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Forte G, Buonadonna AL, Fasano C, Sanese P, Cariola F, Manghisi A, Guglielmi AF, Lepore Signorile M, De Marco K, Grossi V, Disciglio V, Simone C. Clinical and Molecular Characterization of SMAD4 Splicing Variants in Patients with Juvenile Polyposis Syndrome. Int J Mol Sci 2024; 25:7939. [PMID: 39063183 PMCID: PMC11276957 DOI: 10.3390/ijms25147939] [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: 06/14/2024] [Revised: 07/15/2024] [Accepted: 07/18/2024] [Indexed: 07/28/2024] Open
Abstract
Juvenile polyposis syndrome (JPS) is an inherited autosomal dominant condition that predisposes to the development of juvenile polyps throughout the gastrointestinal (GI) tract, and it poses an increased risk of GI malignancy. Germline causative variants were identified in the SMAD4 gene in a subset (20%) of JPS cases. Most SMAD4 germline genetic variants published to date are missense, nonsense, and frameshift mutations. SMAD4 germline alterations predicted to result in aberrant splicing have rarely been reported. Here, we report two unrelated Italian families harboring two different SMAD4 intronic variants, c.424+5G>A and c.425-9A>G, which are clinically associated with colorectal cancer and/or juvenile GI polyps. In silico prediction analysis, in vitro minigene assays, and RT-PCR showed that the identified variants lead to aberrant SMAD4 splicing via the exonization of intronic nucleotides, resulting in a premature stop codon. This is expected to cause the production of a truncated protein. This study expands the landscape of SMAD4 germline genetic variants associated with GI polyposis and/or cancer. Moreover, it emphasizes the importance of the functional characterization of SMAD4 splicing variants through RNA analysis, which can provide new insights into genetic disease variant interpretation, enabling tailored genetic counseling, management, and surveillance of patients with GI polyposis and/or cancer.
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Affiliation(s)
- Giovanna Forte
- Medical Genetics, National Institute of Gastroenterology-IRCCS “Saverio de Bellis” Research Hospital, 70013 Castellana Grotte, Italy; (G.F.); (A.L.B.); (C.F.); (P.S.); (F.C.); (A.M.); (A.F.G.); (M.L.S.); (K.D.M.); (V.G.)
| | - Antonia Lucia Buonadonna
- Medical Genetics, National Institute of Gastroenterology-IRCCS “Saverio de Bellis” Research Hospital, 70013 Castellana Grotte, Italy; (G.F.); (A.L.B.); (C.F.); (P.S.); (F.C.); (A.M.); (A.F.G.); (M.L.S.); (K.D.M.); (V.G.)
| | - Candida Fasano
- Medical Genetics, National Institute of Gastroenterology-IRCCS “Saverio de Bellis” Research Hospital, 70013 Castellana Grotte, Italy; (G.F.); (A.L.B.); (C.F.); (P.S.); (F.C.); (A.M.); (A.F.G.); (M.L.S.); (K.D.M.); (V.G.)
| | - Paola Sanese
- Medical Genetics, National Institute of Gastroenterology-IRCCS “Saverio de Bellis” Research Hospital, 70013 Castellana Grotte, Italy; (G.F.); (A.L.B.); (C.F.); (P.S.); (F.C.); (A.M.); (A.F.G.); (M.L.S.); (K.D.M.); (V.G.)
| | - Filomena Cariola
- Medical Genetics, National Institute of Gastroenterology-IRCCS “Saverio de Bellis” Research Hospital, 70013 Castellana Grotte, Italy; (G.F.); (A.L.B.); (C.F.); (P.S.); (F.C.); (A.M.); (A.F.G.); (M.L.S.); (K.D.M.); (V.G.)
| | - Andrea Manghisi
- Medical Genetics, National Institute of Gastroenterology-IRCCS “Saverio de Bellis” Research Hospital, 70013 Castellana Grotte, Italy; (G.F.); (A.L.B.); (C.F.); (P.S.); (F.C.); (A.M.); (A.F.G.); (M.L.S.); (K.D.M.); (V.G.)
| | - Anna Filomena Guglielmi
- Medical Genetics, National Institute of Gastroenterology-IRCCS “Saverio de Bellis” Research Hospital, 70013 Castellana Grotte, Italy; (G.F.); (A.L.B.); (C.F.); (P.S.); (F.C.); (A.M.); (A.F.G.); (M.L.S.); (K.D.M.); (V.G.)
| | - Martina Lepore Signorile
- Medical Genetics, National Institute of Gastroenterology-IRCCS “Saverio de Bellis” Research Hospital, 70013 Castellana Grotte, Italy; (G.F.); (A.L.B.); (C.F.); (P.S.); (F.C.); (A.M.); (A.F.G.); (M.L.S.); (K.D.M.); (V.G.)
| | - Katia De Marco
- Medical Genetics, National Institute of Gastroenterology-IRCCS “Saverio de Bellis” Research Hospital, 70013 Castellana Grotte, Italy; (G.F.); (A.L.B.); (C.F.); (P.S.); (F.C.); (A.M.); (A.F.G.); (M.L.S.); (K.D.M.); (V.G.)
| | - Valentina Grossi
- Medical Genetics, National Institute of Gastroenterology-IRCCS “Saverio de Bellis” Research Hospital, 70013 Castellana Grotte, Italy; (G.F.); (A.L.B.); (C.F.); (P.S.); (F.C.); (A.M.); (A.F.G.); (M.L.S.); (K.D.M.); (V.G.)
| | - Vittoria Disciglio
- Medical Genetics, National Institute of Gastroenterology-IRCCS “Saverio de Bellis” Research Hospital, 70013 Castellana Grotte, Italy; (G.F.); (A.L.B.); (C.F.); (P.S.); (F.C.); (A.M.); (A.F.G.); (M.L.S.); (K.D.M.); (V.G.)
| | - Cristiano Simone
- Medical Genetics, National Institute of Gastroenterology-IRCCS “Saverio de Bellis” Research Hospital, 70013 Castellana Grotte, Italy; (G.F.); (A.L.B.); (C.F.); (P.S.); (F.C.); (A.M.); (A.F.G.); (M.L.S.); (K.D.M.); (V.G.)
- Medical Genetics, Department of Precision and Regenerative Medicine and Jonic Area (DiMePRe-J), University of Bari Aldo Moro, 70124 Bari, Italy
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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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Papadopulos ME, Plazzer JP, Macrae FA. Genotype-phenotype correlation of BMPR1a disease causing variants in juvenile polyposis syndrome. Hered Cancer Clin Pract 2023; 21:12. [PMID: 37400896 DOI: 10.1186/s13053-023-00255-3] [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: 10/10/2022] [Accepted: 06/07/2023] [Indexed: 07/05/2023] Open
Abstract
BACKGROUND Juvenile Polyposis Syndrome (JPS) is an autosomal dominant condition with hamartomatous polyps in the gastrointestinal tract, associated with an increased risk of gastrointestinal malignancy. Disease causing variants (DCVs) in BMPR1a or SMAD4 account for 45-60% of JPS cases, with BMPR1a DCVs accounting for 17-38% of JPS cases. Within those with either a BMPR1a or SMAD4 DCV, there is phenotypic variability in location of polyps, risk of malignancy and extra-intestinal manifestations with limited published reports of gene-phenotype association or genotype-phenotype correlation. We aimed to identify any gene-phenotype association or genotype-phenotype correlation in BMPR1a to inform surveillance recommendations, and gene-specific modification to the ACMG classification of pathogenicity of DCVs. METHODS A literature search was performed through EMBASE, MEDLINE and PubMed. Studies that were included explored BMPR1a DCV-related JPS or contiguous deletion of PTEN and BMPR1a. Data was also drawn from the BMPR1a specific databases on LOVD and ClinVar. RESULTS There were 211 DCVs in BMPR1a identified, 82 from patients with JPS in the literature, and 17 from LOVD and 112 from ClinVar classified as pathogenic or likely pathogenic. These included missense, nonsense and frameshift variants and large deletions, occurring across all functional domains of the gene. Unlike in SMAD4 carriers, gastric polyposis and malignancy were not identified in our review in BMPR1a carriers, but colonic polyposis and malignancy occurred in carriers of either BMPR1a or SMAD4 DCVs. Those with contiguous deletion of PTEN and BMPR1a can present with JPS of infancy, with a severe phenotype of GI bleeding, diarrhoea, exudative enteropathy and rectal prolapse. No specific BMPR1a genotype-phenotype correlation could be ascertained including by variant type or functional domain. CONCLUSION Phenotypic characteristics cannot be used to inform variant location in BMPR1a. However, the phenotypic characteristics of BMPR1a DCV carriers, being almost exclusively related to the colon and rectum, can assist in pathogenicity assessment of BMPR1a variants. Given these findings, we propose that carriers of BMPR1a DCVs should only require surveillance for colorectal polyps and malignancy, and that surveillance for gastric polyps and malignancy may be unnecessary. However variant location within BMPR1a does not support differential surveillance recommendations.
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Affiliation(s)
- M E Papadopulos
- Department of Medicine, University of Melbourne, The Royal Melbourne Hospital, Melbourne, Australia.
- Department of Colorectal Medicine and Genetics, The Royal Melbourne Hospital, Melbourne, Australia.
| | - J P Plazzer
- Department of Colorectal Medicine and Genetics, The Royal Melbourne Hospital, Melbourne, Australia
| | - F A Macrae
- Department of Medicine, University of Melbourne, The Royal Melbourne Hospital, Melbourne, Australia
- Department of Colorectal Medicine and Genetics, The Royal Melbourne Hospital, Melbourne, Australia
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Shiraishi Y, Okada A, Chiba K, Kawachi A, Omori I, Mateos RN, Iida N, Yamauchi H, Kosaki K, Yoshimi A. Systematic identification of intron retention associated variants from massive publicly available transcriptome sequencing data. Nat Commun 2022; 13:5357. [PMID: 36175409 PMCID: PMC9522810 DOI: 10.1038/s41467-022-32887-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Accepted: 08/23/2022] [Indexed: 12/01/2022] Open
Abstract
Many disease-associated genomic variants disrupt gene function through abnormal splicing. With the advancement of genomic medicine, identifying disease-associated splicing associated variants has become more important than ever. Most bioinformatics approaches to detect splicing associated variants require both genome and transcriptomic data. However, there are not many datasets where both of them are available. In this study, we develop a methodology to detect genomic variants that cause splicing changes (more specifically, intron retention), using transcriptome sequencing data alone. After evaluating its sensitivity and precision, we apply it to 230,988 transcriptome sequencing data from the publicly available repository and identified 27,049 intron retention associated variants (IRAVs). In addition, by exploring positional relationships with variants registered in existing disease databases, we extract 3,000 putative disease-associated IRAVs, which range from cancer drivers to variants linked with autosomal recessive disorders. The in-silico screening framework demonstrates the possibility of near-automatically acquiring medical knowledge, making the most of massively accumulated publicly available sequencing data. Collections of IRAVs identified in this study are available through IRAVDB (https://iravdb.io/). This paper proposed a novel in-silico framework for automatically screening disease-related variants and applied it to over 200,000 transcriptomes, providing an example to acquire medically relevant knowledge from publicly available sequence data.
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Affiliation(s)
- Yuichi Shiraishi
- Division of Genome Analysis Platform Development, National Cancer Center Research Institute, Tokyo, Japan.
| | - Ai Okada
- Division of Genome Analysis Platform Development, National Cancer Center Research Institute, Tokyo, Japan
| | - Kenichi Chiba
- Division of Genome Analysis Platform Development, National Cancer Center Research Institute, Tokyo, Japan
| | - Asuka Kawachi
- Cancer RNA Research Unit, National Cancer Center Research Institute, Tokyo, Japan
| | - Ikuko Omori
- Cancer RNA Research Unit, National Cancer Center Research Institute, Tokyo, Japan
| | - Raúl Nicolás Mateos
- Division of Genome Analysis Platform Development, National Cancer Center Research Institute, Tokyo, Japan
| | - Naoko Iida
- Division of Genome Analysis Platform Development, National Cancer Center Research Institute, Tokyo, Japan
| | - Hirofumi Yamauchi
- Cancer RNA Research Unit, National Cancer Center Research Institute, Tokyo, Japan
| | - Kenjiro Kosaki
- Center for Medical Genetics, Keio University School of Medicine, Tokyo, Japan
| | - Akihide Yoshimi
- Cancer RNA Research Unit, National Cancer Center Research Institute, Tokyo, Japan
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Liu S, Zhang RF, You Y, You W, Ruan GC, Liu YP, Zhang SY, Li Y, Feng YL, Yan XM, Zhou WX, Li JN, Li J, Qian JM. The genomic landscape of Cronkhite-Canada syndrome: Possible clues for pathogenesis. J Dig Dis 2022; 23:288-294. [PMID: 35678525 DOI: 10.1111/1751-2980.13101] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Revised: 05/26/2022] [Accepted: 06/06/2022] [Indexed: 12/11/2022]
Abstract
OBJECTIVES Cronkhite-Canada syndrome (CCS) is a rare hamartomatous polyposis syndrome with a proposed association with chronic autoimmune inflammation. To date, genetic background of patients with CCS remains less investigated. In this study we aimed to explore the genomic landscape of CCS. METHODS Whole exome sequencing was performed on peripheral blood samples extracted from 18 patients with CCS. Potential function-impacting germline variants were filtered by R software. Through systematic data analysis, a number of genetic variants were identified. Enrichment analysis was performed using the R package ClusterProfiler. RESULTS Overall, 3960 low-frequency (<0.05 or not reported in the Exome Aggregation Consortium East Asian, 1000 Genomes, or ESP6500 database) potentially function-impacting germline variants were identified, with 18 genes (FDFT1, LOC400863, MUC3A, MUC4, ZNF806, GXYLT1, MUC6, PABPC3, PSPH, ZFPM1, CIC, LOC283710, ARSD, GOLGA6L2, LOC388282, SLC25A5, TMEM247, WDR89) involved over half the patients. Functional enrichment of these genes revealed several biological processes in relation to innate immune responses and glycosylation. Only one likely pathogenic germline variant of an hamartomatous polyposis syndrome-associated gene, PTCH1, was detected in one patient. CONCLUSIONS CCS has genomic alteration patterns completely distinct from those of traditional hamartomatous polyposis syndrome. The germline mutation landscape indicates potential roles of innate immune responses and glycosylation in the pathogenesis of CCS.
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Affiliation(s)
- Shuang Liu
- Department of Allergy, Chinese Academy of Medical Sciences, Peking Union Medical College Hospital, Beijing, China
| | - Run Feng Zhang
- Department of Gastroenterology, Chinese Academy of Medical Sciences, Peking Union Medical College Hospital, Beijing, China
| | - Yan You
- Department of Gastroenterology, Chinese Academy of Medical Sciences, Peking Union Medical College Hospital, Beijing, China
| | - Wen You
- Department of Gastroenterology, Chinese Academy of Medical Sciences, Peking Union Medical College Hospital, Beijing, China
| | - Ge Chong Ruan
- Department of Gastroenterology, Chinese Academy of Medical Sciences, Peking Union Medical College Hospital, Beijing, China
| | - Ya Ping Liu
- McKusick-Zhang Center for Genetic Medicine, State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing, China
| | - Sheng Yu Zhang
- Department of Gastroenterology, Chinese Academy of Medical Sciences, Peking Union Medical College Hospital, Beijing, China
| | - Yue Li
- Department of Gastroenterology, Chinese Academy of Medical Sciences, Peking Union Medical College Hospital, Beijing, China
| | - Yun Lu Feng
- Department of Gastroenterology, Chinese Academy of Medical Sciences, Peking Union Medical College Hospital, Beijing, China
| | - Xue Min Yan
- Department of Gastroenterology, Chinese Academy of Medical Sciences, Peking Union Medical College Hospital, Beijing, China
| | - Wei Xun Zhou
- Department of Pathology, Chinese Academy of Medical Sciences, Peking Union Medical College Hospital, Beijing, China
| | - Jing Nan Li
- Department of Gastroenterology, Chinese Academy of Medical Sciences, Peking Union Medical College Hospital, Beijing, China
| | - Ji Li
- Department of Gastroenterology, Chinese Academy of Medical Sciences, Peking Union Medical College Hospital, Beijing, China
| | - Jia Ming Qian
- Department of Gastroenterology, Chinese Academy of Medical Sciences, Peking Union Medical College Hospital, Beijing, China
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Jelsig AM, Karstensen JG, Jespersen N, Ketabi Z, Lautrup C, Rønlund K, Sunde L, Wadt K, Thorlacius-Ussing O, Qvist N. Danish guidelines for management of non-APC-associated hereditary polyposis syndromes. Hered Cancer Clin Pract 2021; 19:41. [PMID: 34620187 PMCID: PMC8499431 DOI: 10.1186/s13053-021-00197-8] [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: 06/02/2021] [Accepted: 09/14/2021] [Indexed: 02/06/2023] Open
Abstract
Hereditary Polyposis Syndromes are a group of rare, inherited syndromes characterized by the presence of histopathologically specific or numerous intestinal polyps and an increased risk of cancer. Some polyposis syndromes have been known for decades, but the development in genetic technologies has allowed the identification of new syndromes.. The diagnosis entails surveillance from an early age, but universal guideline on how to manage and surveille these new syndromes are lacking. This paper represents a condensed version of the recent guideline (2020) from a working group appointed by the Danish Society of Medical Genetics and the Danish Society of Surgery on recommendations for the surveillance of patients with hereditary polyposis syndromes, including rare polyposis syndromes.
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Affiliation(s)
- Anne Marie Jelsig
- Department of Clinical Genetics, University Hospital of Copenhagen, Rigshospitalet, Copenhagen, Denmark.
| | - John Gásdal Karstensen
- Danish Polyposis Registry, Gastrounit, Hvidovre Hospital, Hvidovre, Denmark.,Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Niels Jespersen
- Danish Polyposis Registry, Gastrounit, Hvidovre Hospital, Hvidovre, Denmark
| | - Zohreh Ketabi
- Department of Gynecology and Obstetrics, University Hospital of Copenhagen, Rigshospitalet, Copenhagen, Denmark
| | - Charlotte Lautrup
- Department of Clinical Genetics, Aalborg University Hospital, Aalborg, Denmark
| | - Karina Rønlund
- Department of Clinical Genetics, University Hospital of Southern Denmark, Vejle Hospital, Vejle, Denmark
| | - Lone Sunde
- Department of Clinical Genetics, Aalborg University Hospital, Aalborg, Denmark
| | - Karin Wadt
- Department of Clinical Genetics, University Hospital of Copenhagen, Rigshospitalet, Copenhagen, Denmark
| | - Ole Thorlacius-Ussing
- Department of Gastrointestinal Surgery, Aalborg University Hospital, Aalborg, Denmark.,Department of Clinical Medicine, Aalborg University, Aalborg, Denmark
| | - Niels Qvist
- Research Unit for Surgery, Odense University Hospital, Odense, Denmark.,University of Southern Denmark, Odense, Denmark
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Liu Q, Liu M, Liu T, Yu Y. Familial juvenile polyposis syndrome with a de novo germline missense variant in BMPR1A gene: a case report. BMC MEDICAL GENETICS 2020; 21:196. [PMID: 33032550 PMCID: PMC7545562 DOI: 10.1186/s12881-020-01135-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/27/2020] [Accepted: 09/28/2020] [Indexed: 11/10/2022]
Abstract
Background Juvenile polyposis syndrome (JPS) is a rare autosomal dominant hereditary disorder characterized by the development of multiple distinct juvenile polyps in the gastrointestinal tract with an increased risk of colorectal cancer. Germline mutations in two genes, SMAD4 and BMPR1A, have been identified to cause JPS. Case presentation Here, we report a germline heterozygous missense variant (c.299G > A) in exon 3 BMPR1A gene in a family with juvenile polyposis. This variant was absent from the population database, and concluded as de novo compared with the parental sequencing. Further sequencing of the proband’s children confirmed the segregation of this variant with the disease, while the variant was also predicted to have damaging effect based on online prediction tools. Therefore, this variant was classified as likely pathogenic according to the American College of Medical Genetics and Genomics (ACMG) guidelines. Conclusions Germline genetic testing revealed a de novo germline missense variant in BMPR1A gene in a family with juvenile polyposis. Identification of the pathogenic variant facilitates the cancer risk management of at-risk family members, and endoscopic surveillance is recommended for mutation carriers.
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Affiliation(s)
- Qing Liu
- Department of Medical Oncology, Zhongshan Hospital, Fudan University, 180 Fenglin Road, Shanghai, 200032, China
| | - Mengling Liu
- Department of Medical Oncology, Zhongshan Hospital, Fudan University, 180 Fenglin Road, Shanghai, 200032, China
| | - Tianshu Liu
- Department of Medical Oncology, Zhongshan Hospital, Fudan University, 180 Fenglin Road, Shanghai, 200032, China
| | - Yiyi Yu
- Department of Medical Oncology, Zhongshan Hospital, Fudan University, 180 Fenglin Road, Shanghai, 200032, China.
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Rates of Actionable Genetic Findings in Individuals with Colorectal Cancer or Polyps Ascertained from a Community Medical Setting. Am J Hum Genet 2019; 105:526-533. [PMID: 31422818 DOI: 10.1016/j.ajhg.2019.07.012] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2018] [Accepted: 07/18/2019] [Indexed: 12/15/2022] Open
Abstract
As clinical testing for Mendelian causes of colorectal cancer (CRC) is largely driven by recognition of family history and early age of onset, the rates of such findings among individuals with prevalent CRC not recognized to have these features is largely unknown. We evaluated actionable genomic findings in community-based participants ascertained by three phenotypes: (1) CRC, (2) one or more adenomatous colon polyps, and (3) control participants over age 59 years without CRC or colon polyps. These participants underwent sequencing for a panel of genes that included colorectal cancer/polyp (CRC/P)-associated and actionable incidental findings genes. Those with CRC had a 3.8% rate of positive results (pathogenic or likely pathogenic) for a CRC-associated gene variant, despite generally being older at CRC onset (mean 72 years). Those ascertained for polyps had a 0.8% positive rate and those with no CRC/P had a positive rate of 0.2%. Though incidental finding rates unrelated to colon cancer were similar for all groups, our positive rate for cardiovascular findings exceeds disease prevalence, suggesting that variant interpretation challenges or low penetrance in these genes. The rate of HFE c.845G>A (p.Cys282Tyr) homozygotes in the CRC group reinforces a previously reported, but relatively unexplored, association between hemochromatosis and CRC. These results in a general clinical population suggest that current testing strategies could be improved in order to better detect Mendelian CRC-associated conditions. These data also underscore the need for additional functional and familial evidence to clarify the pathogenicity and penetrance of variants deemed pathogenic or likely pathogenic, particularly among the actionable genes associated with cardiovascular disease.
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