that, in addition to mediating recurrent CNVs, L1 and Alu retrotransposons can predispose the human genome to formation of variably sized CNVs, both of clinical and evolutionary relevance. Nonetheless, epigenetic or other genomic features of this locus might also contribute to its increased instability.
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Affiliation(s)
- Przemyslaw Szafranski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Ewelina Kośmider
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas.,Faculty of Mathematics, Informatics and Mechanics, University of Warsaw, Warsaw, Poland
| | - Qian Liu
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Justyna A Karolak
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas.,Department of Genetics and Pharmaceutical Microbiology, Poznan University of Medical Sciences, Poznan, Poland
| | - Lauren Currie
- Maritime Medical Genetics Service, IWK Health Centre, Halifax, Canada
| | - Sandhya Parkash
- Maritime Medical Genetics Service, IWK Health Centre, Halifax, Canada
| | - Stephen G Kahler
- Section of Genetics and Metabolism, Department of Pediatrics, University of Arkansas for Medical Sciences, Little Rock, Arkansas
| | - Elizabeth Roeder
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas.,Department of Pediatrics, Baylor College of Medicine, San Antonio, Texas
| | | | - Thomas S DeNapoli
- Department of Pathology, Children's Hospital of San Antonio, San Antonio, Texas
| | - Felix R Shardonofsky
- Pediatric Pulmonary Center, Children's Hospital of San Antonio, San Antonio, Texas
| | - Cody Henderson
- Department of Pediatrics, Baylor College of Medicine, San Antonio, Texas.,Neonatal-Perinatal Medicine, Children's Hospital of San Antonio, San Antonio, Texas
| | - George Powers
- Department of Pediatrics, Baylor College of Medicine, San Antonio, Texas.,Neonatal-Perinatal Medicine, Children's Hospital of San Antonio, San Antonio, Texas
| | | | | | | | | | - Sandra Janssens
- Center for Medical Genetics, Ghent University, Ghent, Belgium
| | - Kris De Coen
- Department of Neonatal Intensive Care, Ghent University, Ghent, Belgium
| | - Jo Van Dorpe
- Department of Pathology, Ghent University, Ghent, Belgium
| | | | | | | | - Amir M Khan
- McGovern Medical School at UTHealth, Houston, Texas
| | | | - Jennifer Wambach
- Edward Mallinckrodt Department of Pediatrics, Washington University School of Medicine, St. Louis, Missouri
| | - Kathleen A Gibbs
- Children's Hospital of Philadelphia, and University of Pennsylvania, Philadelphia, Pennsylvania
| | - Edwina Popek
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, Texas
| | - Anna Gambin
- Faculty of Mathematics, Informatics and Mechanics, University of Warsaw, Warsaw, Poland
| | - Paweł Stankiewicz
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
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8
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Vetro A, Goidin D, Lesende I, Limongelli I, Ranzani GN, Novara F, Bonaglia MC, Rinaldi B, Franchi F, Manolakos E, Lonardo F, Scarano F, Scarano G, Costantino L, Tedeschi S, Giglio S, Zuffardi O. Diagnostic application of a capture based NGS test for the concurrent detection of variants in sequence and copy number as well as LOH. Clin Genet 2017; 93:545-556. [PMID: 28556904 DOI: 10.1111/cge.13060] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Revised: 05/11/2017] [Accepted: 05/12/2017] [Indexed: 01/08/2023]
Abstract
Whole exome sequencing (WES) has made the identification of causative SNVs/InDels associated with rare Mendelian conditions increasingly accessible. Incorporation of softwares allowing CNVs detection into the WES bioinformatics pipelines may increase the diagnostic yield. However, no standard protocols for this analysis are so far available and CNVs in non-coding regions are totally missed by WES, in spite of their possible role in the regulation of the flanking genes expression. So, in a number of cases the diagnostic workflow contemplates an initial investigation by genomic arrays followed, in the negative cases, by WES. The opposite workflow may also be applied, according to the familial segregation of the disease. We show preliminary results for a diagnostic application of a single next generation sequencing panel permitting the concurrent detection of LOH and variations in sequences and copy number. This approach allowed us to highlight compound heterozygosity for a CNV and a sequence variant in a number of cases, the duplication of a non-coding region responsible for sex reversal, and a whole-chromosome isodisomy causing reduction to homozygosity for a WFS1 variant. Moreover, the panel enabled us to detect deletions, duplications, and amplifications with sensitivity comparable to that of the most widely used array-CGH platforms.
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Affiliation(s)
- A Vetro
- Department of Molecular Medicine, University of Pavia, Pavia, Italy
| | - D Goidin
- Diagnostics and Genomics Group, Agilent Technologies Inc., Santa Clara, California
| | - I Lesende
- Diagnostics and Genomics Group, Agilent Technologies Inc., Santa Clara, California
| | | | - G N Ranzani
- Department of Biology and Biotechnology, University of Pavia, Pavia, Italy
| | - F Novara
- Department of Molecular Medicine, University of Pavia, Pavia, Italy
| | - M C Bonaglia
- Cytogenetics Laboratory, Scientific Institute IRCCS E. Medea, Lecco, Italy
| | - B Rinaldi
- Department of Molecular Medicine, University of Pavia, Pavia, Italy
| | - F Franchi
- Laboratorio Genetica, Azienda Ospedaliera Arcispedale Santa Maria Nuova, Reggio Emilia, Italy
| | - E Manolakos
- Clinical Laboratory Genetics, Access to Genome, Athens, Greece.,Clinical Laboratory Genetics, Access to Genome, Thessaloniki, Greece
| | - F Lonardo
- U.O.S.D. Genetica Medica-A.O.R.N, Benevento, Italy
| | - F Scarano
- U.O.S.D. Genetica Medica-A.O.R.N, Benevento, Italy
| | - G Scarano
- U.O.S.D. Genetica Medica-A.O.R.N, Benevento, Italy
| | - L Costantino
- Medical Genetics Laboratory, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milano, Italy
| | - S Tedeschi
- Medical Genetics Laboratory, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milano, Italy
| | - S Giglio
- Medical Genetics Unit, Meyer Children's University Hospital, Firenze, Italy
| | - O Zuffardi
- Department of Molecular Medicine, University of Pavia, Pavia, Italy
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9
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Marabelli M, Gismondi V, Ricci MT, Vetro A, Abou Khouzam R, Rea V, Vitellaro M, Zuffardi O, Varesco L, Ranzani GN. A novel APC promoter 1B deletion shows a founder effect in Italian patients with classical familial adenomatous polyposis phenotype. Genes Chromosomes Cancer 2017; 56:846-854. [PMID: 28791770 DOI: 10.1002/gcc.22488] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2017] [Revised: 08/05/2017] [Accepted: 08/07/2017] [Indexed: 02/06/2023] Open
Abstract
Familial adenomatous polyposis is a Mendelian syndrome in which germline loss-of-function mutations of APC are associated with multiple adenomatous polyps of the large bowel, a multiplicity of extracolonic features, and a high lifetime risk of colorectal cancer. Different APC germline mutations have been identified, including sequence changes, genomic rearrangements, and expression defects. Recently, very rare families have been associated with constitutive large deletions encompassing the APC-5' regulatory region, while leaving the remaining gene sequence intact; the regulatory region contains a proximal and a distal promoter, called 1A and 1B, respectively. We identified a novel deletion encompassing promoter 1B in a large Italian family that manifested polyposis in three of the six branches descending from a founding couple married in 1797. By combining different molecular approaches on both DNA and RNA, we precisely mapped this deletion (6858 bp in length) that proved to be associated with APC allele silencing. The finding of the same deletion in two additional polyposis families pointed to a founder mutation in Italy. Deletion carriers from the three families all showed a "classical" polyposis phenotype. To explore the molecular mechanisms underlying promoter deletions, we performed an in silico analysis of the breakpoints of 1A and 1B rearrangements so far reported in the literature; moreover, to decipher genotype-phenotype correlations, we critically reviewed current knowledge on deletions versus point mutations in the APC-5' regulatory region.
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Affiliation(s)
- Monica Marabelli
- Department of Biology and Biotechnology, University of Pavia, Pavia, Italy
| | - Viviana Gismondi
- Unit of Hereditary Cancer IRCCS AOU San Martino-IST, Genoa, Italy
| | - Maria Teresa Ricci
- Hereditary Digestive Tract Tumours Unit Department of Preventive and Predictive Medicine, Fondazione IRCCS Istituto Nazionale Tumori, Milan, Italy
| | - Annalisa Vetro
- Department of Molecular Medicine, University of Pavia, Pavia, Italy.,Fondazione IRCCS Policlinico San Matteo Genomics Core Center, Pavia, Italy
| | - Raefa Abou Khouzam
- Department of Biology and Biotechnology, University of Pavia, Pavia, Italy
| | - Valentina Rea
- Unit of Hereditary Cancer IRCCS AOU San Martino-IST, Genoa, Italy
| | - Marco Vitellaro
- Hereditary Digestive Tract Tumours Unit Department of Preventive and Predictive Medicine, Fondazione IRCCS Istituto Nazionale Tumori, Milan, Italy
| | - Orsetta Zuffardi
- Department of Molecular Medicine, University of Pavia, Pavia, Italy
| | - Liliana Varesco
- Unit of Hereditary Cancer IRCCS AOU San Martino-IST, Genoa, Italy
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10
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Yang J, Liu QW, Li LW, Wang QZ, Hong M, Dong J. Familial adenomatous polyposis in China. Oncol Lett 2016; 12:4877-4882. [PMID: 28105195 DOI: 10.3892/ol.2016.5330] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2015] [Accepted: 10/04/2016] [Indexed: 12/11/2022] Open
Abstract
Familial adenomatous polyposis (FAP) is an autosomal dominant disease with a poor prognosis, and has been studied by clinicians and geneticists in China for the past three decades. It is estimated that FAP has an incidence of between 1 in 8,000 and 1 in 10,000 individuals, and accounts for 0.94% of colorectal cancer cases in China. Recent advances in the understanding of FAP suggest that the genotype of the patient may allow for early diagnosis and surveillance, and guide surgical and chemopreventive management. However, the genetic mechanisms of FAP vary between different countries. FAP in China has its own characteristics, and this may be due to ethnic and geographical genetic variation. In the present review the clinical manifestations and genetics of FAP in China are discussed, as well as the surgical strategies, chemotherapeutics and traditional Chinese medicines used in its treatment. Increased insight into the genetic and clinical features of FAP in the Chinese population may aid in the prevention and management of the disorder.
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Affiliation(s)
- Jun Yang
- Department of Oncology, First Affiliated Hospital of Kunming Medical University, Kunming, Yunnan 650032, P.R. China
| | - Qing Wei Liu
- Department of Internal Medicine-Oncology, First Affiliated Hospital of Kunming Medical University, Kunming, Yunnan 650032, P.R. China
| | - Liang Wen Li
- Department of Oncology, First Affiliated Hospital of Kunming Medical University, Kunming, Yunnan 650032, P.R. China
| | - Qiang Zhi Wang
- Department of Oncology, First Affiliated Hospital of Kunming Medical University, Kunming, Yunnan 650032, P.R. China
| | - Min Hong
- Department of Internal Medicine-Oncology, First Affiliated Hospital of Kunming Medical University, Kunming, Yunnan 650032, P.R. China
| | - Jian Dong
- Department of Internal Medicine-Oncology, Third Affiliated Hospital of Kunming Medical University, Kunming, Yunnan 650106, P.R. China
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11
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Abstract
Familial adenomatous polyposis (FAP) is a colorectal cancer predisposition syndrome with considerable genetic and phenotypic heterogeneity, defined by the development of multiple adenomas throughout the colorectum. FAP is caused either by monoallelic mutations in the adenomatous polyposis coli gene APC, or by biallelic germline mutations of MUTYH, this latter usually presenting with milder phenotype. The aim of the present study was to characterize the genotype and phenotype of Hungarian FAP patients. Mutation screening of 87 unrelated probands from FAP families (21 of them presented as the attenuated variant of the disease, showing <100 polyps) was performed using DNA sequencing and multiplex ligation-dependent probe amplification. Twenty-four different pathogenic mutations in APC were identified in 65 patients (75 %), including nine cases (37.5 %) with large genomic alterations. Twelve of the point mutations were novel. In addition, APC-negative samples were also tested for MUTYH mutations and we were able to identify biallelic pathogenic mutations in 23 % of these cases (5/22). Correlations between the localization of APC mutations and the clinical manifestations of the disease were observed, cases with a mutation in the codon 1200-1400 region showing earlier age of disease onset (p < 0.003). There were only a few, but definitive dissimilarities between APC- and MUTYH-associated FAP in our cohort: the age at onset of polyposis was significantly delayed for biallelic MUTYH mutation carriers as compared to patients with an APC mutation. Our data represent the first comprehensive study delineating the mutation spectra of both APC and MUTYH in Hungarian FAP families, and underscore the overlap between the clinical characteristics of APC- and MUTYH-associated phenotypes, necessitating a more appropriate clinical characterization of FAP families.
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12
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Abildinova G, Abdrakhmanova Z, Tuchinsky H, Nesher E, Pinhasov A, Raskin L. Fast detection of deletion breakpoints using quantitative PCR. Genet Mol Biol 2016; 39:365-9. [PMID: 27560363 PMCID: PMC5004823 DOI: 10.1590/1678-4685-gmb-2015-0159] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2015] [Accepted: 12/29/2015] [Indexed: 11/22/2022] Open
Abstract
The routine detection of large and medium copy number variants (CNVs) is well
established. Hemizygotic deletions or duplications in the large Duchenne muscular
dystrophy DMD gene responsible for Duchenne and Becker muscular
dystrophies are routinely identified using multiple ligation probe amplification and
array-based comparative genomic hybridization. These methods only map deleted or
duplicated exons, without providing the exact location of breakpoints. Commonly used
methods for the detection of CNV breakpoints include long-range PCR and primer
walking, their success being limited by the deletion size, GC content and presence of
DNA repeats. Here, we present a strategy for detecting the breakpoints of medium and
large CNVs regardless of their size. The hemizygous deletion of exons 45-50 in the
DMD gene and the large autosomal heterozygous
PARK2 deletion were used to demonstrate the workflow that relies
on real-time quantitative PCR to narrow down the deletion region and Sanger
sequencing for breakpoint confirmation. The strategy is fast, reliable and
cost-efficient, making it amenable to widespread use in genetic laboratories.
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Affiliation(s)
| | | | - Helena Tuchinsky
- Department of Molecular Biology, Ariel University, Ariel, Israel
| | - Elimelech Nesher
- Department of Molecular Biology, Ariel University, Ariel, Israel
| | - Albert Pinhasov
- Department of Molecular Biology, Ariel University, Ariel, Israel
| | - Leon Raskin
- Department of Medicine, Vanderbilt University, Nashville, TN, USA
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13
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Sahnane N, Bernasconi B, Carnevali I, Furlan D, Viel A, Sessa F, Tibiletti MG. Disruption of the APC gene by t(5;7) translocation in a Turcot family. Cancer Genet 2015; 209:107-11. [PMID: 26797314 DOI: 10.1016/j.cancergen.2015.12.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2015] [Revised: 12/04/2015] [Accepted: 12/09/2015] [Indexed: 01/12/2023]
Abstract
Turcot syndrome (TS) refers to the combination of colorectal polyps and primary tumours of the central nervous system. TS is a heterogeneous genetic condition due to APC and/or mismatch repair germline mutations. When APC is involved the vast majority of mutations are truncating, but in approximately 20%-30% of patients with familial polyposis no germline mutation can be found. A 30-year-old Caucasian woman with a positive pedigree for TS was referred to our Genetic Counselling Service. She was negative for APC and MUTYH but showed a reciprocal balanced translocation t(5;7)(q22;p15) at chromosome analysis. FISH analysis using specific BAC probes demonstrated that 5q22 breakpoint disrupted the APC gene. Transcript analysis by MLPA and digital PCR revealed that the cytogenetic rearrangement involving the 3' end of the APC gene caused a defective expression of a truncated transcript. This result allowed cytogenetic analysis to be offered to all the other family members and segregation analysis clearly demonstrated that all the carriers were affected, whereas non-carriers did not have the polyposis. A cytogenetic approach permitted the identification of the mutation-causing disease in this family, and the segregation analysis together with the transcript study supported the pathogenetic role of this mutation. Karyotype analysis was used as a predictive test in all members of this family. This family suggests that clinically positive TS and FAP cases, which test negative with standard molecular analysis, could be easily and cost-effectively resolved by a classical and molecular cytogenetic approach.
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Affiliation(s)
- Nora Sahnane
- Department of Surgical and Morphological Sciences, University of Insubria, via O. Rossi 9, IT-21100 Varese, Italy.
| | - Barbara Bernasconi
- Department of Surgical and Morphological Sciences, University of Insubria, via O. Rossi 9, IT-21100 Varese, Italy
| | - Ileana Carnevali
- Ospedale di Circolo di Varese, Unit of Pathology, via O. Rossi 9, IT-21100 Varese, Italy
| | - Daniela Furlan
- Department of Surgical and Morphological Sciences, University of Insubria, via O. Rossi 9, IT-21100 Varese, Italy
| | - Alessandra Viel
- CRO Aviano National Cancer Institute, Unit of Experimental Oncology 1, via F. Gallini 2, IT-33081 Aviano, PN, Italy
| | - Fausto Sessa
- Department of Surgical and Morphological Sciences, University of Insubria, via O. Rossi 9, IT-21100 Varese, Italy
| | - Maria Grazia Tibiletti
- Ospedale di Circolo di Varese, Unit of Pathology, via O. Rossi 9, IT-21100 Varese, Italy
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