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Yin X, Richardson M, Laner A, Shi X, Ognedal E, Vasta V, Hansen TVO, Pineda M, Ritter D, den Dunnen JT, Hassanin E, Lyman Lin W, Borras E, Krahn K, Nordling M, Martins A, Mahmood K, Nadeau EAW, Beshay V, Tops C, Genuardi M, Pesaran T, Frayling IM, Capellá G, Latchford A, Tavtigian SV, Maj C, Plon SE, Greenblatt MS, Macrae FA, Spier I, Aretz S. Systematic large-scale application of ClinGen InSiGHT APC -specific ACMG/AMP variant classification criteria substantially alleviates the burden of variants of uncertain significance in ClinVar and LOVD databases. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.05.03.24306761. [PMID: 38746299 PMCID: PMC11092726 DOI: 10.1101/2024.05.03.24306761] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
Background Pathogenic constitutional APC variants underlie familial adenomatous polyposis, the most common hereditary gastrointestinal polyposis syndrome. To improve variant classification and resolve the interpretative challenges of variants of uncertain significance (VUS), APC-specific ACMG/AMP variant classification criteria were developed by the ClinGen-InSiGHT Hereditary Colorectal Cancer/Polyposis Variant Curation Expert Panel (VCEP). Methods A streamlined algorithm using the APC -specific criteria was developed and applied to assess all APC variants in ClinVar and the InSiGHT international reference APC LOVD variant database. Results A total of 10,228 unique APC variants were analysed. Among the ClinVar and LOVD variants with an initial classification of (Likely) Benign or (Likely) Pathogenic, 94% and 96% remained in their original categories, respectively. In contrast, 41% ClinVar and 61% LOVD VUS were reclassified into clinically actionable classes, the vast majority as (Likely) Benign. The total number of VUS was reduced by 37%. In 21 out of 36 (58%) promising APC variants that remained VUS despite evidence for pathogenicity, a data mining-driven work-up allowed their reclassification as (Likely) Pathogenic. Conclusions The application of APC -specific criteria substantially reduced the number of VUS in ClinVar and LOVD. The study also demonstrated the feasibility of a systematic approach to variant classification in large datasets, which might serve as a generalisable model for other gene-/disease-specific variant interpretation initiatives. It also allowed for the prioritization of VUS that will benefit from in-depth evidence collection. This subset of APC variants was approved by the VCEP and made publicly available through ClinVar and LOVD for widespread clinical use.
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Li J, He C, Gong J, Wang X, Liu C, Deng A, Zhu L. Identification of a novel CNV at the APC gene in a Chinese family with familial adenomatous polyposis. Front Mol Biosci 2023; 10:1234296. [PMID: 37577746 PMCID: PMC10415011 DOI: 10.3389/fmolb.2023.1234296] [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: 06/04/2023] [Accepted: 07/10/2023] [Indexed: 08/15/2023] Open
Abstract
Introduction: Familial adenomatous polyposis (FAP) is the second most commonly inherited colorectal cancer (CRC) predisposition caused by germline mutations within the adenomatous polyposis coli (APC) gene. The molecular defects and clinical manifestations of two FAP families were analyzed, and individual prevention strategies suitable for mutation carriers in different families were proposed. Methods and results: The pathogenic gene mutations were identified among the two families using whole-exome sequencing and verified with Sanger sequencing or quantitative polymerase chain reaction (qPCR). One novel (GRCh37:Chr5: 112145676-112174368, del, 28,692 bp) and a known (c.C847T:p.R283X) mutation in the APC gene were pathogenic mutations for FAP, according to the sequencing data and tumorigenesis pattern among the family members. The two mutations led to a premature translational stop signal, synthesizing an absent or disrupted protein product. Conclusion: Our findings expand the known germline mutation spectrum of the APC gene among the Chinese population. This reaffirms the importance of genetic testing in FAP. Genetic consultation and regular follow-ups are necessary for the individualized treatment of cancer-afflicted families with APC expression deficiency. Additional work is required to develop safe and effective chemotherapy and immunotherapy for FAP based on the mutation type.
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Affiliation(s)
- Juyi Li
- Department of Pharmacy, The Central Hospital of Wuhan, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Chengzhi He
- Department of Gastrointestinal Surgery, The Central Hospital of Wuhan, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Jing Gong
- Department of Gastroenterology, The Central Hospital of Wuhan, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Xiufang Wang
- Department of Pain, The Central Hospital of Wuhan, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Chao Liu
- Hubei Key Laboratory of Diabetes and Angiopathy, Hubei University of Science and Technology, Xianning, Hubei, China
| | - Aiping Deng
- Department of Pharmacy, The Central Hospital of Wuhan, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Lin Zhu
- Department of Pediatrics, Tongji Hospital, Huazhong University of Science and Technology, Wuhan, Hubei, China
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Bozsik A, Butz H, Grolmusz VK, Polgár C, Patócs A, Papp J. Genome sequencing-based discovery of a novel deep intronic APC pathogenic variant causing exonization. Eur J Hum Genet 2023; 31:841-845. [PMID: 36828923 PMCID: PMC10326037 DOI: 10.1038/s41431-023-01322-y] [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: 12/26/2022] [Revised: 02/09/2023] [Accepted: 02/13/2023] [Indexed: 02/26/2023] Open
Abstract
Familial adenomatous polyposis (FAP) is a hereditary cancer syndrome that occurs as a result of germline mutations in the APC gene. Despite a clear clinical diagnosis of FAP, a certain proportion of the APC variants are not readily detectable through conventional genotyping routines. We accomplished genome sequencing in duo of the disease-affected proband and non-affected sibling followed by in silico predictions and a series of RNA-based assays clarifying variant functionality. By prioritizing variants obtained by genome sequencing, we discovered the novel deep intronic alteration APC:c.531 + 1482 A > G that was demonstrated to cause out-of-frame exonization of 56 base pairs from intron 5 of the gene. Further cDNA assays confirmed, that the aberrant splicing event was complete and its splice product was subject to nonsense-mediated decay. Co-segregation was observed between the variant carrier status and the disease phenotype. Cumulative evidence confirmed that APC:c.531 + 1482 A > G is a pathogenic variant causative of the disease.
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Affiliation(s)
- Anikó Bozsik
- Department of Molecular Genetics, National Institute of Oncology, Ráth György út 7-9, Budapest, H-1122, Hungary.
- Hereditary Cancers Research Group, Hungarian Academy of Sciences - Semmelweis University, Nagyvárad tér 4, Budapest, H-1089, Hungary.
- National Tumorbiology Laboratory, National Institute of Oncology, Ráth György út 7-9, Budapest, H-1122, Hungary.
| | - Henriett Butz
- Department of Molecular Genetics, National Institute of Oncology, Ráth György út 7-9, Budapest, H-1122, Hungary
- Hereditary Cancers Research Group, Hungarian Academy of Sciences - Semmelweis University, Nagyvárad tér 4, Budapest, H-1089, Hungary
- National Tumorbiology Laboratory, National Institute of Oncology, Ráth György út 7-9, Budapest, H-1122, Hungary
| | - Vince Kornél Grolmusz
- Department of Molecular Genetics, National Institute of Oncology, Ráth György út 7-9, Budapest, H-1122, Hungary
- Hereditary Cancers Research Group, Hungarian Academy of Sciences - Semmelweis University, Nagyvárad tér 4, Budapest, H-1089, Hungary
- National Tumorbiology Laboratory, National Institute of Oncology, Ráth György út 7-9, Budapest, H-1122, Hungary
| | - Csaba Polgár
- National Tumorbiology Laboratory, National Institute of Oncology, Ráth György út 7-9, Budapest, H-1122, Hungary
- Center of Radiotherapy, National Institute of Oncology, Ráth György út 7-9, Budapest, H-1122, Hungary
- Department of Oncology, Semmelweis University, Ráth György út 7-9, Budapest, H-1122, Hungary
| | - Attila Patócs
- Department of Molecular Genetics, National Institute of Oncology, Ráth György út 7-9, Budapest, H-1122, Hungary
- Hereditary Cancers Research Group, Hungarian Academy of Sciences - Semmelweis University, Nagyvárad tér 4, Budapest, H-1089, Hungary
- National Tumorbiology Laboratory, National Institute of Oncology, Ráth György út 7-9, Budapest, H-1122, Hungary
| | - János Papp
- Department of Molecular Genetics, National Institute of Oncology, Ráth György út 7-9, Budapest, H-1122, Hungary
- Hereditary Cancers Research Group, Hungarian Academy of Sciences - Semmelweis University, Nagyvárad tér 4, Budapest, H-1089, Hungary
- National Tumorbiology Laboratory, National Institute of Oncology, Ráth György út 7-9, Budapest, H-1122, Hungary
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Germline mutations of the adenomatous polyposis coli (APC) gene in Algerian familial adenomatous polyposis cohort: first report. Mol Biol Rep 2022; 49:3823-3837. [PMID: 35142982 DOI: 10.1007/s11033-022-07228-0] [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: 11/17/2021] [Accepted: 02/03/2022] [Indexed: 10/19/2022]
Abstract
BACKGROUND Familial adenomatous polyposis (known also as classical or severe FAP) is a rare autosomal dominant colorectal cancer predisposition syndrome, characterized by the presence of hundreds to thousands of adenomatous polyps in the colon and rectum from an early age. In the absence of prophylactic surgery, colorectal cancer (CRC) is the inevitable consequence of FAP. The vast majority of FAP is caused by germline mutations in the adenomatous polyposis coli (APC) tumor suppressor gene (5q21). To date, most of the germline mutations in classical FAP result in truncation of the APC protein and 60% are mainly located within exon 15. MATERIAL AND METHODS In this first nationwide study, we investigated the clinical and genetic features of 52 unrelated Algerian FAP families. We screened by PCR-direct sequencing the entire exon 15 of APC gene in 50 families and two families have been analyzed by NGS using a cancer panel of 30 hereditary cancer genes. RESULTS Among 52 FAP index cases, 36 had 100 or more than 100 polyps, 37 had strong family history of FAP, 5 developed desmoids tumors, 15 had extra colonic manifestations and 21 had colorectal cancer. We detected 13 distinct germline mutations in 17 FAP families. Interestingly, 4 novel APC germline pathogenic variants never described before have been identified in our study. CONCLUSIONS The accumulating knowledge about the prevalence and nature of APC variants in Algerian population will contribute in the near future to the implementation of genetic testing and counseling for FAP patients.
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Garcia-Pelaez J, Barbosa-Matos R, São José C, Sousa S, Gullo I, Hoogerbrugge N, Carneiro F, Oliveira C. Gastric cancer genetic predisposition and clinical presentations: Established heritable causes and potential candidate genes. Eur J Med Genet 2021; 65:104401. [PMID: 34871783 DOI: 10.1016/j.ejmg.2021.104401] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2021] [Revised: 11/10/2021] [Accepted: 11/28/2021] [Indexed: 12/12/2022]
Abstract
Tumour risk syndromes (TRS) are characterized by an increased risk of early-onset cancers in a familial context. High cancer risk is mostly driven by loss-of-function variants in a single cancer-associated gene. Presently, predisposition to diffuse gastric cancer (DGC) is explained by CDH1 and CTNNA1 pathogenic and likely pathogenic variants (P/LP), causing Hereditary Diffuse Gastric Cancer (HDGC); while APC promoter 1B single nucleotide variants predispose to Gastric Adenocarcinoma and Proximal Polyposis of the Stomach (GAPPS). Familial Intestinal Gastric Cancer (FIGC), recognized as a GC-predisposing disease, remains understudied and genetically unsolved. GC can also occur in the spectrum of other TRS. Identification of heritable causes allows defining diagnostic testing criteria, helps to clinically classify GC families into the appropriate TRS, and allows performing pre-symptomatic testing identifying at-risk individuals for downstream surveillance, risk reduction and/or treatment. However, most of HDGC, some GAPPS, and most FIGC patients/families remain unsolved, expecting a heritable factor to be discovered. The missing heritability in GC-associated tumour risk syndromes (GC-TRS) is likely explained not by a single major gene, but by a diversity of genes, some, predisposing to other TRS. This would gain support if GC-enriched small families or apparently isolated early-onset GC cases were hiding a family history compatible with another TRS. Herein, we revisited current knowledge on GC-TRS, and searched in the literature for individuals/families bearing P/LP variants predisposing for other TRS, but whose probands display a clinical presentation and/or family history also fitting GC-TRS criteria. We found 27 families with family history compatible with HDGC or FIGC, harbouring 28 P/LP variants in 16 TRS-associated genes, mainly associated with DNA repair. PALB2 or BRCA2 were the most frequently mutated candidate genes in individuals with family history compatible with HDGC and FIGC, respectively. Consolidation of PALB2 and BRCA2 as HDGC- or FIGC-associated genes, respectively, holds promise and worth additional research. This analysis further highlighted the influence, that proband's choice and small or unreported family history have, for a correct TRS diagnosis, genetic screening, and disease management. In this review, we provide a rational for identification of particularly relevant candidate genes in GC-TRS.
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Affiliation(s)
- José Garcia-Pelaez
- i3S - Instituto de Investigação e Inovação em Saúde, Porto, Portugal; IPATIMUP - Instituto de Patologia e Imunologia Molecular da Universidade do Porto, Porto, Portugal; Doctoral Programme in Biomedicine, Faculty of Medicine, University of Porto, Porto, Portugal
| | - Rita Barbosa-Matos
- i3S - Instituto de Investigação e Inovação em Saúde, Porto, Portugal; IPATIMUP - Instituto de Patologia e Imunologia Molecular da Universidade do Porto, Porto, Portugal; International Doctoral Programme in Molecular and Cellular Biotechnology Applied to Health Sciences from Institute of Biomedical Sciences Abel Salazar (ICBAS), University of Porto, Porto, Portugal
| | - Celina São José
- i3S - Instituto de Investigação e Inovação em Saúde, Porto, Portugal; IPATIMUP - Instituto de Patologia e Imunologia Molecular da Universidade do Porto, Porto, Portugal; Doctoral Programme in Biomedicine, Faculty of Medicine, University of Porto, Porto, Portugal
| | - Sónia Sousa
- i3S - Instituto de Investigação e Inovação em Saúde, Porto, Portugal; IPATIMUP - Instituto de Patologia e Imunologia Molecular da Universidade do Porto, Porto, Portugal
| | - Irene Gullo
- i3S - Instituto de Investigação e Inovação em Saúde, Porto, Portugal; IPATIMUP - Instituto de Patologia e Imunologia Molecular da Universidade do Porto, Porto, Portugal; FMUP - Faculty of Medicine of the University of Porto, Porto, Portugal; Centro Hospitalar e Universitário S. João, Porto, Portugal
| | - Nicoline Hoogerbrugge
- Department of Human Genetics, Radboud University Medical Center, Radboud Institute for Molecular Life Sciences, Nijmegen, the Netherlands
| | - Fátima Carneiro
- i3S - Instituto de Investigação e Inovação em Saúde, Porto, Portugal; IPATIMUP - Instituto de Patologia e Imunologia Molecular da Universidade do Porto, Porto, Portugal; FMUP - Faculty of Medicine of the University of Porto, Porto, Portugal; Centro Hospitalar e Universitário S. João, Porto, Portugal
| | - Carla Oliveira
- i3S - Instituto de Investigação e Inovação em Saúde, Porto, Portugal; IPATIMUP - Instituto de Patologia e Imunologia Molecular da Universidade do Porto, Porto, Portugal; FMUP - Faculty of Medicine of the University of Porto, Porto, Portugal.
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Arruda KAR, Normando AGC, Pacheco-Pereira C, Amorim Dos Santos J, Yamaguti PM, Mazzeu JF, Almeida FT, Acevedo AC, Guerra ENS. Phenotypic dento-osseous characterization of a Brazilian family with Familial Adenomatous Polyposis. Arch Oral Biol 2021; 129:105206. [PMID: 34224960 DOI: 10.1016/j.archoralbio.2021.105206] [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: 03/09/2021] [Revised: 06/17/2021] [Accepted: 06/28/2021] [Indexed: 10/21/2022]
Abstract
OBJECTIVE To perform a phenotypic characterization of the dento-osseous anomalies in a Brazilian family with Familial Adenomatous Polyposis (FAP) and to investigate the adenomatous polyposis coli (APC) causative variant. DESIGN The study included a family of 14 individuals (Group A: affected; Group B: non-affected). The frequency of radiographic findings in both groups was evaluated according to the Dental Panoramic Radiograph Score (DPRS) diagnostic method. The accuracy and reproducibility of DPRS were tested. The DNA was isolated from the index patient's saliva and submitted to whole-exome and Sanger sequencing approach. RESULTS DPRS ≥ 7 was observed in 80 % of Group A but in none of Group B. The most common findings in Group A were dense bone islands (60 %), hazy sclerosis (40 %), osteomas (40 %), and supernumerary tooth (20 %). DPRS has proved to be a reliable method while DPRS ≥ 5 and DPRS ≥ 7 were taken as positive for FAP, and reproducible diagnosis test considering that the evaluators correctly identified the affected patients (Kappa agreement>0.8, p = 0.002). A nonsense heterozygous mutation in the APC gene (c.1370C > G; p.Ser457*) of the index case was detected. CONCLUSION FAP patients have a higher frequency of dento-osseous anomalies (p = 0.005). Bone abnormalities were more prevalent than dental anomalies (p = 0.001). Thus, FAP patients should be referred for dental examination and genetic counseling to perform early diagnosis of dento-osseous anomalies and evaluate the implications of the molecular findings in each particular family.
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Affiliation(s)
- Karen Ariely Rocha Arruda
- Laboratory of Oral Histopathology, Health Sciences Faculty and Oral Care Center for Inherited Diseases, University of Brasilia, Brasília, Brazil
| | - Ana Gabriela Costa Normando
- Laboratory of Oral Histopathology, Health Sciences Faculty and Oral Care Center for Inherited Diseases, University of Brasilia, Brasília, Brazil
| | - Camila Pacheco-Pereira
- School of Dentistry, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Canada
| | - Juliana Amorim Dos Santos
- Laboratory of Oral Histopathology, Health Sciences Faculty and Oral Care Center for Inherited Diseases, University of Brasilia, Brasília, Brazil
| | - Paulo Marcio Yamaguti
- Laboratory of Oral Histopathology, Health Sciences Faculty and Oral Care Center for Inherited Diseases, University of Brasilia, Brasília, Brazil
| | - Juliana Forte Mazzeu
- Laboratory of Clinical Genetics, Faculty of Medicine, University of Brasilia, Brasilia, Brazil
| | | | - Ana Carolina Acevedo
- Laboratory of Oral Histopathology, Health Sciences Faculty and Oral Care Center for Inherited Diseases, University of Brasilia, Brasília, Brazil
| | - Eliete Neves Silva Guerra
- Laboratory of Oral Histopathology, Health Sciences Faculty and Oral Care Center for Inherited Diseases, University of Brasilia, Brasília, Brazil.
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Zhu L, Li X, Yuan Y, Dong C, Yang M. APC Promoter Methylation in Gastrointestinal Cancer. Front Oncol 2021; 11:653222. [PMID: 33968756 PMCID: PMC8103321 DOI: 10.3389/fonc.2021.653222] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Accepted: 03/30/2021] [Indexed: 12/30/2022] Open
Abstract
The adenomatous polyposis coli (APC) gene, known as tumor suppressor gene, has the two promoters 1A and 1B. Researches on APC have usually focused on its loss-of-function variants causing familial adenomatous polyposis. Hypermethylation, however, which is one of the key epigenetic alterations of the APC CpG sequence, is also associated with carcinogenesis in various cancers. Accumulating studies have successively explored the role of APC hypermethylation in gastrointestinal (GI) tumors, such as in esophageal, colorectal, gastric, pancreatic, and hepatic cancer. In sporadic colorectal cancer, the hypermethylation of CpG island in APC is even considered as one of the primary causative factors. In this review, we systematically summarized the distribution of APC gene methylation in various GI tumors, and attempted to provide an improved general understanding of DNA methylation in GI tumors. In addition, we included a robust overview of demethylating agents available for both basic and clinical researches. Finally, we elaborated our findings and perspectives on the overall situation of APC gene methylation in GI tumors, aiming to explore the potential research directions and clinical values.
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Affiliation(s)
- Lila Zhu
- Department of Medical Oncology, Key Laboratory of Cancer Prevention and Intervention, Ministry of Education, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Xinyu Li
- Department of Medical Oncology, Key Laboratory of Cancer Prevention and Intervention, Ministry of Education, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Ying Yuan
- Department of Medical Oncology, Key Laboratory of Cancer Prevention and Intervention, Ministry of Education, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China.,Cancer Institute, Key Laboratory of Cancer Prevention and Intervention, Ministry of Education, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Caixia Dong
- Department of Medical Oncology, Key Laboratory of Cancer Prevention and Intervention, Ministry of Education, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Mengyuan Yang
- Department of Medical Oncology, Key Laboratory of Cancer Prevention and Intervention, Ministry of Education, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China.,Cancer Institute, Key Laboratory of Cancer Prevention and Intervention, Ministry of Education, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
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Disciglio V, Forte G, Fasano C, Sanese P, Lepore Signorile M, De Marco K, Grossi V, Cariola F, Simone C. APC Splicing Mutations Leading to In-Frame Exon 12 or Exon 13 Skipping Are Rare Events in FAP Pathogenesis and Define the Clinical Outcome. Genes (Basel) 2021; 12:genes12030353. [PMID: 33670833 PMCID: PMC7997234 DOI: 10.3390/genes12030353] [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: 12/31/2020] [Revised: 02/22/2021] [Accepted: 02/22/2021] [Indexed: 11/16/2022] Open
Abstract
Familial adenomatous polyposis (FAP) is caused by germline mutations in the tumor suppressor gene APC. To date, nearly 2000 APC mutations have been described in FAP, most of which are predicted to result in truncated protein products. Mutations leading to aberrant APC splicing have rarely been reported. Here, we characterized a novel germline heterozygous splice donor site mutation in APC exon 12 (NM_000038.5: c.1621_1626+7del) leading to exon 12 skipping in an Italian family with the attenuated FAP (AFAP) phenotype. Moreover, we performed a literature meta-analysis of APC splicing mutations. We found that 119 unique APC splicing mutations, including the one described here, have been reported in FAP patients, 69 of which have been characterized at the mRNA level. Among these, only a small proportion (9/69) results in an in-frame protein, with four mutations causing skipping of exon 12 or 13 with loss of armadillo repeat 2 (ARM2) and 3 (ARM3), and five mutations leading to skipping of exon 5, 7, 8, or (partially) 9 with loss of regions not encompassing known functional domains. The APC splicing mutations causing skipping of exon 12 or 13 considered in this study cluster with the AFAP phenotype and reveal a potential molecular mechanism of pathogenesis in FAP disease.
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Affiliation(s)
- Vittoria Disciglio
- Medical Genetics, National Institute of Gastroenterology “S. de Bellis” Research Hospital, Castellana Grotte, 70013 Bari, Italy; (G.F.); (C.F.); (P.S.); (M.L.S.); (K.D.M.); (V.G.); (F.C.)
- Correspondence: (V.D.); (C.S.)
| | - Giovanna Forte
- Medical Genetics, National Institute of Gastroenterology “S. de Bellis” Research Hospital, Castellana Grotte, 70013 Bari, Italy; (G.F.); (C.F.); (P.S.); (M.L.S.); (K.D.M.); (V.G.); (F.C.)
| | - Candida Fasano
- Medical Genetics, National Institute of Gastroenterology “S. de Bellis” Research Hospital, Castellana Grotte, 70013 Bari, Italy; (G.F.); (C.F.); (P.S.); (M.L.S.); (K.D.M.); (V.G.); (F.C.)
| | - Paola Sanese
- Medical Genetics, National Institute of Gastroenterology “S. de Bellis” Research Hospital, Castellana Grotte, 70013 Bari, Italy; (G.F.); (C.F.); (P.S.); (M.L.S.); (K.D.M.); (V.G.); (F.C.)
| | - Martina Lepore Signorile
- Medical Genetics, National Institute of Gastroenterology “S. de Bellis” Research Hospital, Castellana Grotte, 70013 Bari, Italy; (G.F.); (C.F.); (P.S.); (M.L.S.); (K.D.M.); (V.G.); (F.C.)
| | - Katia De Marco
- Medical Genetics, National Institute of Gastroenterology “S. de Bellis” Research Hospital, Castellana Grotte, 70013 Bari, Italy; (G.F.); (C.F.); (P.S.); (M.L.S.); (K.D.M.); (V.G.); (F.C.)
| | - Valentina Grossi
- Medical Genetics, National Institute of Gastroenterology “S. de Bellis” Research Hospital, Castellana Grotte, 70013 Bari, Italy; (G.F.); (C.F.); (P.S.); (M.L.S.); (K.D.M.); (V.G.); (F.C.)
| | - Filomena Cariola
- Medical Genetics, National Institute of Gastroenterology “S. de Bellis” Research Hospital, Castellana Grotte, 70013 Bari, Italy; (G.F.); (C.F.); (P.S.); (M.L.S.); (K.D.M.); (V.G.); (F.C.)
| | - Cristiano Simone
- Medical Genetics, National Institute of Gastroenterology “S. de Bellis” Research Hospital, Castellana Grotte, 70013 Bari, Italy; (G.F.); (C.F.); (P.S.); (M.L.S.); (K.D.M.); (V.G.); (F.C.)
- Department of Biomedical Sciences and Human Oncology (DIMO), Medical Genetics, University of Bari Aldo Moro, 70124 Bari, Italy
- Correspondence: (V.D.); (C.S.)
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Gastric adenocarcinoma and proximal polyposis of the stomach (GAPPS) - A Helicobacter-opposite point. Best Pract Res Clin Gastroenterol 2021; 50-51:101728. [PMID: 33975682 DOI: 10.1016/j.bpg.2021.101728] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Accepted: 02/08/2021] [Indexed: 01/31/2023]
Abstract
Gastric adenocarcinoma and proximal polyposis of the stomach (GAPPS) is a rare familial gastric cancer syndrome with an autosomal dominant pattern of inheritance. It is characterised by fundic gland polyposis of the gastric body and is associated with a significant risk of gastric adenocarcinoma. Unlike sporadic gastric cancer, Helicobacter pylori is usually absent in patients with GAPPS. This opposite-point finding has so far not been fully clarified. Prophylactic total gastrectomy is indicated in all cases of GAPPS with fundic gland polyposis and the presence of any dysplasia. If no dysplasia is found at histology, prophylactic gastrectomy is suggested at between 30 and 35 years of age, or at five years earlier than the age at which the youngest family member developed gastric cancer. Different phenotypes of GAPPS demand an individual approach to particular family members.
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Aitchison A, Hakkaart C, Day RC, Morrin HR, Frizelle FA, Keenan JI. APC Mutations Are Not Confined to Hotspot Regions in Early-Onset Colorectal Cancer. Cancers (Basel) 2020; 12:cancers12123829. [PMID: 33352971 PMCID: PMC7766084 DOI: 10.3390/cancers12123829] [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: 11/11/2020] [Revised: 12/07/2020] [Accepted: 12/15/2020] [Indexed: 02/07/2023] Open
Abstract
Simple Summary Mutation of the APC gene is a common early event in colorectal cancer, however lower rates have been reported in younger cohorts of colorectal cancer patients. In sporadic cancer, mutations are typically clustered around a mutation cluster region, a narrowly defined hotspot within the APC gene. In this study we used a sequencing strategy aimed at identifying mutations more widely throughout the APC gene in patients aged 50 years or under. We found high rates of APC mutation in our young cohort that were similar to rates seen in older patients but the mutations we found were spread throughout the gene in a pattern more similar to that seen in inherited rather than sporadic mutations. Our study has implications both for the sequencing of the APC gene in early-onset colorectal cancer and for the etiology of this disease. Abstract While overall colorectal cancer (CRC) cases have been declining worldwide there has been an increase in the incidence of the disease among patients under 50 years of age. Mutation of the APC gene is a common early event in CRC but is reported at lower rates in early-onset colorectal cancer (EOCRC) than in older patients. Here we investigate the APC mutation status of a cohort of EOCRC patients in New Zealand using a novel sequencing approach targeting regions of the gene encompassing the vast majority of known APC mutations. Using this strategy we find a higher rate (72%) of APC mutation than previously reported in EOCRC with mutations being spread throughout the gene rather than clustered in hotspots as seen with sporadic mutations in older patients. The rate of mutations falling within hotspots was similar to those previously seen in EOCRC and as such our study has implications for sequencing strategies for EOCRC patients. Overall there were low rates of both loss of heterozygosity and microsatellite instability whereas a relatively high rate (40%) of APC promoter methylation was found, possibly reflecting increasing exposure of young people to pro-oncogenic lifestyle factors.
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Affiliation(s)
- Alan Aitchison
- Department of Surgery, University of Otago Christchurch, Christchurch 8011, New Zealand; (F.A.F.); (J.I.K.)
- Correspondence:
| | - Christopher Hakkaart
- Mackenzie Cancer Research Group, Department of Pathology and Biomedical Science, University of Otago Christchurch, Christchurch 8011, New Zealand;
| | - Robert C. Day
- Department of Biochemistry, University of Otago, Dunedin 9054, New Zealand;
| | - Helen R. Morrin
- Cancer Society Tissue Bank, University of Otago Christchurch, Christchurch 8011, New Zealand;
| | - Frank A. Frizelle
- Department of Surgery, University of Otago Christchurch, Christchurch 8011, New Zealand; (F.A.F.); (J.I.K.)
| | - Jacqueline I. Keenan
- Department of Surgery, University of Otago Christchurch, Christchurch 8011, New Zealand; (F.A.F.); (J.I.K.)
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11
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Tanabe H, Moriichi K, Takahashi K, Ono Y, Kobayashi Y, Murakami Y, Iwama T, Kunogi T, Sasaki T, Ando K, Ueno N, Kashima S, Takei H, Mizukami Y, Fujiya M, Okumura T. Genetic alteration of colorectal adenoma-carcinoma sequence among gastric adenocarcinoma and dysplastic lesions in a patient with attenuated familial adenomatous polyposis. Mol Genet Genomic Med 2020; 8:e1348. [PMID: 32543103 PMCID: PMC7507424 DOI: 10.1002/mgg3.1348] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Revised: 05/19/2020] [Accepted: 05/21/2020] [Indexed: 12/25/2022] Open
Abstract
Background Familial adenomatous polyposis (FAP) is characterized by colorectal polyposis and adenocarcinoma that is frequently accompanied by extracolonic neoplasm. The risk of gastric carcinoma is increasing in Western FAP patients as well as Asian patients. Methods We report the case of an FAP patient with fundic gland polyposis who developed gastric adenocarcinoma and metachronous pyloric gland adenomas. These tumors were endoscopically resected, and immunohistochemistry with gastric mucin (i.e., MUC6, MUC5AC) showed that the tumors belonged to the gastric subtype. Somatic mutation profiles were determined by target amplicon sequencing using a next‐generation sequencer. Results Germline APC variant c.5782delC was found by direct sequencing and somatic KRAS mutations in these tumors were identified by next‐generation sequencing. Different KRAS mutation alleles (KRAS p.Gly12Ala, p.Gly12Arg, and p.Gly12Asp) indicated these dysplastic lesions developed from a distinct origin in fundic gland polyposis. Sequential mutations of the APC and KRAS were judged—based on a database search—to be characteristic of the adenoma‐carcinoma sequence in colorectal carcinogenesis. Conclusion The colonic adenoma‐carcinoma sequence among gastric adenocarcinoma and dysplastic lesions was indicated in FAP‐associated gastric carcinogenesis.
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Affiliation(s)
- Hiroki Tanabe
- Division of Gastroenterology and Hematology/Oncology, Department of Medicine, Asahikawa Medical University, Asahikawa, Hokkaido, Japan
| | - Kentaro Moriichi
- Division of Gastroenterology and Hematology/Oncology, Department of Medicine, Asahikawa Medical University, Asahikawa, Hokkaido, Japan
| | - Keitaro Takahashi
- Division of Gastroenterology and Hematology/Oncology, Department of Medicine, Asahikawa Medical University, Asahikawa, Hokkaido, Japan
| | - Yusuke Ono
- Institute of Biomedical Research, Sapporo-Higashi Tokushukai Hospital, Sapporo, Hokkaido, Japan
| | - Yu Kobayashi
- Division of Gastroenterology and Hematology/Oncology, Department of Medicine, Asahikawa Medical University, Asahikawa, Hokkaido, Japan
| | - Yuki Murakami
- Division of Gastroenterology and Hematology/Oncology, Department of Medicine, Asahikawa Medical University, Asahikawa, Hokkaido, Japan
| | - Takuya Iwama
- Division of Gastroenterology and Hematology/Oncology, Department of Medicine, Asahikawa Medical University, Asahikawa, Hokkaido, Japan
| | - Takehito Kunogi
- Division of Gastroenterology and Hematology/Oncology, Department of Medicine, Asahikawa Medical University, Asahikawa, Hokkaido, Japan
| | - Takahiro Sasaki
- Division of Gastroenterology and Hematology/Oncology, Department of Medicine, Asahikawa Medical University, Asahikawa, Hokkaido, Japan
| | - Katsuyoshi Ando
- Division of Gastroenterology and Hematology/Oncology, Department of Medicine, Asahikawa Medical University, Asahikawa, Hokkaido, Japan
| | - Nobuhiro Ueno
- Division of Gastroenterology and Hematology/Oncology, Department of Medicine, Asahikawa Medical University, Asahikawa, Hokkaido, Japan
| | - Shin Kashima
- Division of Gastroenterology and Hematology/Oncology, Department of Medicine, Asahikawa Medical University, Asahikawa, Hokkaido, Japan
| | - Hidehiro Takei
- Department of Diagnostic Pathology, Asahikawa Medical University, Asahikawa, Hokkaido, Japan
| | - Yusuke Mizukami
- Division of Gastroenterology and Hematology/Oncology, Department of Medicine, Asahikawa Medical University, Asahikawa, Hokkaido, Japan.,Institute of Biomedical Research, Sapporo-Higashi Tokushukai Hospital, Sapporo, Hokkaido, Japan
| | - Mikihiro Fujiya
- Division of Gastroenterology and Hematology/Oncology, Department of Medicine, Asahikawa Medical University, Asahikawa, Hokkaido, Japan
| | - Toshikatsu Okumura
- Division of Gastroenterology and Hematology/Oncology, Department of Medicine, Asahikawa Medical University, Asahikawa, Hokkaido, Japan
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12
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Li N, Kang Q, Yang L, Zhao XJ, Xue LJ, Wang X, Li AQ, Li CG, Sheng JQ. Clinical characterization and mutation spectrum in patients with familial adenomatous polyposis in China. J Gastroenterol Hepatol 2019; 34:1497-1503. [PMID: 31062380 DOI: 10.1111/jgh.14704] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Revised: 04/25/2019] [Accepted: 04/30/2019] [Indexed: 12/30/2022]
Abstract
BACKGROUND AND AIM Familial adenomatous polyposis (FAP) is the most common adenomatous polyposis syndrome. Patients with FAP are screened for germline mutations of two genes, APC and MUTYH. However, limited data exist on the clinical characterization and genotypic spectrum of FAP in China. This study was aimed to determine APC and MUTYH mutational status in a small cohort of FAP probands in China and to characterize the genotype-phenotype correlation in mutated patients. METHODS Mutation screening of 46 unrelated probands was performed using multigene panels by next-generation sequencing. Clinical data of the index were used to assess genotype-phenotype correlations. RESULTS Overall, 42 out of 46 (91.30%) unrelated probands found mutations, including 35 (76.09%) with APC mutations, 3 (6.52%) with MUTYH mutations, and 4 (8.70%) with both APC and MUTYH mutations. Ten APC genetic alterations variants were novel. The hereditary pattern of the family with both APC and MUTYH mutations was autosomal dominant inheritance. Upper gastrointestinal polyp was the most common extracolonic manifestations. The onset time for patients with both APC and MUTYH mutations was earlier than MUTYH mutation carriers and similar to APC mutation carriers. But the age of carcinogenesis for patients with both APC and MUTYH mutations was later than APC mutation carriers and similar to MUTYH mutation carriers. CONCLUSION In this study, we show the importance of using multigene panels that allow for a parallel comprehensive screening. We suggest that genetic testing of patients with suspected adenomatous polyposis syndromes should include APC and MUTYH gene mutation analyses simultaneously.
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Affiliation(s)
- Na Li
- Medical School of Chinese PLA, Beijing, China.,Department of Gastroenterology, The Seventh Medical Center of PLA General Hospital, Beijing, China
| | - Qian Kang
- Department of Gastroenterology, The Seventh Medical Center of PLA General Hospital, Beijing, China
| | - Lang Yang
- Department of Gastroenterology, The Seventh Medical Center of PLA General Hospital, Beijing, China
| | - Xiao-Jun Zhao
- Department of Gastroenterology, The Seventh Medical Center of PLA General Hospital, Beijing, China
| | - Li-Jun Xue
- Department of Gastroenterology, The Seventh Medical Center of PLA General Hospital, Beijing, China
| | - Xin Wang
- Department of Gastroenterology, The Seventh Medical Center of PLA General Hospital, Beijing, China
| | - Ai-Qin Li
- Department of Gastroenterology, The Seventh Medical Center of PLA General Hospital, Beijing, China
| | - Chen-Guang Li
- Department of Gastroenterology, The Seventh Medical Center of PLA General Hospital, Beijing, China
| | - Jian-Qiu Sheng
- Medical School of Chinese PLA, Beijing, China.,Department of Gastroenterology, The Seventh Medical Center of PLA General Hospital, Beijing, China
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13
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Rudloff U. Gastric adenocarcinoma and proximal polyposis of the stomach: diagnosis and clinical perspectives. Clin Exp Gastroenterol 2018; 11:447-459. [PMID: 30584346 PMCID: PMC6284852 DOI: 10.2147/ceg.s163227] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Gastric adenocarcinoma and proximal polyposis of the stomach (GAPPS) is a recently described, rare gastric polyposis syndrome. It is characterized by extensive involvement of the fundus and body of the stomach with fundic gland polyps sparing the antrum and lesser curvature, an autosomal dominant inheritance pattern with incomplete penetrance, and a significant predisposition for the development of gastric adenocarcinoma. Due to the recent discovery of APC promotor IB mutations (c.-191T>C, c.-192A>G, and c.-195A>C), which reduce binding of the transcription factor Yin Yang 1 (YY1) and transcriptional activity of the promotor, as its underlying genetic perturbation, GAPPS has been added to the growing molecular class of APC-associated disorders. Recent reports on family members afflicted by gastric polyposis due to GAPPS have described the development of metastatic cancer or the presence of invasive gastric adenocarcinoma in total gastrectomy specimens after variable periods of endoscopic surveillance emphasizing the need for an improved understanding of the to-date poorly characterized natural history of the syndrome. There are, however, currently no guidelines on screening, timing of prophylactic gastrectomy, or endoscopic surveillance for GAPPS available. In this review, we summarize the clinical, pathological, and genetic aspects of GAPPS as well as management approaches to this rare cancer predisposition syndrome, highlighting the need for early recognition, a multidisciplinary approach, and the creation of prospective family registries and consensus guidelines in the near future.
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Affiliation(s)
- Udo Rudloff
- Rare Tumor Initiative, Pediatric Oncology Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA,
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14
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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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15
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Macagno N, Fina F, Penel N, Bouvier C, Nanni I, Duffaud F, Rouah R, Lacarelle B, Ouafik L, Bonvalot S, Salas S. Proof of concept: prognostic value of the plasmatic concentration of circulating cell free DNA in desmoid tumors using ddPCR. Oncotarget 2018; 9:18296-18308. [PMID: 29719606 PMCID: PMC5915073 DOI: 10.18632/oncotarget.24817] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2017] [Accepted: 02/25/2018] [Indexed: 12/18/2022] Open
Abstract
Since desmoid tumors (DT) exhibit an unpredictable clinical course, with stabilization and/or spontaneous regression, an initial "wait-and-see" policy is the new standard of care-thus, the actual challenge is to identify early factors of progression. We present a method of detection of CTNNB1 mutations using a targeted digital droplet PCR (ddPCR) on cell-free DNA (cfDNA) extracted from blood samples of 31 DT patients. Furthermore, we analyzed the correlation between DT evolution and plasmatic concentration of total and mutated cfDNA at the time of diagnosis. Circulating copies of CTNNB1 mutants (ctDNA) were detected in the plasma of 6 patients (33%) but their concentration was not correlated with evolution of the tumor. Concentration of total cfDNA was higher in the plasma of patients with progressive desmoids (p = 0,0009). Using a threshold <900 copies/mL of plasma to detect indolent desmoid and a threshold >1375, it was possible to predict desmoid evolution for 65% of patients by measuring the quantity of circulating DNA in their plasma as early as the time of diagnosis. Albeit showing that the detection of CTNNB1 mutants is possible in the plasma of patients harboring a desmoid tumor, the results of this preliminary study raise the hypothesis that most of the circulating DNA detected in their plasma is derived from non-neoplastic cells, most likely normal neighboring tissues being actively invaded. Our results open the perspective of using cfDNA as a biomarker to predict prognosis at the time of diagnosis and assess tumor dynamics to optimize the treatment strategy.
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Affiliation(s)
- Nicolas Macagno
- Department of Pathology, Assistance Publique Hôpitaux de Marseille Timone Hospital, Marseille, France.,Aix-Marseille University, Medical Faculty, CRO2, UMR 911 (Equipe IV), Marseille, France
| | - Frédéric Fina
- Department of Pathology, Assistance Publique Hôpitaux de Marseille Timone Hospital, Marseille, France.,ID-Solutions, Grabels, France
| | - Nicolas Penel
- Department of General Oncology, Oscar Lambret Center, Lille, France
| | - Corinne Bouvier
- Department of Pathology, Assistance Publique Hôpitaux de Marseille Timone Hospital, Marseille, France.,Aix-Marseille University, Medical Faculty, CRO2, UMR 911 (Equipe IV), Marseille, France
| | - Isabelle Nanni
- Department of Molecular Oncology, Assistance Publique Hôpitaux de Marseille, Marseille, France
| | - Florence Duffaud
- Department of Oncology, Assistance Publique Hôpitaux de Marseille Timone Hospital, Marseille, France.,Aix-Marseille University, Medical Faculty, Marseille, France
| | - Raquel Rouah
- Department of Molecular Oncology, Assistance Publique Hôpitaux de Marseille, Marseille, France
| | - Bruno Lacarelle
- Department of Medical Biology, Assistance Publique Hôpitaux de Marseille Timone Hospital, Marseille, France
| | - L'houcine Ouafik
- Department of Molecular Oncology, Assistance Publique Hôpitaux de Marseille, Marseille, France
| | - Sylvie Bonvalot
- Department of Surgery, Institut Curie, PSL Univeristy, Paris, France
| | - Sébastien Salas
- Department of Oncology, Assistance Publique Hôpitaux de Marseille Timone Hospital, Marseille, France.,Aix-Marseille University, Medical Faculty, Marseille, France
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16
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Yanus G, Akhapkina T, Ivantsov A, Preobrazhenskaya E, Aleksakhina S, Bizin I, Sokolenko A, Mitiushkina N, Kuligina E, Suspitsin E, Venina A, Holmatov M, Zaitseva O, Yatsuk O, Pashkov D, Belyaev A, Togo A, Imyanitov E, Iyevleva A. Spectrum of APC and MUTYH germ-line mutations in Russian patients with colorectal malignancies. Clin Genet 2018; 93:1015-1021. [DOI: 10.1111/cge.13228] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2017] [Revised: 01/28/2018] [Accepted: 01/31/2018] [Indexed: 12/14/2022]
Affiliation(s)
- G.A. Yanus
- N.N. Petrov Institute of Oncology, Laboratory of Molecular Oncology; St.-Petersburg 197758 Russia
- St.-Petersburg Pediatric Medical University, Department of Medical Genetics; St.-Petersburg 194100 Russia
| | - T.A. Akhapkina
- N.N. Petrov Institute of Oncology, Laboratory of Molecular Oncology; St.-Petersburg 197758 Russia
- St.-Petersburg Pediatric Medical University, Department of Medical Genetics; St.-Petersburg 194100 Russia
| | - A.O. Ivantsov
- N.N. Petrov Institute of Oncology, Laboratory of Molecular Oncology; St.-Petersburg 197758 Russia
- St.-Petersburg Pediatric Medical University, Department of Medical Genetics; St.-Petersburg 194100 Russia
| | - E.V. Preobrazhenskaya
- N.N. Petrov Institute of Oncology, Laboratory of Molecular Oncology; St.-Petersburg 197758 Russia
- St.-Petersburg Pediatric Medical University, Department of Medical Genetics; St.-Petersburg 194100 Russia
| | - S.N. Aleksakhina
- N.N. Petrov Institute of Oncology, Laboratory of Molecular Oncology; St.-Petersburg 197758 Russia
| | - I.V. Bizin
- Peter the Great St.-Petersburg Polytechnic University, Department of Bioinformatics; St.-Petersburg 195251 Russia
| | - A.P. Sokolenko
- N.N. Petrov Institute of Oncology, Laboratory of Molecular Oncology; St.-Petersburg 197758 Russia
- St.-Petersburg Pediatric Medical University, Department of Medical Genetics; St.-Petersburg 194100 Russia
| | - N.V. Mitiushkina
- N.N. Petrov Institute of Oncology, Laboratory of Molecular Oncology; St.-Petersburg 197758 Russia
| | - E.Sh. Kuligina
- N.N. Petrov Institute of Oncology, Laboratory of Molecular Oncology; St.-Petersburg 197758 Russia
| | - E.N. Suspitsin
- N.N. Petrov Institute of Oncology, Laboratory of Molecular Oncology; St.-Petersburg 197758 Russia
- St.-Petersburg Pediatric Medical University, Department of Medical Genetics; St.-Petersburg 194100 Russia
| | - A.R. Venina
- N.N. Petrov Institute of Oncology, Laboratory of Molecular Oncology; St.-Petersburg 197758 Russia
| | - M.M. Holmatov
- N.N. Petrov Institute of Oncology, Laboratory of Molecular Oncology; St.-Petersburg 197758 Russia
- St.-Petersburg Pediatric Medical University, Department of Medical Genetics; St.-Petersburg 194100 Russia
| | - O.A. Zaitseva
- N.N. Petrov Institute of Oncology, Laboratory of Molecular Oncology; St.-Petersburg 197758 Russia
| | - O.S. Yatsuk
- N.N. Petrov Institute of Oncology, Laboratory of Molecular Oncology; St.-Petersburg 197758 Russia
| | - D.V. Pashkov
- S.M. Kirov Military Medical Academy, Department of Surgery; St.-Petersburg 194044 Russia
| | - A.M. Belyaev
- N.N. Petrov Institute of Oncology, Laboratory of Molecular Oncology; St.-Petersburg 197758 Russia
- S.M. Kirov Military Medical Academy, Department of Surgery; St.-Petersburg 194044 Russia
| | - A.V. Togo
- N.N. Petrov Institute of Oncology, Laboratory of Molecular Oncology; St.-Petersburg 197758 Russia
| | - E.N. Imyanitov
- N.N. Petrov Institute of Oncology, Laboratory of Molecular Oncology; St.-Petersburg 197758 Russia
- St.-Petersburg Pediatric Medical University, Department of Medical Genetics; St.-Petersburg 194100 Russia
- I.I. Mechnikov North-Western Medical University, Department of Oncology; St.-Petersburg 191015 Russia
- St.-Petersburg State University, Faculty of Medicine, Department of Oncology; St.-Petersburg 199034 Russia
| | - A.G. Iyevleva
- N.N. Petrov Institute of Oncology, Laboratory of Molecular Oncology; St.-Petersburg 197758 Russia
- St.-Petersburg Pediatric Medical University, Department of Medical Genetics; St.-Petersburg 194100 Russia
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17
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Neoplastic Lesions of Gastric Adenocarcinoma and Proximal Polyposis Syndrome (GAPPS) Are Gastric Phenotype. Am J Surg Pathol 2017; 42:1-8. [PMID: 29112017 DOI: 10.1097/pas.0000000000000924] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Neoplastic lesions of gastric adenocarcinoma and proximal polyposis of the stomach (GAPPS) are gastric phenotype. GAPPS was reported in 2011 as a new autosomal dominant gastric polyposis syndrome characterized by involvement of the gastric body/fundus with sparing of the antrum by multiple polyps, reported to be primarily fundic gland polyps (FGPs), with progression to dysplasia and adenocarcinoma of intestinal type. Our series consists of 51 endoscopic biopsies and 5 gastrectomy specimens from 25 patients belonging to a previously defined GAPPS family. Slides were reviewed and further stains performed. Endoscopy was abnormal in 15 of the 25 patients: carpeting polyposis of the gastric body and fundus in 14 and a gastric mass without polyposis in one. The most common polypoid lesion (seen in 12 patients) was a disorganized proliferation of specialized/oxyntic glands high up in the mucosa involving the attenuated foveolar region around the gastric pits, which we have termed "hyperproliferative aberrant pits". Well developed FGP were seen in 10 patients. Established neoplastic lesions seen in 9 patients were: (1) discrete gastric adenomas, (2) multifocal "flat" dysplasia in the setting of hyperproliferative aberrant pits +/- FGPs, (3) adenomatous tissue associated with adenocarcinoma. All cases of dysplasia were of gastric phenotype based on morphology and mucin immunohistochemistry. IN CONCLUSION (1) the spectrum of gastric pathology associated with GAPPS is wider than previously reported, (2) the earliest microscopic clue is the finding of hyperproliferative aberrant pits, and (3) the dysplasia is gastric phenotype and the subsequent adenocarcinoma may follow the gastric pathway of carcinogenesis.
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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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Lopez NE, Peterson CY. Advances in Biomarkers: Going Beyond the Carcinoembryonic Antigen. Clin Colon Rectal Surg 2016; 29:196-204. [PMID: 27582644 DOI: 10.1055/s-0036-1584289] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Using biologically available markers to guide treatment decisions in colorectal cancer care is becoming increasingly common, though our understanding of these biomarkers is in its infancy. In this article, we will discuss how this area is rapidly changing, review important biomarkers being used currently, and explain how the results influence clinical decision-making. We will also briefly discuss the possibility of a liquid biopsy and explore several exciting and new options.
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Affiliation(s)
- Nicole E Lopez
- Division of Surgical Oncology, University of North Carolina, Chapel Hill, North Carolina
| | - Carrie Y Peterson
- Division of Colorectal Surgery, Medical College of Wisconsin, Milwaukee, Wisconsin
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Abstract
BACKGROUND Patients with multiple colorectal adenomas (MCRA) without genetic cause are increasingly being diagnosed. The characteristics and natural history of this condition are not well studied. MATERIALS AND METHODS Twenty-seven patients with MCRA, with cumulatively 10 to 99 colorectal adenomas and without deleterious mutations of APC or MYH genes, were investigated. Results of colonoscopies with a mean follow-up of 4.9 years (range, 0 to 27 y) were evaluated. Findings from esophagogastroduodenoscopy and extracolonic manifestations were assessed. RESULTS The mean age at polyp diagnosis and MCRA diagnosis was 47.8±13.1 years (range, 21 to 72 y) and 50.4±14.6 years (range, 21 to 72 y), respectively. In 22% of patients another family member had MCRA. At first colonoscopy, the mean number of adenomas was 35.0±35.9 (range, 0 to 99). Serrated polyps were rare. Esophagogastroduodenoscopy revealed 47% of patients had upper tract neoplasia. Patients with upper tract findings were diagnosed with MCRA at significantly younger mean age than those without findings, P<0.05. Eighteen patients (67%) underwent colectomy with a mean time from diagnosis of MCRA of 3.1±1.3 years. After surgery, surveyed patients developed recurrent adenomas in retained colorectum. Nine patients (33%) had extracolonic cancers. CONCLUSIONS MCRA patients have a similar clinicopathologic phenotype to known syndromes of attenuated adenomatous polyposis and the majority have need for colectomy. The management of MCRA patients and families should parallel that of attenuated familial adenomatous polyposis and MUTYH-associated polyposis including surveillance of the upper tract.
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Li J, Woods SL, Healey S, Beesley J, Chen X, Lee JS, Sivakumaran H, Wayte N, Nones K, Waterfall JJ, Pearson J, Patch AM, Senz J, Ferreira MA, Kaurah P, Mackenzie R, Heravi-Moussavi A, Hansford S, Lannagan TRM, Spurdle AB, Simpson PT, da Silva L, Lakhani SR, Clouston AD, Bettington M, Grimpen F, Busuttil RA, Di Costanzo N, Boussioutas A, Jeanjean M, Chong G, Fabre A, Olschwang S, Faulkner GJ, Bellos E, Coin L, Rioux K, Bathe OF, Wen X, Martin HC, Neklason DW, Davis SR, Walker RL, Calzone KA, Avital I, Heller T, Koh C, Pineda M, Rudloff U, Quezado M, Pichurin PN, Hulick PJ, Weissman SM, Newlin A, Rubinstein WS, Sampson JE, Hamman K, Goldgar D, Poplawski N, Phillips K, Schofield L, Armstrong J, Kiraly-Borri C, Suthers GK, Huntsman DG, Foulkes WD, Carneiro F, Lindor NM, Edwards SL, French JD, Waddell N, Meltzer PS, Worthley DL, Schrader KA, Chenevix-Trench G. Point Mutations in Exon 1B of APC Reveal Gastric Adenocarcinoma and Proximal Polyposis of the Stomach as a Familial Adenomatous Polyposis Variant. Am J Hum Genet 2016; 98:830-842. [PMID: 27087319 DOI: 10.1016/j.ajhg.2016.03.001] [Citation(s) in RCA: 138] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2016] [Accepted: 03/02/2016] [Indexed: 12/15/2022] Open
Abstract
Gastric adenocarcinoma and proximal polyposis of the stomach (GAPPS) is an autosomal-dominant cancer-predisposition syndrome with a significant risk of gastric, but not colorectal, adenocarcinoma. We mapped the gene to 5q22 and found loss of the wild-type allele on 5q in fundic gland polyps from affected individuals. Whole-exome and -genome sequencing failed to find causal mutations but, through Sanger sequencing, we identified point mutations in APC promoter 1B that co-segregated with disease in all six families. The mutations reduced binding of the YY1 transcription factor and impaired activity of the APC promoter 1B in luciferase assays. Analysis of blood and saliva from carriers showed allelic imbalance of APC, suggesting that these mutations lead to decreased allele-specific expression in vivo. Similar mutations in APC promoter 1B occur in rare families with familial adenomatous polyposis (FAP). Promoter 1A is methylated in GAPPS and sporadic FGPs and in normal stomach, which suggests that 1B transcripts are more important than 1A in gastric mucosa. This might explain why all known GAPPS-affected families carry promoter 1B point mutations but only rare FAP-affected families carry similar mutations, the colonic cells usually being protected by the expression of the 1A isoform. Gastric polyposis and cancer have been previously described in some FAP-affected individuals with large deletions around promoter 1B. Our finding that GAPPS is caused by point mutations in the same promoter suggests that families with mutations affecting the promoter 1B are at risk of gastric adenocarcinoma, regardless of whether or not colorectal polyps are present.
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Affiliation(s)
- Jun Li
- Department of Genetics and Computational Biology, QIMR Berghofer, Herston, QLD 4029, Australia
| | - Susan L Woods
- School of Medicine, University of Adelaide and Cancer Theme, SAHMRI, Adelaide, SA 5000, Australia
| | - Sue Healey
- Department of Genetics and Computational Biology, QIMR Berghofer, Herston, QLD 4029, Australia
| | - Jonathan Beesley
- Department of Genetics and Computational Biology, QIMR Berghofer, Herston, QLD 4029, Australia
| | - Xiaoqing Chen
- Department of Genetics and Computational Biology, QIMR Berghofer, Herston, QLD 4029, Australia
| | - Jason S Lee
- Department of Genetics and Computational Biology, QIMR Berghofer, Herston, QLD 4029, Australia
| | - Haran Sivakumaran
- Department of Genetics and Computational Biology, QIMR Berghofer, Herston, QLD 4029, Australia
| | - Nicci Wayte
- Department of Genetics and Computational Biology, QIMR Berghofer, Herston, QLD 4029, Australia
| | - Katia Nones
- Department of Genetics and Computational Biology, QIMR Berghofer, Herston, QLD 4029, Australia
| | - Joshua J Waterfall
- Genetics Branch, Center for Cancer Research (CCR), National Cancer Institute (NCI), NIH, Bethesda, MD 20892, USA
| | - John Pearson
- Department of Genetics and Computational Biology, QIMR Berghofer, Herston, QLD 4029, Australia; Institute for Molecular Bioscience, The University of Queensland, St Lucia, QLD 4072, Australia
| | - Anne-Marie Patch
- Department of Genetics and Computational Biology, QIMR Berghofer, Herston, QLD 4029, Australia
| | - Janine Senz
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC V6T 2B5, Canada
| | - Manuel A Ferreira
- Department of Genetics and Computational Biology, QIMR Berghofer, Herston, QLD 4029, Australia
| | - Pardeep Kaurah
- Department of Medical Genetics, University of British Columbia, Vancouver, BC V6H 3N1, Canada
| | - Robertson Mackenzie
- Department of Molecular Oncology, BC Cancer Research Centre, Vancouver, BC V5Z 1L3, Canada
| | | | - Samantha Hansford
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC V6T 2B5, Canada
| | - Tamsin R M Lannagan
- School of Medicine, University of Adelaide and Cancer Theme, SAHMRI, Adelaide, SA 5000, Australia
| | - Amanda B Spurdle
- Department of Genetics and Computational Biology, QIMR Berghofer, Herston, QLD 4029, Australia
| | - Peter T Simpson
- UQ Centre for Clinical Research, The University of Queensland, Brisbane, QLD 4029, Australia; School of Medicine, The University of Queensland, Brisbane, QLD 4006, Australia
| | - Leonard da Silva
- UQ Centre for Clinical Research, The University of Queensland, Brisbane, QLD 4029, Australia; School of Medicine, The University of Queensland, Brisbane, QLD 4006, Australia
| | - Sunil R Lakhani
- UQ Centre for Clinical Research, The University of Queensland, Brisbane, QLD 4029, Australia; School of Medicine, The University of Queensland, Brisbane, QLD 4006, Australia; Anatomical Pathology, Pathology Queensland, Royal Brisbane and Women's Hospital, Brisbane, QLD 4029, Australia
| | - Andrew D Clouston
- Centre for Liver Disease Research, TRI Building, University of Queensland, Woolloongabba, QLD 4102, Australia; Envoi Specialist Pathologists, Bishop Street, Kelvin Grove, QLD 4059, Australia
| | - Mark Bettington
- School of Medicine, The University of Queensland, Brisbane, QLD 4006, Australia; Envoi Specialist Pathologists, Bishop Street, Kelvin Grove, QLD 4059, Australia; The Conjoint Gastroenterology Laboratory, QIMR Berghofer, Herston, QLD 4029, Australia
| | - Florian Grimpen
- Departments of Gastroenterology and Hepatology, Royal Brisbane and Women's Hospital, Brisbane, QLD 4006, Australia
| | - Rita A Busuttil
- Cancer Genetics and Genomics Laboratory, Peter MacCallum Cancer Centre, Locked Bag 1, Melbourne, VIC 8006, Australia; Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, VIC 3010, Australia; Department of Medicine, Royal Melbourne Hospital, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Natasha Di Costanzo
- Cancer Genetics and Genomics Laboratory, Peter MacCallum Cancer Centre, Locked Bag 1, Melbourne, VIC 8006, Australia
| | - Alex Boussioutas
- Cancer Genetics and Genomics Laboratory, Peter MacCallum Cancer Centre, Locked Bag 1, Melbourne, VIC 8006, Australia; Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, VIC 3010, Australia; Department of Medicine, Royal Melbourne Hospital, The University of Melbourne, Parkville, VIC 3010, Australia; Department of Gastroenterology, Royal Melbourne Hospital, Parkville, VIC 3010, Australia
| | - Marie Jeanjean
- Lady Davis Institute, Segal Cancer Centre, Jewish General Hospital, Montreal, QC H3T 1E2, Canada
| | - George Chong
- Molecular Pathology Centre, Department of Pathology, Jewish General Hospital - McGill University, Montreal, QC H3T 1E2, Canada
| | - Aurélie Fabre
- AP-HM Timone, Medical Genetics Department, 13385 Marseille, France; Aix Marseille Université, INSERM, GMGF UMR_S 910, 13385 Marseille, France; Oncology Unit, Generale de Sante, Clairval Hospital, 13009 Marseille, France
| | - Sylviane Olschwang
- AP-HM Timone, Medical Genetics Department, 13385 Marseille, France; Aix Marseille Université, INSERM, GMGF UMR_S 910, 13385 Marseille, France; Oncology Unit, Generale de Sante, Clairval Hospital, 13009 Marseille, France
| | - Geoffrey J Faulkner
- Mater Research Institute, University of Queensland, TRI Building, Woolloongabba, QLD 4102, Australia
| | - Evangelos Bellos
- Institute for Molecular Bioscience, The University of Queensland, St Lucia, QLD 4072, Australia; Department of Genomics of Common Disease, Imperial College London, London W12 0NN, UK
| | - Lachlan Coin
- Institute for Molecular Bioscience, The University of Queensland, St Lucia, QLD 4072, Australia
| | - Kevin Rioux
- Department of Medicine, Division of Gastroenterology, Department of Microbiology and Infectious Diseases, Gastrointestinal Research Group, University of Calgary, Calgary, AB T2N 4N1, Canada
| | - Oliver F Bathe
- Departments of Surgery and Oncology, University of Calgary, Calgary, AB T2N 4N1, Canada; Division of Surgical Oncology, Tom Baker Cancer Centre, 1331 29(th) St NW, Calgary, AB T2N 4N1, Canada
| | - Xiaogang Wen
- Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP)/Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto 4200-135, Portugal; Centro Hospitalar Vila Nova de Gaia/Espinho, Porto 4430-027, Portugal
| | - Hilary C Martin
- Wellcome Trust Centre for Human Genetics, Oxford OX3 7BN, UK
| | - Deborah W Neklason
- Department of Internal Medicine, Huntsman Cancer Institute at University of Utah, Salt Lake City, UT 84112, USA
| | - Sean R Davis
- Genetics Branch, Center for Cancer Research (CCR), National Cancer Institute (NCI), NIH, Bethesda, MD 20892, USA
| | - Robert L Walker
- Genetics Branch, Center for Cancer Research (CCR), National Cancer Institute (NCI), NIH, Bethesda, MD 20892, USA
| | - Kathleen A Calzone
- Genetics Branch, Center for Cancer Research (CCR), National Cancer Institute (NCI), NIH, Bethesda, MD 20892, USA
| | - Itzhak Avital
- Department of Surgery, Saint Peter's University Hospital, Rutgers University, New Brunswick, NJ 08901, USA
| | - Theo Heller
- Liver Diseases Branch, National Institute of Diabetes and Digestive and Kidney Disease (NIDDK), NIH, Bethesda, MD 20892, USA
| | - Christopher Koh
- Liver Diseases Branch, National Institute of Diabetes and Digestive and Kidney Disease (NIDDK), NIH, Bethesda, MD 20892, USA
| | - Marbin Pineda
- Genetics Branch, Center for Cancer Research (CCR), National Cancer Institute (NCI), NIH, Bethesda, MD 20892, USA
| | - Udo Rudloff
- Thoracic and Gastrointestinal Oncology Branch, Center for Cancer Research (CCR), National Cancer Institute (NCI), NIH, Bethesda, MD 20892, USA
| | - Martha Quezado
- Laboratory of Pathology, Center for Cancer Research (CCR), National Cancer Institute (NCI), NIH, Bethesda, MD 20892, USA
| | - Pavel N Pichurin
- Department of Medical Genetics, Mayo Clinic, Rochester, MN 55905, USA
| | - Peter J Hulick
- Center for Medical Genetics, NorthShore University HealthSystem, Evanston, IL 60201, USA
| | | | - Anna Newlin
- Center for Medical Genetics, NorthShore University HealthSystem, Evanston, IL 60201, USA
| | - Wendy S Rubinstein
- National Center for Biotechnology Information (NCBI), National Library of Medicine (NLM), NIH, Bethesda, MD 20892, USA
| | - Jone E Sampson
- Department of Molecular and Medical Genetics, Oregon Health & Science University, Portland, OR 97239, USA
| | - Kelly Hamman
- Department of Molecular and Medical Genetics, Oregon Health & Science University, Portland, OR 97239, USA
| | - David Goldgar
- Department of Dermatology and Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | - Nicola Poplawski
- Adult Genetics Unit, SA Pathology at the Women's and Children's Hospital, North Adelaide, SA 5006, Australia; University Department of Paediatrics, University of Adelaide, Adelaide, SA 5005, Australia
| | - Kerry Phillips
- Adult Genetics Unit, SA Pathology at the Women's and Children's Hospital, North Adelaide, SA 5006, Australia; University Department of Paediatrics, University of Adelaide, Adelaide, SA 5005, Australia
| | - Lyn Schofield
- Genetic Services of Western Australia, King Edward Memorial Hospital, Subiaco, WA 6008, Australia
| | - Jacqueline Armstrong
- Adult Genetics Unit, SA Pathology at the Women's and Children's Hospital, North Adelaide, SA 5006, Australia
| | - Cathy Kiraly-Borri
- Genetic Services of Western Australia, King Edward Memorial Hospital, Subiaco, WA 6008, Australia
| | - Graeme K Suthers
- University Department of Paediatrics, University of Adelaide, Adelaide, SA 5005, Australia
| | - David G Huntsman
- Department of Molecular Oncology, BC Cancer Research Centre, Vancouver, BC V5Z 1L3, Canada; Department of Pathology and Obstetrics and Gynaecology, University of British Columbia, Vancouver, BC V6Z 2K5, Canada
| | - William D Foulkes
- Lady Davis Institute, Segal Cancer Centre, Jewish General Hospital, Montreal, QC H3T 1E2, Canada; Program in Cancer Genetics, Departments of Oncology and Human Genetics, McGill University, Montreal, QC H3A 1B1, Canada
| | - Fatima Carneiro
- Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP)/Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto 4200-135, Portugal; Medical Faculty of the University of Porto/Centro Hospitalar São João, Porto 4200-319, Portugal
| | - Noralane M Lindor
- Department of Health Sciences Research, Mayo Clinic, Scottsdale, AZ 85259, USA
| | - Stacey L Edwards
- Department of Genetics and Computational Biology, QIMR Berghofer, Herston, QLD 4029, Australia
| | - Juliet D French
- Department of Genetics and Computational Biology, QIMR Berghofer, Herston, QLD 4029, Australia
| | - Nicola Waddell
- Department of Genetics and Computational Biology, QIMR Berghofer, Herston, QLD 4029, Australia; Institute for Molecular Bioscience, The University of Queensland, St Lucia, QLD 4072, Australia
| | - Paul S Meltzer
- Genetics Branch, Center for Cancer Research (CCR), National Cancer Institute (NCI), NIH, Bethesda, MD 20892, USA
| | - Daniel L Worthley
- School of Medicine, University of Adelaide and Cancer Theme, SAHMRI, Adelaide, SA 5000, Australia
| | - Kasmintan A Schrader
- Department of Medical Genetics, University of British Columbia, Vancouver, BC V6H 3N1, Canada; Department of Molecular Oncology, BC Cancer Research Centre, Vancouver, BC V5Z 1L3, Canada
| | - Georgia Chenevix-Trench
- Department of Genetics and Computational Biology, QIMR Berghofer, Herston, QLD 4029, Australia.
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High-resolution melting (HRM) re-analysis of a polyposis patients cohort reveals previously undetected heterozygous and mosaic APC gene mutations. Fam Cancer 2016; 14:247-57. [PMID: 25604157 PMCID: PMC4430602 DOI: 10.1007/s10689-015-9780-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Familial adenomatous polyposis is most frequently caused by pathogenic variants in either the APC gene or the MUTYH gene. The detection rate of pathogenic variants depends on the severity of the phenotype and sensitivity of the screening method, including sensitivity for mosaic variants. For 171 patients with multiple colorectal polyps without previously detectable pathogenic variant, APC was reanalyzed in leukocyte DNA by one uniform technique: high-resolution melting (HRM) analysis. Serial dilution of heterozygous DNA resulted in a lowest detectable allelic fraction of 6 % for the majority of variants. HRM analysis and subsequent sequencing detected pathogenic fully heterozygous APC variants in 10 (6 %) of the patients and pathogenic mosaic variants in 2 (1 %). All these variants were previously missed by various conventional scanning methods. In parallel, HRM APC scanning was applied to DNA isolated from polyp tissue of two additional patients with apparently sporadic polyposis and without detectable pathogenic APC variant in leukocyte DNA. In both patients a pathogenic mosaic APC variant was present in multiple polyps. The detection of pathogenic APC variants in 7 % of the patients, including mosaics, illustrates the usefulness of a complete APC gene reanalysis of previously tested patients, by a supplementary scanning method. HRM is a sensitive and fast pre-screening method for reliable detection of heterozygous and mosaic variants, which can be applied to leukocyte and polyp derived DNA.
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23
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Spier I, Drichel D, Kerick M, Kirfel J, Horpaopan S, Laner A, Holzapfel S, Peters S, Adam R, Zhao B, Becker T, Lifton RP, Perner S, Hoffmann P, Kristiansen G, Timmermann B, Nöthen MM, Holinski-Feder E, Schweiger MR, Aretz S. Low-level APC mutational mosaicism is the underlying cause in a substantial fraction of unexplained colorectal adenomatous polyposis cases. J Med Genet 2015; 53:172-9. [PMID: 26613750 DOI: 10.1136/jmedgenet-2015-103468] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2015] [Accepted: 10/22/2015] [Indexed: 12/20/2022]
Abstract
BACKGROUND In 30-50% of patients with colorectal adenomatous polyposis, no germline mutation in the known genes APC, causing familial adenomatous polyposis, MUTYH, causing MUTYH-associated polyposis, or POLE or POLD1, causing polymerase-proofreading-associated polyposis can be identified, although a hereditary aetiology is likely. This study aimed to explore the impact of APC mutational mosaicism in unexplained polyposis. METHODS To comprehensively screen for somatic low-level APC mosaicism, high-coverage next-generation sequencing of the APC gene was performed using DNA from leucocytes and a total of 53 colorectal tumours from 20 unrelated patients with unexplained sporadic adenomatous polyposis. APC mosaicism was assumed if the same loss-of-function APC mutation was present in ≥ 2 anatomically separated colorectal adenomas/carcinomas per patient. All mutations were validated using diverse methods. RESULTS In 25% (5/20) of patients, somatic mosaicism of a pathogenic APC mutation was identified as underlying cause of the disease. In 2/5 cases, the mosaic level in leucocyte DNA was slightly below the sensitivity threshold of Sanger sequencing; while in 3/5 cases, the allelic fraction was either very low (0.1-1%) or no mutations were detectable. The majority of mosaic mutations were located outside the somatic mutation cluster region of the gene. CONCLUSIONS The present data indicate a high prevalence of pathogenic mosaic APC mutations below the detection thresholds of routine diagnostics in adenomatous polyposis, even if high-coverage sequencing of leucocyte DNA alone is taken into account. This has important implications for both routine work-up and strategies to identify new causative genes in this patient group.
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Affiliation(s)
- Isabel Spier
- Institute of Human Genetics, University of Bonn, Bonn, Germany Center for Hereditary Tumor Syndromes, University of Bonn, Bonn, Germany
| | - Dmitriy Drichel
- German Center for Neurodegenerative Diseases (DZNE), 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
| | - Jutta Kirfel
- Center for Hereditary Tumor Syndromes, University of Bonn, Bonn, Germany Institute of Pathology, University of Bonn, Bonn, Germany
| | - Sukanya Horpaopan
- Institute of Human Genetics, University of Bonn, Bonn, Germany Department of Anatomy, Faculty of Medical Science, Naresuan University, Phitsanulok, Thailand
| | - Andreas Laner
- Medizinische Klinik-Campus Innenstadt, Klinikum der LMU, Munich, Germany MGZ-Center of Medical Genetics, Munich, Germany
| | - Stefanie Holzapfel
- Institute of Human Genetics, University of Bonn, Bonn, Germany Center for Hereditary Tumor Syndromes, University of Bonn, Bonn, Germany
| | - Sophia Peters
- Institute of Human Genetics, University of Bonn, Bonn, Germany
| | - Ronja Adam
- Institute of Human Genetics, University of Bonn, 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, Connecticut, 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, Connecticut, USA
| | - Sven Perner
- Section for Prostate Cancer Research, Institute of Pathology, Center for Integrated Oncology Cologne/Bonn, University Hospital of Bonn, Bonn, Germany
| | - Per Hoffmann
- Institute of Human Genetics, University of Bonn, Bonn, Germany Department of Genomics, Life & Brain Center, University of Bonn, Bonn, Germany Division of Medical Genetics, University Hospital Basel and Department of Biomedicine, University of Basel, Basel, Switzerland
| | - Glen Kristiansen
- Center for Hereditary Tumor Syndromes, University of Bonn, Bonn, Germany Institute of Pathology, University of Bonn, Bonn, Germany
| | - Bernd Timmermann
- Next Generation Sequencing Group, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Markus M Nöthen
- Institute of Human Genetics, University of Bonn, Bonn, Germany Department of Genomics, Life & Brain Center, University of Bonn, Bonn, Germany
| | - Elke Holinski-Feder
- Medizinische Klinik-Campus Innenstadt, Klinikum der LMU, Munich, Germany MGZ-Center of Medical Genetics, Munich, 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, Bonn, Germany Center for Hereditary Tumor Syndromes, University of Bonn, Bonn, Germany
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Mutation spectrum in the Wnt/β-catenin signaling pathway in gastric fundic gland-associated neoplasms/polyps. Virchows Arch 2015; 467:27-38. [PMID: 25820416 DOI: 10.1007/s00428-015-1753-4] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2014] [Revised: 02/05/2015] [Accepted: 03/06/2015] [Indexed: 01/02/2023]
Abstract
Frequent activation of the Wnt/β-catenin signaling pathway has recently been demonstrated in gastric adenocarcinoma/neoplasia of chief cell predominant type (GA-CCP/GN-CCP) with submucosal involvement. In this study, we examined the activation status of the Wnt/β-catenin signaling pathway in GN-CCP without submucosal involvement, which is referred to as gastric dysplasia-CCP (GD-CCP). We also examined β-catenin expression and the mutation spectrum of PPP2R1A and Wnt pathway genes in 11 cases of GD-CCP, 25 cases of gastric polyps of fundic gland type (GPs-FG), and 21 cases of GPs-FG with dysplasia (GP-FGD). β-catenin nuclear staining was observed in 3 cases of GD-CCP, none of GPs-FG, and 6 cases of GPs-FGD. Mutations in Wnt pathway genes, including PPP2R1A, were observed in 4 cases of GDs-CCP, 10 cases of GPs-FG, and 7 cases of GPs-FGD. Two of these seven GPs-FGD cases showed β-catenin nuclear staining. However, none of the 4 GD-CCP cases with mutations or the 10 GPs-FG cases with mutations showed β-catenin nuclear staining. PPP2R1A mutations were observed in 1 GD-CCP case and 1 GPs-FGD case. Although the mutation spectra of the Wnt pathway genes in GD-CCP and GP-FG differed, based on the absence of β-catenin nuclear staining despite the genetic alterations, GD-CCP is more similar to GP-FG than to GN-CCP, which shows β-catenin nuclear staining and submucosal involvement. Activation of the Wnt/β-catenin signaling by the β-catenin nuclear transition may be required during progression from GD-CCP to GN-CCP. Furthermore, this is the first report describing PPP2R1A mutations in gastric fundic gland-associated neoplasms.
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25
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Aretz S, Vasen HFA, Olschwang S. Clinical Utility Gene Card for: Familial adenomatous polyposis (FAP) and attenuated FAP (AFAP)--update 2014. Eur J Hum Genet 2014; 23:ejhg2014193. [PMID: 25248397 DOI: 10.1038/ejhg.2014.193] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2014] [Revised: 07/08/2014] [Accepted: 08/21/2014] [Indexed: 11/09/2022] Open
Affiliation(s)
- Stefan Aretz
- Institute of Human Genetics, University of Bonn, Bonn, Germany
| | - Hans F A Vasen
- Department of Gastroenterology & Hepatology, Leiden University Medical Centre, Leiden, The Netherlands
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26
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Grandval P, Blayau M, Buisine MP, Coulet F, Maugard C, Pinson S, Remenieras A, Tinat J, Uhrhammer N, Béroud C, Olschwang S. The UMD-APC database, a model of nation-wide knowledge base: update with data from 3,581 variations. Hum Mutat 2014; 35:532-6. [PMID: 24599579 DOI: 10.1002/humu.22539] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2013] [Accepted: 02/21/2014] [Indexed: 12/13/2022]
Abstract
Familial adenomatous polyposis (FAP) is a rare autosomal-inherited disease that highly predisposes to colorectal cancer, characterized by a diffuse duodenal and colorectal polyposis associated with various extradigestive tumors and linked to germline mutations within the APC gene. A French consortium of laboratories involved in APC mutation screening has progressively improved the description of the variation spectrum, inferred functional significance of nontruncating variations, and delineated phenotypic characteristics of the disease. The current version of the UMD-APC database is described here. The total number of variations has risen to 5,453 representing 1,473 distinct variations. The published records initially registered into the database were extended with 3,581 germline variations found through genetic testing performed by the eight licensed laboratories belonging to the French APC network. Sixty six of 149 variations of previously unknown significance have now been classified as (likely) causal or neutral. The database is available on the Internet (http://www.umd.be/APC/) and updated twice per year according to the consensus rules of the network. The UMD-APC database is thus expected to facilitate functional classification of rare synonymous, nonsynonymous, and intronic mutations and consequently improve genetic counseling and medical care in FAP families.
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Affiliation(s)
- Philippe Grandval
- UMR_S910, INSERM, Marseille, France; AP-HM La Timone, Gastroenterology Department, Marseille, France
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27
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Rouleau E, Zattara H, Lefol C, Noguchi T, Briaux A, Buecher B, Bourdon V, Sobol H, Lidereau R, Olschwang S. First large rearrangement in the MUTYH gene and attenuated familial adenomatous polyposis syndrome. Clin Genet 2011; 80:301-3. [PMID: 21815886 DOI: 10.1111/j.1399-0004.2011.01699.x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- E Rouleau
- Germline and Somatic Oncogenetic Laboratory, Institut Curie, Hôpital René Huguenin, Saint-Cloud, France CHU Timone, Medical Genetic Department, Assistance Publique des Hôpitaux de Marseille, Marseille, France Oncogenetic Laboratory, Institut Paoli Calmettes, Marseille, France Medical Oncogenetic Department, Institut Curie, Paris, France
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28
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Li M, Gerber DA, Koruda M, O'Neil BH. Hepatocelluar carcinoma associated with attenuated familial adenomatous polyposis: a case report and review of the literature. Clin Colorectal Cancer 2011; 11:77-81. [PMID: 21813337 DOI: 10.1016/j.clcc.2011.05.007] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2011] [Revised: 05/03/2011] [Accepted: 05/16/2011] [Indexed: 01/28/2023]
Affiliation(s)
- Mingqing Li
- Division of Hematology/Oncology, Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.
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A systematic study of gene mutations in urothelial carcinoma; inactivating mutations in TSC2 and PIK3R1. PLoS One 2011; 6:e18583. [PMID: 21533174 PMCID: PMC3077383 DOI: 10.1371/journal.pone.0018583] [Citation(s) in RCA: 87] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2010] [Accepted: 03/04/2011] [Indexed: 02/07/2023] Open
Abstract
Background Urothelial carcinoma (UC) is characterized by frequent gene mutations of which activating mutations in FGFR3 are the most frequent. Several downstream targets of FGFR3 are also mutated in UC, e.g., PIK3CA, AKT1, and RAS. Most mutation studies of UCs have been focused on single or a few genes at the time or been performed on small sample series. This has limited the possibility to investigate co-occurrence of mutations. Methodology/Principal Findings We performed mutation analyses of 16 genes, FGFR3, PIK3CA, PIK3R1 PTEN, AKT1, KRAS, HRAS, NRAS, BRAF, ARAF, RAF1, TSC1, TSC2, APC, CTNNB1, and TP53, in 145 cases of UC. We show that FGFR3 and PIK3CA mutations are positively associated. In addition, we identified PIK3R1 as a target for mutations. We demonstrate a negative association at borderline significance between FGFR3 and RAS mutations, and show that these mutations are not strictly mutually exclusive. We show that mutations in BRAF, ARAF, RAF1 rarely occurs in UC. Our data emphasize the possible importance of APC signaling as 6% of the investigated tumors either showed inactivating APC or activating CTNNB1 mutations. TSC1, as well as TSC2, that constitute the mTOR regulatory tuberous sclerosis complex were found to be mutated at a combined frequency of 15%. Conclusions/Significance Our data demonstrate a significant association between FGFR3 and PIK3CA mutations in UC. Moreover, the identification of mutations in PIK3R1 further emphasizes the importance of the PI3-kinase pathway in UC. The presence of TSC2 mutations, in addition to TSC1 mutations, underlines the involvement of mTOR signaling in UC.
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Ivanov D, Hamby SE, Stenson PD, Phillips AD, Kehrer-Sawatzki H, Cooper DN, Chuzhanova N. Comparative analysis of germline and somatic microlesion mutational spectra in 17 human tumor suppressor genes. Hum Mutat 2011; 32:620-32. [PMID: 21432943 DOI: 10.1002/humu.21483] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2010] [Accepted: 02/07/2011] [Indexed: 12/17/2022]
Abstract
Mutations associated with tumorigenesis may either arise somatically or can be inherited through the germline. We performed a comparison of somatic, germline, shared (found in both soma and germline) and somatic recurrent mutational spectra for 17 human tumor suppressor genes, which focused upon missense single base-pair substitutions and microdeletions/microinsertions. Somatic and germline mutational spectra were similar in relation to C.G>T.A transitions but differed with respect to the frequency of A.T>G.C, A.T>T.A, and C.G>A.T substitutions. Shared missense mutations were characterized by higher mutability rates, greater physicochemical differences between wild-type and mutant residues, and a tendency to occur in evolutionarily conserved residues and within CpG/CpHpG oligonucleotides. Mononucleotide runs (≥4 bp) were identified as hotspots for shared microdeletions/microinsertions. Both germline and somatic microdeletions/microinsertions were found to be significantly overrepresented within the "indel-hotspot" motif, GTAAGT. Using a naïve Bayes' classifier trained to discriminate between five missense mutation groups, 63% of mutations in our dataset were on average correctly recognized. Applying this classifier to an independent dataset of probable driver mutations, we concluded that ∼50% of these somatic missense mutations possess features consistent with their being either shared or recurrent, suggesting that a disproportionate number of such lesions are likely to be drivers of tumorigenesis.
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Affiliation(s)
- Dobril Ivanov
- Institute of Medical Genetics, School of Medicine, Cardiff University, Cardiff, United Kingdom
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Clinical utility gene card for: familial adenomatous polyposis (FAP) and attenuated FAP (AFAP). Eur J Hum Genet 2011; 19:ejhg20117. [PMID: 21368914 DOI: 10.1038/ejhg.2011.7] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
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