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Pantaleo A, Forte G, Fasano C, Lepore Signorile M, Sanese P, De Marco K, Di Nicola E, Latrofa M, Grossi V, Disciglio V, Simone C. Understanding the Genetic Landscape of Pancreatic Ductal Adenocarcinoma to Support Personalized Medicine: A Systematic Review. Cancers (Basel) 2023; 16:56. [PMID: 38201484 PMCID: PMC10778202 DOI: 10.3390/cancers16010056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Revised: 12/13/2023] [Accepted: 12/15/2023] [Indexed: 01/12/2024] Open
Abstract
Pancreatic ductal adenocarcinoma (PDAC) is one of the most fatal malignancies worldwide. While population-wide screening recommendations for PDAC in asymptomatic individuals are not achievable due to its relatively low incidence, pancreatic cancer surveillance programs are recommended for patients with germline causative variants in PDAC susceptibility genes or a strong family history. In this study, we sought to determine the prevalence and significance of germline alterations in major genes (ATM, BRCA1, BRCA2, CDKN2A, EPCAM, MLH1, MSH2, MSH6, PALB2, PMS2, STK11, TP53) involved in PDAC susceptibility. We performed a systematic review of PubMed publications reporting germline variants identified in these genes in PDAC patients. Overall, the retrieved articles included 1493 PDAC patients. A high proportion of these patients (n = 1225/1493, 82%) were found to harbor alterations in genes (ATM, BRCA1, BRCA2, PALB2) involved in the homologous recombination repair (HRR) pathway. Specifically, the remaining PDAC patients were reported to carry alterations in genes playing a role in other cancer pathways (CDKN2A, STK11, TP53; n = 181/1493, 12.1%) or in the mismatch repair (MMR) pathway (MLH1, MSH2, MSH6, PMS2; n = 87/1493, 5.8%). Our findings highlight the importance of germline genetic characterization in PDAC patients for better personalized targeted therapies, clinical management, and surveillance.
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Affiliation(s)
- Antonino Pantaleo
- Medical Genetics, National Institute of Gastroenterology-IRCCS “Saverio de Bellis” Research Hospital, 70013 Bari, Italy; (A.P.); (G.F.); (C.F.); (M.L.S.); (P.S.); (K.D.M.); (E.D.N.); (M.L.); (V.G.)
| | - Giovanna Forte
- Medical Genetics, National Institute of Gastroenterology-IRCCS “Saverio de Bellis” Research Hospital, 70013 Bari, Italy; (A.P.); (G.F.); (C.F.); (M.L.S.); (P.S.); (K.D.M.); (E.D.N.); (M.L.); (V.G.)
| | - Candida Fasano
- Medical Genetics, National Institute of Gastroenterology-IRCCS “Saverio de Bellis” Research Hospital, 70013 Bari, Italy; (A.P.); (G.F.); (C.F.); (M.L.S.); (P.S.); (K.D.M.); (E.D.N.); (M.L.); (V.G.)
| | - Martina Lepore Signorile
- Medical Genetics, National Institute of Gastroenterology-IRCCS “Saverio de Bellis” Research Hospital, 70013 Bari, Italy; (A.P.); (G.F.); (C.F.); (M.L.S.); (P.S.); (K.D.M.); (E.D.N.); (M.L.); (V.G.)
| | - Paola Sanese
- Medical Genetics, National Institute of Gastroenterology-IRCCS “Saverio de Bellis” Research Hospital, 70013 Bari, Italy; (A.P.); (G.F.); (C.F.); (M.L.S.); (P.S.); (K.D.M.); (E.D.N.); (M.L.); (V.G.)
| | - Katia De Marco
- Medical Genetics, National Institute of Gastroenterology-IRCCS “Saverio de Bellis” Research Hospital, 70013 Bari, Italy; (A.P.); (G.F.); (C.F.); (M.L.S.); (P.S.); (K.D.M.); (E.D.N.); (M.L.); (V.G.)
| | - Elisabetta Di Nicola
- Medical Genetics, National Institute of Gastroenterology-IRCCS “Saverio de Bellis” Research Hospital, 70013 Bari, Italy; (A.P.); (G.F.); (C.F.); (M.L.S.); (P.S.); (K.D.M.); (E.D.N.); (M.L.); (V.G.)
| | - Marialaura Latrofa
- Medical Genetics, National Institute of Gastroenterology-IRCCS “Saverio de Bellis” Research Hospital, 70013 Bari, Italy; (A.P.); (G.F.); (C.F.); (M.L.S.); (P.S.); (K.D.M.); (E.D.N.); (M.L.); (V.G.)
| | - Valentina Grossi
- Medical Genetics, National Institute of Gastroenterology-IRCCS “Saverio de Bellis” Research Hospital, 70013 Bari, Italy; (A.P.); (G.F.); (C.F.); (M.L.S.); (P.S.); (K.D.M.); (E.D.N.); (M.L.); (V.G.)
| | - Vittoria Disciglio
- Medical Genetics, National Institute of Gastroenterology-IRCCS “Saverio de Bellis” Research Hospital, 70013 Bari, Italy; (A.P.); (G.F.); (C.F.); (M.L.S.); (P.S.); (K.D.M.); (E.D.N.); (M.L.); (V.G.)
| | - Cristiano Simone
- Medical Genetics, National Institute of Gastroenterology-IRCCS “Saverio de Bellis” Research Hospital, 70013 Bari, Italy; (A.P.); (G.F.); (C.F.); (M.L.S.); (P.S.); (K.D.M.); (E.D.N.); (M.L.); (V.G.)
- Medical Genetics, Department of Precision and Regenerative Medicine and Jonic Area (DiMePRe-J), University of Bari Aldo Moro, 70124 Bari, Italy
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Lu M, Zhang X, Chu Q, Chen Y, Zhang P. Susceptibility Genes Associated with Multiple Primary Cancers. Cancers (Basel) 2023; 15:5788. [PMID: 38136334 PMCID: PMC10741435 DOI: 10.3390/cancers15245788] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2023] [Revised: 11/29/2023] [Accepted: 12/05/2023] [Indexed: 12/24/2023] Open
Abstract
With advancements in treatment and screening techniques, we have been witnessing an era where more cancer survivors harbor multiple primary cancers (MPCs), affecting approximately one in six patients. Identifying MPCs is crucial for tumor staging and subsequent treatment choices. However, the current clinicopathological criteria for clinical application are limited and insufficient, making it challenging to differentiate them from recurrences or metastases. The emergence of next-generation sequencing (NGS) technology has provided a genetic perspective for defining multiple primary cancers. Researchers have found that, when considering multiple tumor pairs, it is crucial not only to examine well-known essential mutations like MLH1/MSH2, EGFR, PTEN, BRCA1/2, CHEK2, and TP53 mutations but also to explore certain pleiotropic loci. Moreover, specific deleterious mutations may serve as regulatory factors in second cancer development following treatment. This review aims to discuss these susceptibility genes and provide an explanation of their functions based on the signaling pathway background. Additionally, the association network between genetic signatures and different tumor pairs will be summarized.
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Affiliation(s)
| | | | | | | | - Peng Zhang
- Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China; (M.L.)
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Chrysafi P, Jani CT, Lotz M, Al Omari O, Singh H, Stafford K, Agarwal L, Rupal A, Dar AQ, Dangelo A, Lam P. Prevalence of Variants of Uncertain Significance in Patients Undergoing Genetic Testing for Hereditary Breast and Ovarian Cancer and Lynch Syndrome. Cancers (Basel) 2023; 15:5762. [PMID: 38136308 PMCID: PMC10742236 DOI: 10.3390/cancers15245762] [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: 11/03/2023] [Revised: 11/27/2023] [Accepted: 12/04/2023] [Indexed: 12/24/2023] Open
Abstract
Hereditary Breast and Ovarian Cancer (HBOC) and Lynch Syndrome (LS) are the most common inherited cancer syndromes identified with genetic testing. Testing, though, commonly reveals variants of uncertain significance (VUSs). This is a retrospective observational study designed to determine the prevalence of pathogenic mutations and VUSs in patients tested for HBOC and/or LS and to explore the characteristics of the VUS population. Patients 18-80 years old that met NCCN criteria for HBOC and/or LS genetic screening were tested between 2006 and 2020 at Mount Auburn Hospital in Cambridge, Massachusetts. A total of 663 patients were included in the study, with a mean age of 50 years old and 90% being females. Pathogenic mutations were identified in 12.5% and VUSs in 28.3%. VUS prevalence was associated with race (p-value = 0.019), being particularly higher in Asian populations. Patients with a personal history of breast cancer or family history of breast or ovarian cancer were more likely to have a VUS (personal breast: OR: 1.55; CI: 1.08-2.25; family breast: OR: 1.68; CI: 1.08-2.60, family ovarian OR: 2.29; CI: 1.04-5.45). In conclusion, VUSs appear to be detected in almost one third patients tested for cancer genetic syndromes, and thus future work is warranted to determine their significance in cancer development.
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Affiliation(s)
- Pavlina Chrysafi
- Department of Medicine, Mount Auburn Hospital, Cambridge, MA 02138, USA; (P.C.); (M.L.); (K.S.); (A.D.); (P.L.)
- Department of Medicine, Harvard Medical School, Boston, MA 02129, USA
| | - Chinmay T. Jani
- Department of Medicine, Mount Auburn Hospital, Cambridge, MA 02138, USA; (P.C.); (M.L.); (K.S.); (A.D.); (P.L.)
- Department of Medicine, Harvard Medical School, Boston, MA 02129, USA
- Sylvester Comprehensive Cancer Center, University of Miami, Miami, FL 33146, USA
| | - Margaret Lotz
- Department of Medicine, Mount Auburn Hospital, Cambridge, MA 02138, USA; (P.C.); (M.L.); (K.S.); (A.D.); (P.L.)
- Division of Hematology and Oncology, Mount Auburn Hospital, Cambridge, MA 02138, USA
| | - Omar Al Omari
- Department of Pulmonary and Critical Care, Temple University, Philadelphia, PA 19122, USA;
| | - Harpreet Singh
- Department of Pulmonary and Critical Care, Medical College of Wisconsin, Milwaukee, WI 53226, USA;
| | - Katherine Stafford
- Department of Medicine, Mount Auburn Hospital, Cambridge, MA 02138, USA; (P.C.); (M.L.); (K.S.); (A.D.); (P.L.)
- Department of Medicine, Harvard Medical School, Boston, MA 02129, USA
| | - Lipisha Agarwal
- Department of Pulmonary and Critical Care, University of Vermont, Burlington, VT 05405, USA;
| | - Arashdeep Rupal
- Department of Pulmonary and Critical Care, University of South Florida, Tampa, FL 33620, USA;
| | - Abdul Qadir Dar
- Department of Medicine, Lahey Medical Center, Burlington, MA 01805, USA;
| | - Abby Dangelo
- Department of Medicine, Mount Auburn Hospital, Cambridge, MA 02138, USA; (P.C.); (M.L.); (K.S.); (A.D.); (P.L.)
- Division of Hematology and Oncology, Mount Auburn Hospital, Cambridge, MA 02138, USA
| | - Prudence Lam
- Department of Medicine, Mount Auburn Hospital, Cambridge, MA 02138, USA; (P.C.); (M.L.); (K.S.); (A.D.); (P.L.)
- Department of Medicine, Harvard Medical School, Boston, MA 02129, USA
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Li Y, Yu L, Cui J, Yin J, Wu W. The MSH2 c.793-1G>A variant disrupts normal splicing and is associated with Lynch syndrome. Front Oncol 2023; 13:1131011. [PMID: 37538120 PMCID: PMC10395827 DOI: 10.3389/fonc.2023.1131011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2022] [Accepted: 06/05/2023] [Indexed: 08/05/2023] Open
Abstract
Instruction Lynch syndrome (LS) is the most common inherited cancer predisposition disorder of colorectal cancer (CRC) which is associated with pathogenic variants in 4 mismatch repair (MMR) genes. Here, we reported a multi-generation Chinese family clinically diagnosed with LS. Methods To identify the underlying pathogenic gene variants, 30 whole blood samples and 4 colorectal cancer tissue samples and their clinical data were obtained from this four-generation family. Microsatellite instability-high (MSI) testing, immunohistochemistry (IHC), and Whole-Exome Sequencing (WES) were performed to identify the MMR/MSI and the underlying gene variants. The minigene splicing assay and in vitro splicing assay were used to explore the function of this variant. Results MSI-H and dMMR was revealed by the MSI testing and IHC, Whole-Exome Sequencing (WES) in 3 patients successfully identified a splicing variant (c.793-1G>A) in intron 4 of MSH2. Sanger sequencing validated the WES results, and all the "healthy" individuals carrying the variant have been identified in the family by PCR. Bioinformatics analysis and in vitro minigene assay showed that the pathogenic variant affected the splicing process of MSH2 gene to generate 2 kinds defective transcription products, and consequently reduced the expression of MSH2 protein. The mutation carriers were later recommended for colonoscopy and other important cancer diagnostic inspections every 1-2 years because they both have a higher risk of LS. Discussion We found a pathogenic splicing variant (rs863225397, c.793-1G>A) of MSH2 gene, and furtherly confirmed that this mutation plays an important role in LS patients of this pedigree based on the vitro study. Our study indicates that one splicing mutation in the MSH2 gene (c.793-1G>A) causes LS and highlights the importance of LS gene testing.
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Affiliation(s)
- Yiming Li
- Department of Geratic Surgery, Xiangya Hospital, Central South University, Changsha, Hunan, China
- Department of General Surgery, Xiangya Hospital, Central South University, Changsha, Hunan, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Lulu Yu
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha, Hunan, China
- Institute of Clinical Pharmacology, Central South University, Hunan Key Laboratory of Pharmacogenetics, Changsha, Hunan, China
- Engineering Research Center of Applied Technology of Pharmacogenomics, Ministry of Education, Changsha, Hunan, China
| | - Jiajia Cui
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha, Hunan, China
- Institute of Clinical Pharmacology, Central South University, Hunan Key Laboratory of Pharmacogenetics, Changsha, Hunan, China
- Engineering Research Center of Applied Technology of Pharmacogenomics, Ministry of Education, Changsha, Hunan, China
| | - Jiye Yin
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha, Hunan, China
- Institute of Clinical Pharmacology, Central South University, Hunan Key Laboratory of Pharmacogenetics, Changsha, Hunan, China
- Engineering Research Center of Applied Technology of Pharmacogenomics, Ministry of Education, Changsha, Hunan, China
| | - Wei Wu
- Department of Geratic Surgery, Xiangya Hospital, Central South University, Changsha, Hunan, China
- Department of General Surgery, Xiangya Hospital, Central South University, Changsha, Hunan, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, China
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Kansikas M, Vähätalo L, Kantelinen J, Kasela M, Putula J, Døhlen A, Paloviita P, Kärkkäinen E, Lahti N, Arnez P, Kilpinen S, Alcala-Repo B, Pylvänäinen K, Pöyhönen M, Peltomäki P, Järvinen HJ, Seppälä TT, Renkonen-Sinisalo L, Lepistö A, Mecklin JP, Nyström M. Tumor-independent Detection of Inherited Mismatch Repair Deficiency for the Diagnosis of Lynch Syndrome with High Specificity and Sensitivity. CANCER RESEARCH COMMUNICATIONS 2023; 3:361-370. [PMID: 36875157 PMCID: PMC9979712 DOI: 10.1158/2767-9764.crc-22-0384] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 12/20/2022] [Accepted: 02/07/2023] [Indexed: 06/18/2023]
Abstract
UNLABELLED Lynch syndrome (LS) is the most common hereditary cancer syndrome. Early diagnosis improves prognosis and reduces health care costs, through existing cancer surveillance methods. The problem is finding and diagnosing the cancer predisposing genetic condition. The current workup involves a complex array of tests that combines family cancer history and clinical phenotypes with tumor characteristics and sequencing data, followed by a challenging task to interpret the found variant(s). On the basis of the knowledge that an inherited mismatch repair (MMR) deficiency is a hallmark of LS, we have developed and validated a functional MMR test, DiagMMR, that detects inherited MMR deficiency directly from healthy tissue without need of tumor and variant information. The validation included 119 skin biopsies collected from clinically pathogenic MMR variant carriers (MSH2, MSH6) and controls, and was followed by a small clinical pilot study. The repair reaction was performed on proteins extracted from primary fibroblasts and the interpretation was based on the MMR capability of the sample in relation to cutoff, which distinguishes MMR proficient (non-LS) from MMR deficient (LS) function. The results were compared with the reference standard (germline NGS). The test was shown to have exceptional specificity (100%) with high sensitivity (89%) and accuracy (97%). The ability to efficiently distinguish LS carriers from controls was further shown with a high area under the receiving operating characteristic (AUROC) value (0.97). This test offers an excellent tool for detecting inherited MMR deficiency linked to MSH2 or MSH6 and can be used alone or with conventional tests to recognize genetically predisposed individuals. SIGNIFICANCE Clinical validation of DiagMMR shows high accuracy in distinguishing individuals with hereditary MSH2 or MSH6 MMR deficiency (i.e., LS). The method presented overcomes challenges faced by the complexity of current methods and can be used alone or with conventional tests to improve the ability to recognize genetically predisposed individuals.
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Affiliation(s)
- Minttu Kansikas
- LS CancerDiag Ltd., Helsinki, Finland
- Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | - Laura Vähätalo
- LS CancerDiag Ltd., Helsinki, Finland
- Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | - Jukka Kantelinen
- LS CancerDiag Ltd., Helsinki, Finland
- Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | - Mariann Kasela
- LS CancerDiag Ltd., Helsinki, Finland
- Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | - Jaana Putula
- LS CancerDiag Ltd., Helsinki, Finland
- Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | - Anni Døhlen
- LS CancerDiag Ltd., Helsinki, Finland
- Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | - Pauliina Paloviita
- LS CancerDiag Ltd., Helsinki, Finland
- Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | - Emmi Kärkkäinen
- LS CancerDiag Ltd., Helsinki, Finland
- Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | - Niklas Lahti
- LS CancerDiag Ltd., Helsinki, Finland
- Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | - Philippe Arnez
- LS CancerDiag Ltd., Helsinki, Finland
- Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | - Sami Kilpinen
- Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | | | - Kirsi Pylvänäinen
- Department of Education and Science, Nova Hospital, Central Finland Health Care District, Jyväskylä, Finland
| | - Minna Pöyhönen
- Department of Genetics, HUSLAB, Helsinki University Hospital Diagnostic Center, Helsinki, Finland
- Department of Medical and Clinical Genetics, University of Helsinki, Helsinki, Finland
- Applied Tumor Genomics, Research Programs Unit, University of Helsinki, Helsinki, Finland
| | - Päivi Peltomäki
- Department of Medical and Clinical Genetics, University of Helsinki, Helsinki, Finland
| | | | - Toni T. Seppälä
- Department of Surgery, Helsinki University Hospital, Helsinki, Finland
- Applied Tumor Genomics, Research Programs Unit, University of Helsinki, Helsinki, Finland
- Faculty of Medicine and Medical Technology, University of Tampere, Tampere, Finland
- Department of Gastroenterology and Alimentary Tract Surgery, Tampere University Hospital, Tampere, Finland
| | - Laura Renkonen-Sinisalo
- Department of Surgery, Helsinki University Hospital, Helsinki, Finland
- Applied Tumor Genomics, Research Programs Unit, University of Helsinki, Helsinki, Finland
| | - Anna Lepistö
- Department of Surgery, Helsinki University Hospital, Helsinki, Finland
- Applied Tumor Genomics, Research Programs Unit, University of Helsinki, Helsinki, Finland
| | - Jukka-Pekka Mecklin
- Department of Education and Science, Nova Hospital, Central Finland Health Care District, Jyväskylä, Finland
- Faculty of Sports and Health Sciences, University of Jyväskylä, Jyväskylä, Finland
| | - Minna Nyström
- Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
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Pan S, Cox H, Willmott J, Mundt E, Gorringe H, Landon M, Bowles KR, Coffee B, Roa BB, Mancini-DiNardo D. Discordance between germline genetic findings and abnormal tumor immunohistochemistry staining of mismatch repair proteins in individuals with suspected Lynch syndrome. Front Oncol 2023; 13:1069467. [PMID: 36793599 PMCID: PMC9923021 DOI: 10.3389/fonc.2023.1069467] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Accepted: 01/11/2023] [Indexed: 01/31/2023] Open
Abstract
Background and Aims Tumor immunohistochemical staining (IHC) of DNA mismatch repair (MMR) proteins is often used to guide germline genetic testing and variant classification for patients with suspected Lynch syndrome. This analysis examined the spectrum of germline findings in a cohort of individuals showing abnormal tumor IHC. Methods We assessed individuals with reported abnormal IHC findings and referred for testing with a six-gene syndrome-specific panel (n=703). Pathogenic variants (PVs) and variants of uncertain significance (VUS) in MMR genes were designated expected/unexpected relative to IHC results. Results The PV positive rate was 23.2% (163/703; 95% confidence interval [CI], 20.1%-26.5%); 8.0% (13/163; 95% CI, 4.3%-13.3%) of PV carriers had a PV in an unexpected MMR gene. Overall, 121 individuals carried VUS in MMR genes expected to be mutated based on IHC results. Based on independent evidence, in 47.1% (57/121; 95% CI, 38.0%-56.4%) of these individuals the VUSs were later reclassified as benign and in 14.0% (17/121; 95% CI, 8.4%-21.5%) of these individuals the VUSs were reclassified as pathogenic. Conclusions Among patients with abnormal IHC findings, IHC-guided single-gene genetic testing may miss 8% of individuals with Lynch syndrome. In addition, in patients with VUS identified in MMR genes predicted to be mutated by IHC, extreme caution must be taken when the IHC results are considered in variant classification.
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Affiliation(s)
- Shujuan Pan
- Myriad Genetic Laboratories, Inc., Salt Lake City, UT, United States
| | - Hannah Cox
- Myriad Genetic Laboratories, Inc., Salt Lake City, UT, United States
| | - Jamie Willmott
- Myriad Genetic Laboratories, Inc., Salt Lake City, UT, United States
| | - Erin Mundt
- Myriad Genetic Laboratories, Inc., Salt Lake City, UT, United States
| | - Heidi Gorringe
- Myriad Genetic Laboratories, Inc., Salt Lake City, UT, United States
| | - Michelle Landon
- Myriad Genetic Laboratories, Inc., Salt Lake City, UT, United States
| | - Karla R Bowles
- Myriad Genetic Laboratories, Inc., Salt Lake City, UT, United States
| | - Bradford Coffee
- Myriad Genetic Laboratories, Inc., Salt Lake City, UT, United States
| | - Benjamin B Roa
- Myriad Genetic Laboratories, Inc., Salt Lake City, UT, United States
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Vogelaar IP, Greer S, Wang F, Shin G, Lau B, Hu Y, Haraldsdottir S, Alvarez R, Hazelett D, Nguyen P, Aguirre FP, Guindi M, Hendifar A, Balcom J, Leininger A, Fairbank B, Ji H, Hitchins MP. Large Cancer Pedigree Involving Multiple Cancer Genes including Likely Digenic MSH2 and MSH6 Lynch Syndrome (LS) and an Instance of Recombinational Rescue from LS. Cancers (Basel) 2022; 15:cancers15010228. [PMID: 36612224 PMCID: PMC9818763 DOI: 10.3390/cancers15010228] [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: 11/17/2022] [Revised: 12/26/2022] [Accepted: 12/28/2022] [Indexed: 12/31/2022] Open
Abstract
Lynch syndrome (LS), caused by heterozygous pathogenic variants affecting one of the mismatch repair (MMR) genes (MSH2, MLH1, MSH6, PMS2), confers moderate to high risks for colorectal, endometrial, and other cancers. We describe a four-generation, 13-branched pedigree in which multiple LS branches carry the MSH2 pathogenic variant c.2006G>T (p.Gly669Val), one branch has this and an additional novel MSH6 variant c.3936_4001+8dup (intronic), and other non-LS branches carry variants within other cancer-relevant genes (NBN, MC1R, PTPRJ). Both MSH2 c.2006G>T and MSH6 c.3936_4001+8dup caused aberrant RNA splicing in carriers, including out-of-frame exon-skipping, providing functional evidence of their pathogenicity. MSH2 and MSH6 are co-located on Chr2p21, but the two variants segregated independently (mapped in trans) within the digenic branch, with carriers of either or both variants. Thus, MSH2 c.2006G>T and MSH6 c.3936_4001+8dup independently confer LS with differing cancer risks among family members in the same branch. Carriers of both variants have near 100% risk of transmitting either one to offspring. Nevertheless, a female carrier of both variants did not transmit either to one son, due to a germline recombination within the intervening region. Genetic diagnosis, risk stratification, and counseling for cancer and inheritance were highly individualized in this family. The finding of multiple cancer-associated variants in this pedigree illustrates a need to consider offering multicancer gene panel testing, as opposed to targeted cascade testing, as additional cancer variants may be uncovered in relatives.
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Affiliation(s)
- Ingrid P. Vogelaar
- Department of Medicine (Oncology), Stanford Cancer Institute, Stanford University, Stanford, CA 94305, USA
| | - Stephanie Greer
- Department of Medicine (Oncology), Stanford Cancer Institute, Stanford University, Stanford, CA 94305, USA
| | - Fan Wang
- Department of Medicine (Oncology), Stanford Cancer Institute, Stanford University, Stanford, CA 94305, USA
- School of Public Health (Epidemiology), Harbin Medical University, Harbin 150088, China
| | - GiWon Shin
- Department of Medicine (Oncology), Stanford Cancer Institute, Stanford University, Stanford, CA 94305, USA
| | - Billy Lau
- Department of Medicine (Oncology), Stanford Cancer Institute, Stanford University, Stanford, CA 94305, USA
| | - Yajing Hu
- Department of Medicine (Oncology), Stanford Cancer Institute, Stanford University, Stanford, CA 94305, USA
| | - Sigurdis Haraldsdottir
- Department of Medicine (Oncology), Stanford Cancer Institute, Stanford University, Stanford, CA 94305, USA
| | - Rocio Alvarez
- Bioinformatics and Functional Genomics Center, Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Dennis Hazelett
- Bioinformatics and Functional Genomics Center, Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Peter Nguyen
- Bioinformatics and Functional Genomics Center, Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Francesca P. Aguirre
- Bioinformatics and Functional Genomics Center, Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Maha Guindi
- Department of Pathology and Laboratory Medicine, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Andrew Hendifar
- Samuel Oschin Cancer Center, Cedars-Sinai Medical Center, 8700 Beverly Blvd, Los Angeles, CA 90048, USA
| | - Jessica Balcom
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN 55902, USA
| | | | - Beth Fairbank
- Lynch Syndrome Australia, The Summit, QLD 4377, Australia
| | - Hanlee Ji
- Department of Medicine (Oncology), Stanford Cancer Institute, Stanford University, Stanford, CA 94305, USA
- Stanford Genome Technology Center West, 1050 Arastradero, Palo Alto, CA 94304, USA
| | - Megan P. Hitchins
- Department of Medicine (Oncology), Stanford Cancer Institute, Stanford University, Stanford, CA 94305, USA
- Bioinformatics and Functional Genomics Center, Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
- Lowy Cancer Research Centre, University of New South Wales, Sydney, NSW 2052, Australia
- Correspondence: ; Tel.: +310-423-8785
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Scott A, Hernandez F, Chamberlin A, Smith C, Karam R, Kitzman JO. Saturation-scale functional evidence supports clinical variant interpretation in Lynch syndrome. Genome Biol 2022; 23:266. [PMID: 36550560 PMCID: PMC9773515 DOI: 10.1186/s13059-022-02839-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Accepted: 12/13/2022] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Lynch syndrome (LS) is a cancer predisposition syndrome affecting more than 1 in every 300 individuals worldwide. Clinical genetic testing for LS can be life-saving but is complicated by the heavy burden of variants of uncertain significance (VUS), especially missense changes. RESULT To address this challenge, we leverage a multiplexed analysis of variant effect (MAVE) map covering >94% of the 17,746 possible missense variants in the key LS gene MSH2. To establish this map's utility in large-scale variant reclassification, we overlay it on clinical databases of >15,000 individuals with LS gene variants uncovered during clinical genetic testing. We validate these functional measurements in a cohort of individuals with paired tumor-normal test results and find that MAVE-based function scores agree with the clinical interpretation for every one of the MSH2 missense variants with an available classification. We use these scores to attempt reclassification for 682 unique missense VUS, among which 34 scored as deleterious by our function map, in line with previously published rates for other cancer predisposition genes. Combining functional data and other evidence, ten missense VUS are reclassified as pathogenic/likely pathogenic, and another 497 could be moved to benign/likely benign. Finally, we apply these functional scores to paired tumor-normal genetic tests and identify a subset of patients with biallelic somatic loss of function, reflecting a sporadic Lynch-like Syndrome with distinct implications for treatment and relatives' risk. CONCLUSION This study demonstrates how high-throughput functional assays can empower scalable VUS resolution and prospectively generate strong evidence for variant classification.
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Affiliation(s)
- Anthony Scott
- grid.214458.e0000000086837370Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI 48109 USA ,grid.214458.e0000000086837370Division of Genetic Medicine, Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI 48109 USA
| | - Felicia Hernandez
- grid.465138.d0000 0004 0455 211XAmbry Genetics, Aliso Viejo, CA 92656 USA
| | - Adam Chamberlin
- grid.465138.d0000 0004 0455 211XAmbry Genetics, Aliso Viejo, CA 92656 USA
| | - Cathy Smith
- grid.214458.e0000000086837370Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI 48109 USA ,grid.214458.e0000000086837370Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, MI 48109 USA
| | - Rachid Karam
- grid.465138.d0000 0004 0455 211XAmbry Genetics, Aliso Viejo, CA 92656 USA ,grid.214458.e0000000086837370Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, MI 48109 USA
| | - Jacob O. Kitzman
- grid.214458.e0000000086837370Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI 48109 USA ,grid.214458.e0000000086837370Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, MI 48109 USA
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9
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Rath A, Radecki AA, Rahman K, Gilmore RB, Hudson JR, Cenci M, Tavtigian SV, Grady JP, Heinen CD. A calibrated cell-based functional assay to aid classification of MLH1 DNA mismatch repair gene variants. Hum Mutat 2022; 43:2295-2307. [PMID: 36054288 PMCID: PMC9772141 DOI: 10.1002/humu.24462] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Revised: 06/21/2022] [Accepted: 08/30/2022] [Indexed: 01/25/2023]
Abstract
Functional assays provide important evidence for classifying the disease significance of germline variants in DNA mismatch repair genes. Numerous laboratories, including our own, have developed functional assays to study mismatch repair gene variants. However, previous assays are limited due to the model system employed, the manner of gene expression, or the environment in which function is assessed. Here, we developed a human cell-based approach for testing the function of variants of uncertain significance (VUS) in the MLH1 gene. Using clustered regularly interspaced short palindromic repeats gene editing, we knocked in MLH1 VUS into the endogenous MLH1 loci in human embryonic stem cells. We examined their impact on RNA and protein, including their ability to prevent microsatellite instability and instigate a DNA damage response. A statistical clustering analysis determined the range of functions associated with known pathogenic or benign variants, and linear regression was performed using existing odds in favor of pathogenicity scores for these control variants to calibrate our functional assay results. By converting the functional outputs into a single odds in favor of pathogenicity score, variant classification expert panels can use these results to readily reassess these VUS. Ultimately, this information will guide proper diagnosis and disease management for suspected Lynch syndrome patients.
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Affiliation(s)
- Abhijit Rath
- Center for Molecular Oncology, UConn Health, Farmington, CT
| | | | - Kaussar Rahman
- Center for Molecular Oncology, UConn Health, Farmington, CT
| | - Rachel B. Gilmore
- Department of Genetics and Genome Sciences, UConn Health, Farmington, CT
| | - Jonathan R. Hudson
- Department of Genetics and Genome Sciences, UConn Health, Farmington, CT
| | - Matthew Cenci
- Center for Molecular Oncology, UConn Health, Farmington, CT
| | - Sean V. Tavtigian
- Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, UT
| | - James P. Grady
- Connecticut Institute for Clinical and Translational Science, UConn Health, Farmington, CT
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10
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Mahdouani M, Ben Ahmed S, Hmila F, Rais H, Ben Sghaier R, Saad H, Ben Said M, Masmoudi S, Hmida D, Brieger A, Zeuzem S, Saad A, Gribaa M, Plotz G. Functional characterization of MLH1 missense variants unveils mechanisms of pathogenicity and clarifies role in cancer. PLoS One 2022; 17:e0278283. [PMID: 36454741 PMCID: PMC9714755 DOI: 10.1371/journal.pone.0278283] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Accepted: 10/28/2022] [Indexed: 12/05/2022] Open
Abstract
Lynch syndrome is a heritable condition caused by a heterozygous germline inactivating mutation of the DNA mismatch repair (MMR) genes, most commonly the MLH1 gene. However, one third of the identified alterations are missense variants, for which the clinical significance is unclear in many cases. We have identified three MLH1 missense alterations (p.(Glu736Lys), p.(Pro640Thr) and p.(Leu73Pro)) in six individuals from large Tunisian families. For none of these alterations, a classification of pathogenicity was available, consequently diagnosis, predictive testing and targeted surveillance in affected families was impossible. We therefore performed functional laboratory testing using a system testing stability as well as catalytic activity that includes clinically validated reference variants. Both p.(Leu73Pro) and p.(Pro640Thr) were found to be non-functional due to severe defects in protein stability and catalytic activity. In contrast, p.(Glu736Lys) was comparable to the wildtype protein and therefore considered a neutral substitution. Analysis of residue conservation and of the structural roles of the substituted residues corroborated these findings. In conjunction with the available clinical data, two variants fulfil classification criteria for class 4 "likely pathogenic". The findings of this work clarify the mechanism of pathogenicity of two unclear MLH1 variants and enables predictive testing and targeted surveillance in members of carrier families worldwide.
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Affiliation(s)
- Marwa Mahdouani
- Laboratory of Human Cytogenetics, Molecular Genetics and Reproductive Biology, Farhat Hached University Hospital, Sousse, Tunisia
- Higher Institute of Biotechnology of Monastir, University of Monastir, Monastir, Tunisia
| | - Slim Ben Ahmed
- Department of Oncology, Farhat Hached University Hospital, Sousse, Tunisia
- Faculty of Medicine Ibn El Jazzar of Sousse, University of Sousse, Sousse, Tunisia
| | - Fahmi Hmila
- Faculty of Medicine Ibn El Jazzar of Sousse, University of Sousse, Sousse, Tunisia
- Department of General and Digestive Surgery, Farhat Hached University Hospital, Sousse, Tunisia
| | - Henda Rais
- Medical Service, Salah Azaiez Institute, Tunis, Tunisia
| | - Rihab Ben Sghaier
- Laboratory of Human Cytogenetics, Molecular Genetics and Reproductive Biology, Farhat Hached University Hospital, Sousse, Tunisia
- Higher Institute of Biotechnology of Monastir, University of Monastir, Monastir, Tunisia
| | - Hanene Saad
- Laboratory of Human Cytogenetics, Molecular Genetics and Reproductive Biology, Farhat Hached University Hospital, Sousse, Tunisia
- Higher Institute of Biotechnology of Monastir, University of Monastir, Monastir, Tunisia
| | - Mariem Ben Said
- Laboratory of Molecular and Cellular Screening Processes, Centre of Biotechnology of Sfax, Sfax, Tunisia
| | - Saber Masmoudi
- Laboratory of Molecular and Cellular Screening Processes, Centre of Biotechnology of Sfax, Sfax, Tunisia
| | - Dorra Hmida
- Laboratory of Human Cytogenetics, Molecular Genetics and Reproductive Biology, Farhat Hached University Hospital, Sousse, Tunisia
- Faculty of Medicine Ibn El Jazzar of Sousse, University of Sousse, Sousse, Tunisia
| | - Angela Brieger
- Biomedical Research Laboratory, Department of Internal Medicine 1, University Hospital, Goethe University, Frankfurt am Main, Germany
| | - Stefan Zeuzem
- Biomedical Research Laboratory, Department of Internal Medicine 1, University Hospital, Goethe University, Frankfurt am Main, Germany
| | - Ali Saad
- Laboratory of Human Cytogenetics, Molecular Genetics and Reproductive Biology, Farhat Hached University Hospital, Sousse, Tunisia
- Faculty of Medicine Ibn El Jazzar of Sousse, University of Sousse, Sousse, Tunisia
| | - Moez Gribaa
- Laboratory of Human Cytogenetics, Molecular Genetics and Reproductive Biology, Farhat Hached University Hospital, Sousse, Tunisia
- Faculty of Medicine Ibn El Jazzar of Sousse, University of Sousse, Sousse, Tunisia
| | - Guido Plotz
- Biomedical Research Laboratory, Department of Internal Medicine 1, University Hospital, Goethe University, Frankfurt am Main, Germany
- * E-mail:
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11
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Morak M, Pineda M, Martins A, Gaildrat P, Tubeuf H, Drouet A, Gómez C, Dámaso E, Schaefer K, Steinke-Lange V, Koehler U, Laner A, Hauchard J, Chauris K, Holinski-Feder E, Capellá G. Splicing analyses for variants in MMR genes: best practice recommendations from the European Mismatch Repair Working Group. Eur J Hum Genet 2022; 30:1051-1059. [PMID: 35676339 PMCID: PMC9437034 DOI: 10.1038/s41431-022-01106-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2021] [Revised: 03/20/2022] [Accepted: 04/11/2022] [Indexed: 11/09/2022] Open
Abstract
Over 20% of the DNA mismatch repair (MMR) germline variants in suspected Lynch syndrome patients are classified as variants of uncertain significance (VUS). Well-established functional assays are pivotal for assessing the biological impact of these variants and provide relevant evidence for clinical classification. In our collaborative European Mismatch Repair Working Group (EMMR-WG) we compared three different experimental approaches for evaluating the effect of seven variants on mRNA splicing in MMR genes: (i) RT-PCR of full-length transcripts (FLT), (ii) RT-PCR of targeted transcript sections (TTS), both from patient biological samples and (iii) minigene splicing assays. An overall good concordance was observed between splicing patterns in TTS, FLT and minigene analyses for all variants. The FLT analysis depicted a higher number of different isoforms and mitigated PCR-bias towards shorter isoforms. TTS analyses may miss aberrant isoforms and minigene assays may under/overestimate the severity of certain splicing defects. The interpretation of the experimental findings must be cautious to adequately discriminate abnormal events from physiological complex alternative splicing patterns. A consensus strategy for investigating the impact of MMR variants on splicing was defined. First, RNA should be obtained from patient's cell cultures (such as fresh lymphocyte cultures) incubated with/without a nonsense-mediated decay inhibitor. Second, FLT RT-PCR analysis is recommended to oversee all generated isoforms. Third, TTS analysis and minigene assays are useful independent approaches for verifying and clarifying FLT results. The use of several methodologies is likely to increase the strength of the experimental evidence which contributes to improve variant interpretation.
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Affiliation(s)
- Monika Morak
- Medizinische Klinik und Poliklinik IV, Campus Innenstadt, Klinikum der Universität München, Munich, Germany.,MGZ - Medizinisch Genetisches Zentrum, Munich, Germany
| | - Marta Pineda
- Hereditary Cancer Program, Catalan Institute of Oncology-IDIBELL, ONCOBELL Program, L'Hospitalet, Barcelona, Spain.,Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
| | | | | | - Hélène Tubeuf
- Inserm U1245, UNIROUEN, Normandie Univ, F-76000, Rouen, France.,Interactive Biosoftware, Rouen, France
| | - Aurélie Drouet
- Inserm U1245, UNIROUEN, Normandie Univ, F-76000, Rouen, France
| | - Carolina Gómez
- Hereditary Cancer Program, Catalan Institute of Oncology-IDIBELL, ONCOBELL Program, L'Hospitalet, Barcelona, Spain
| | - Estela Dámaso
- Hereditary Cancer Program, Catalan Institute of Oncology-IDIBELL, ONCOBELL Program, L'Hospitalet, Barcelona, Spain
| | - Kerstin Schaefer
- Medizinische Klinik und Poliklinik IV, Campus Innenstadt, Klinikum der Universität München, Munich, Germany
| | - Verena Steinke-Lange
- Medizinische Klinik und Poliklinik IV, Campus Innenstadt, Klinikum der Universität München, Munich, Germany.,MGZ - Medizinisch Genetisches Zentrum, Munich, Germany
| | - Udo Koehler
- MGZ - Medizinisch Genetisches Zentrum, Munich, Germany
| | - Andreas Laner
- MGZ - Medizinisch Genetisches Zentrum, Munich, Germany
| | - Julie Hauchard
- Inserm U1245, UNIROUEN, Normandie Univ, F-76000, Rouen, France
| | - Karine Chauris
- Inserm U1245, UNIROUEN, Normandie Univ, F-76000, Rouen, France
| | - Elke Holinski-Feder
- Medizinische Klinik und Poliklinik IV, Campus Innenstadt, Klinikum der Universität München, Munich, Germany. .,MGZ - Medizinisch Genetisches Zentrum, Munich, Germany.
| | - Gabriel Capellá
- Hereditary Cancer Program, Catalan Institute of Oncology-IDIBELL, ONCOBELL Program, L'Hospitalet, Barcelona, Spain. .,Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain.
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12
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Yang C, Sheehan M, Borras E, Cadoo K, Offit K, Zhang L. Characterization of a germline splice site variant MLH1 c.678-3T>A in a Lynch syndrome family. Fam Cancer 2021; 19:315-322. [PMID: 32356167 DOI: 10.1007/s10689-020-00180-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Germline mutations in the DNA mismatch repair (MMR) genes cause Lynch syndrome. Classification and interpretation of intronic variants, especially those outside the consensus ± 1 ~ 2 splice sites are challenging as it is uncertain whether such variants would affect splicing accuracy and efficiency. The assessment of the pathogenicity of splice site variants in MLH1 is further complicated by the various isoforms due to alternative splicing. In this report, we describe a 42-year-old female with Lynch syndrome who carries a germline variant, MLH1 c.678-3T>A, in the splice acceptor site of intron 8. Functional studies and semiquantitative analysis demonstrated that this variant causes a significant increase in the transcripts with exon 9 or exon 9 and 10 deletions, which presumably leads to premature protein truncation or abnormal protein. In addition, we also observed MSI-H and loss of MLH1 by IHC in patient's tumor tissue. This variant also segregated with Lynch Syndrome related cancers in three affected family members. Based on these evidence, the MLH1 c.678-3T>A variant is considered pathogenic.
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Affiliation(s)
- Ciyu Yang
- Departments of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Margaret Sheehan
- Departments of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Ester Borras
- Departments of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Karen Cadoo
- Departments of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Kenneth Offit
- Departments of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Liying Zhang
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California at Los Angeles (UCLA), 10833 Le Conte Ave, Los Angeles, CA, 90095, USA.
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13
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14
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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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15
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Picó MD, Sánchez-Heras AB, Castillejo A, Giner-Calabuig M, Alustiza M, Sánchez A, Moreira L, Pellise M, Castells A, Llort G, Yagüe C, Ramon y Cajal T, Gisbert-Beamud A, Cubiella J, Rivas L, Herraiz M, Garau C, Salces I, Carrillo-Palau M, Bujanda L, López-Fernández A, Alvarez-Urturi C, López MJ, Alenda C, Zapater P, Lacueva FJ, Balaguer F, Soto JL, Murcia Ó, Jover R. Risk of Cancer in Family Members of Patients with Lynch-Like Syndrome. Cancers (Basel) 2020; 12:cancers12082225. [PMID: 32784934 PMCID: PMC7466118 DOI: 10.3390/cancers12082225] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2020] [Revised: 07/31/2020] [Accepted: 08/05/2020] [Indexed: 12/15/2022] Open
Abstract
Lynch syndrome (LS) is a common cause of hereditary colorectal cancer (CRC). Some CRC patients develop mismatch repair deficiency without germline pathogenic mutation, known as Lynch-like syndrome (LLS). We compared the risk of CRC in first-degree relatives (FDRs) in LLS and LS patients. LLS was diagnosed when tumors showed immunohistochemical loss of MSH2, MSH6, and PMS2; or loss of MLH1 with BRAF wild type; and/or no MLH1 methylation and absence of pathogenic mutation in these genes. CRC and other LS-related neoplasms were followed in patients diagnosed with LS and LLS and among their FDRs. Standardized incidence ratios (SIRs) were calculated for CRC and other neoplasms associated with LS among FDRs of LS and LLS patients. In total, 205 LS (1205 FDRs) and 131 LLS families (698 FDRs) had complete pedigrees. FDRs of patients with LLS had a high incidence of CRC (SIR, 2.08; 95% confidence interval (CI), 1.56–2.71), which was significantly lower than that in FDRs of patients with LS (SIR, 4.25; 95% CI, 3.67–4.90; p < 0.001). The risk of developing other neoplasms associated with LS also increased among FDR of LLS patients (SIR, 2.04; 95% CI, 1.44–2.80) but was lower than that among FDR of patients with LS (SIR, 5.01, 95% CI, 4.26–5.84; p < 0.001). FDRs with LLS have an increased risk of developing CRC as well as LS-related neoplasms, although this risk is lower than that of families with LS. Thus, their management should take into account this increased risk.
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Affiliation(s)
- María Dolores Picó
- Servicio de Medicina Digestiva, Hospital General Universitario de Elche, Elche, 03203 Alicante, Spain;
| | - Ana Beatriz Sánchez-Heras
- Servicio de Oncología Médica, Hospital General Universitario de Elche, Elche, 03203 Alicante, Spain;
| | - Adela Castillejo
- Unidad de Genética Molecular, Hospital General Universitario de Elche, 03203 Alicante, Spain; (A.C.); (J.-L.S.)
| | - Mar Giner-Calabuig
- Servicio de Medicina Digestiva, Hospital General Universitario de Alicante, Instituto de Investigación Sanitaria ISABIAL, 03010 Alicante, Spain; (M.G.-C.); (M.A.)
| | - Miren Alustiza
- Servicio de Medicina Digestiva, Hospital General Universitario de Alicante, Instituto de Investigación Sanitaria ISABIAL, 03010 Alicante, Spain; (M.G.-C.); (M.A.)
| | - Ariadna Sánchez
- Servicio de Medicina Digestiva, Hospital Clínic de Barcelona, IDIBAPS, CIBERehd. University of Barcelona, 08036 Barcelona, Spain; (A.S.); (L.M.); (M.P.); (A.C.); (F.B.)
| | - Leticia Moreira
- Servicio de Medicina Digestiva, Hospital Clínic de Barcelona, IDIBAPS, CIBERehd. University of Barcelona, 08036 Barcelona, Spain; (A.S.); (L.M.); (M.P.); (A.C.); (F.B.)
| | - María Pellise
- Servicio de Medicina Digestiva, Hospital Clínic de Barcelona, IDIBAPS, CIBERehd. University of Barcelona, 08036 Barcelona, Spain; (A.S.); (L.M.); (M.P.); (A.C.); (F.B.)
| | - Antoni Castells
- Servicio de Medicina Digestiva, Hospital Clínic de Barcelona, IDIBAPS, CIBERehd. University of Barcelona, 08036 Barcelona, Spain; (A.S.); (L.M.); (M.P.); (A.C.); (F.B.)
| | - Gemma Llort
- Servicio de Oncología Médica, Hospital Universitari Parc Taulí, Sabadell, Consorci Sanitari de Terrassa, Terrassa, 08208 Barcelona, Spain; (G.L.); (C.Y.)
| | - Carmen Yagüe
- Servicio de Oncología Médica, Hospital Universitari Parc Taulí, Sabadell, Consorci Sanitari de Terrassa, Terrassa, 08208 Barcelona, Spain; (G.L.); (C.Y.)
| | - Teresa Ramon y Cajal
- Servicio de Medicina Digestiva, Hospital de la Santa Creu i Sant Pau, 08041 Barcelona, Spain; (T.R.yC.); (A.G.-B.)
| | - Alexandra Gisbert-Beamud
- Servicio de Medicina Digestiva, Hospital de la Santa Creu i Sant Pau, 08041 Barcelona, Spain; (T.R.yC.); (A.G.-B.)
| | - Joaquin Cubiella
- Servicio de Medicina Digestiva, Complexo Hospitalario Universitario de Ourense, Instituto de Investigación Sanitaria Galicia Sur, CIBERehd, 32005 Ourense, Spain; (J.C.); (L.R.)
| | - Laura Rivas
- Servicio de Medicina Digestiva, Complexo Hospitalario Universitario de Ourense, Instituto de Investigación Sanitaria Galicia Sur, CIBERehd, 32005 Ourense, Spain; (J.C.); (L.R.)
| | - Maite Herraiz
- Servicio de Medicina Digestiva, Clínica Universidad de Navarra, 31008 Navarra, Spain;
| | - Catalina Garau
- Servicio de Medicina Digestiva, Hospital de Son Llàtzer, 07198 Palma de Mallorca, Spain;
| | - Inmaculada Salces
- Servicio de Medicina Digestiva, Hospital 12 de Octubre, 28041 Madrid, Spain;
| | - Marta Carrillo-Palau
- Servicio de Medicina Digestiva, Hospital Universitario de Canarias, 38320 Tenerife, Spain;
| | - Luis Bujanda
- Servicio de Medicina Digestiva, Hospital Donostia/Instituto Biodonostia, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Universidad del País Vasco (UPV/EHU), 20014 San Sebastián, Spain;
| | - Adriá López-Fernández
- Unidad de Alto Riesgo y Prevención del Cáncer, Hospital Universitario Vall d’Hebron, 08035 Barcelona, Spain;
| | | | - María Jesús López
- Servicio de Medicina Digestiva, Hospital Universitario Marqués de Valdecilla, 39008 Santandercity, Spain;
| | - Cristina Alenda
- Servicio de Anatomía Patológica, Hospital General Universitario de Alicante, Instituto de Investigación Sanitaria ISABIAL, 03010 Alicante, Spain;
| | - Pedro Zapater
- Servicio de Farmacología Clínica, Hospital General Universitario de Alicante, ISABIAL, CIBERehd, IDiBE, UMH, 03010 Alicante, Spain;
| | - Francisco Javier Lacueva
- Servicio de Cirugía general, Hospital General Universitario de Elche, Elche, 03203 Alicante, Spain;
| | - Francesc Balaguer
- Servicio de Medicina Digestiva, Hospital Clínic de Barcelona, IDIBAPS, CIBERehd. University of Barcelona, 08036 Barcelona, Spain; (A.S.); (L.M.); (M.P.); (A.C.); (F.B.)
| | - Jose-Luis Soto
- Unidad de Genética Molecular, Hospital General Universitario de Elche, 03203 Alicante, Spain; (A.C.); (J.-L.S.)
| | - Óscar Murcia
- Servicio de Medicina Digestiva, Hospital General Universitario de Alicante, Instituto de Investigación Sanitaria ISABIAL, 03010 Alicante, Spain; (M.G.-C.); (M.A.)
- Correspondence: (Ó.M.); or (R.J.); Fax: +34-965-933-468 (Ó.M. & R.J.)
| | - Rodrigo Jover
- Servicio de Medicina Digestiva, Hospital General Universitario de Alicante, Instituto de Investigación Sanitaria ISABIAL, 03010 Alicante, Spain; (M.G.-C.); (M.A.)
- Correspondence: (Ó.M.); or (R.J.); Fax: +34-965-933-468 (Ó.M. & R.J.)
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16
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Wang A, Li Z, Wang M, Jia S, Chen J, Ji K, Ji X, Zong X, Wu X, Zhang J, Li Z, Zhang L, Hu Y, Bu Z, Zheng Q, Ji J. Molecular characteristics of synchronous multiple gastric cancer. Theranostics 2020; 10:5489-5500. [PMID: 32373223 PMCID: PMC7196298 DOI: 10.7150/thno.42814] [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: 12/07/2019] [Accepted: 03/15/2020] [Indexed: 12/24/2022] Open
Abstract
Rationale: Multiple gastric cancer (MGC) is characterized by the presence of more than two different tumors in the stomach. However, the clonal relationship and carcinogenesis of MGC remain unclear. We investigated the clonal relationship and role of germline mutations in the carcinogenesis of MGC. Methods: We gathered 16 multiple gastric cancer patients. Thirty-three tumor samples and sixteen normal gastric tissue or blood samples were obtained from January 2016 to December 2017. We also conducted analyses for 208 gastric cancer and 49 esophagogastric junction cancer (GC-EGJ) tumors from TCGA. DNA extraction from our samples was conducted for whole-exome sequencing (WES). Results: Tumor mutation burden (TMB) was not statistically significant within database and our data in the GC-EGJ (P=0.0591) and GC groups (P=0.3113). The mutation spectrum and signatures also showed uniform distributions in GC and GC-EGJ groups within our data and TCGA database. Among sixteen patients, four were identified as monoclonal, in which 11, 10, 26 and 6 somatic mutations were shared within different tumors of P7, P8, P9 and P16, respectively. However, no common mutation between different tumors of the same patient was found among the other 12 patients. After identifying predisposing genes, we found that germline MSH2 and NCOR2 mutations were significantly dominant in 8/12 and 10/12 of genetic MGC patients. Additionally, all patients were identified with MSH2 mutations in cancer samples of those genetic MGC patients. Taking genetic MGCs as a whole, we identified that TP53 were significantly mutated in 14 of 25 tumor samples. Main conclusions: WES analyses are suggestive of monoclonal and polyclonal origin of MGC, which may promote the classification of MGC into genetic and metastatic MGC. For patients with genetic MGC, germline MSH2 X314_splice variants may contribute to carcinogenesis, thus prompting the consideration of more radical surgery and/or anti-PD-1/PD-L1 therapy.
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17
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Rath A, Mishra A, Ferreira VD, Hu C, Omerza G, Kelly K, Hesse A, Reddi HV, Grady JP, Heinen CD. Functional interrogation of Lynch syndrome-associated MSH2 missense variants via CRISPR-Cas9 gene editing in human embryonic stem cells. Hum Mutat 2019; 40:2044-2056. [PMID: 31237724 DOI: 10.1002/humu.23848] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2018] [Revised: 05/08/2019] [Accepted: 06/19/2019] [Indexed: 12/18/2022]
Abstract
Lynch syndrome (LS) predisposes patients to cancer and is caused by germline mutations in the DNA mismatch repair (MMR) genes. Identifying the deleterious mutation, such as a frameshift or nonsense mutation, is important for confirming an LS diagnosis. However, discovery of a missense variant is often inconclusive. The effects of these variants of uncertain significance (VUS) on disease pathogenesis are unclear, though understanding their impact on protein function can help determine their significance. Laboratory functional studies performed to date have been limited by their artificial nature. We report here an in-cellulo functional assay in which we engineered site-specific MSH2 VUS using clustered regularly interspaced short palindromic repeats-Cas9 gene editing in human embryonic stem cells. This approach introduces the variant into the endogenous MSH2 loci, while simultaneously eliminating the wild-type gene. We characterized the impact of the variants on cellular MMR functions including DNA damage response signaling and the repair of DNA microsatellites. We classified the MMR functional capability of eight of 10 VUS providing valuable information for determining their likelihood of being bona fide pathogenic LS variants. This human cell-based assay system for functional testing of MMR gene VUS will facilitate the identification of high-risk LS patients.
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Affiliation(s)
- Abhijit Rath
- Center for Molecular Oncology and Institute for Systems Genomics, UConn Health, Farmington, Connecticut
| | - Akriti Mishra
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, Connecticut
| | | | - Chaoran Hu
- Department of Statistics, University of Connecticut, Storrs, Connecticut.,Connecticut Institute for Clinical and Translational Science, UConn Health, Farmington, Connecticut
| | - Gregory Omerza
- Clinical Genomics Laboratory, The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut
| | - Kevin Kelly
- Clinical Genomics Laboratory, The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut
| | - Andrew Hesse
- Clinical Genomics Laboratory, The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut
| | - Honey V Reddi
- Clinical Genomics Laboratory, The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut
| | - James P Grady
- Connecticut Institute for Clinical and Translational Science, UConn Health, Farmington, Connecticut
| | - Christopher D Heinen
- Center for Molecular Oncology and Institute for Systems Genomics, UConn Health, Farmington, Connecticut
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18
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Ito T, Yamaguchi T, Wakatsuki T, Suzuki T, Eguchi H, Okazaki Y, Yamamoto G, Tachikawa T, Kawakami S, Sasaki A, Akagi K, Ishida H. The single-base-pair deletion, MSH2 c.2635-3delC affecting intron 15 splicing can be a cause of Lynch syndrome. Jpn J Clin Oncol 2019; 49:477-480. [PMID: 30882153 DOI: 10.1093/jjco/hyz031] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2018] [Revised: 01/08/2019] [Accepted: 02/19/2019] [Indexed: 01/03/2023] Open
Abstract
The proband was a 62-year-old man with ureter cancer. He had a history of metachronous colorectal and gastric cancer. Immunohistochemical staining showed the absence of both MSH2 and MSH6 proteins in the ureter cancer and other available cancer tissue specimens. Genetic testing was conducted to identify the causative genes of hereditary gastrointestinal cancer syndromes including mismatch repair genes. We detected a germline variant, c.2635-3delC, within the splice acceptor site of exon 16, in the MSH2 gene. To investigate whether this variant affected splicing of the gene, RNA sequencing was performed using blood samples. We observed a substantial amount of the transcripts that lacked proper splicing of intron 15 in the indexed case, whereas, a very low amount of such aberrant transcripts was detected in the controls, strongly indicating an association between the variant and splicing defect. These results indicate that MSH2 c.2635-3delC affects normal splicing and might be a cause of Lynch syndrome.
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Affiliation(s)
- Tetsuya Ito
- Department of Digestive Tract and General Surgery, Saitama Medical Center, Saitama Medical University, Saitama, Japan
| | - Tatsuro Yamaguchi
- Department of Surgery, Tokyo Metropolitan Cancer and Infectious Diseases Center Komagome Hospital, Tokyo, Japan
| | - Tomokazu Wakatsuki
- Division of Molecular Diagnosis and Cancer Prevention, Saitama Cancer Center, Saitama, Japan
| | - Tsuyoshi Suzuki
- Department of Digestive Tract and General Surgery, Saitama Medical Center, Saitama Medical University, Saitama, Japan
| | - Hidetaka Eguchi
- Diagnosis and Therapeutics of Intractable Disease, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Yasushi Okazaki
- Diagnosis and Therapeutics of Intractable Disease, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Gou Yamamoto
- Division of Molecular Diagnosis and Cancer Prevention, Saitama Cancer Center, Saitama, Japan
| | - Tetsuhiko Tachikawa
- Division of Molecular Diagnosis and Cancer Prevention, Saitama Cancer Center, Saitama, Japan
| | - Satoru Kawakami
- Department of Urology, Saitama Medical Center, Saitama Medical University, Saitama, Japan
| | - Astushi Sasaki
- Department of Pathology, Saitama Medical University, Moroyama, Saitama, Japan
| | - Kiwamu Akagi
- Division of Molecular Diagnosis and Cancer Prevention, Saitama Cancer Center, Saitama, Japan
| | - Hideyuki Ishida
- Department of Digestive Tract and General Surgery, Saitama Medical Center, Saitama Medical University, Saitama, Japan
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19
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Valle L, Vilar E, Tavtigian SV, Stoffel EM. Genetic predisposition to colorectal cancer: syndromes, genes, classification of genetic variants and implications for precision medicine. J Pathol 2019; 247:574-588. [PMID: 30584801 PMCID: PMC6747691 DOI: 10.1002/path.5229] [Citation(s) in RCA: 100] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2018] [Revised: 12/21/2018] [Accepted: 12/23/2018] [Indexed: 12/15/2022]
Abstract
This article reviews genes and syndromes associated with predisposition to colorectal cancer (CRC), with an overview of gene variant classification. We include updates on the application of preventive and therapeutic measures, focusing on the use of non-steroidal anti-inflammatory drugs (NSAIDs) and immunotherapy. Germline pathogenic variants in genes conferring high or moderate risk to cancer are detected in 6-10% of all CRCs and 20% of those diagnosed before age 50. CRC syndromes can be subdivided into nonpolyposis and polyposis entities, the most common of which are Lynch syndrome and familial adenomatous polyposis, respectively. In addition to known and novel genes associated with highly penetrant CRC risk, identification of pathogenic germline variants in genes associated with moderate-penetrance cancer risk and/or hereditary cancer syndromes not traditionally linked to CRC may have an impact on genetic testing, counseling, and surveillance. The use of multigene panels in genetic testing has exposed challenges in the classification of variants of uncertain significance. We provide an overview of the main classification systems and strategies for improving these. Finally, we highlight approaches for integrating chemoprevention in the care of individuals with genetic predisposition to CRC and use of targeted agents and immunotherapy for treatment of mismatch repair-deficient and hypermutant tumors. Copyright © 2018 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.
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Affiliation(s)
- Laura Valle
- Hereditary Cancer Program, Catalan Institute of Oncology, IDIBELL, Barcelona, Spain
- Program in Molecular Mechanisms and Experimental Therapy in Oncology (Oncobell), IDIBELL, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Spain
| | - Eduardo Vilar
- Departments of Clinical Cancer Prevention, GI Medical Oncology and Clinical Cancer Genetics Program, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
- Graduate School of Biomedical Sciences, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Sean V. Tavtigian
- Department of Oncological Sciences, University of Utah School of Medicine, Salt Lake City, UT, United States
- Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, United States
| | - Elena M. Stoffel
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI, United States
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20
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Rañola JMO, Liu Q, Rosenthal EA, Shirts BH. A comparison of cosegregation analysis methods for the clinical setting. Fam Cancer 2019; 17:295-302. [PMID: 28695303 DOI: 10.1007/s10689-017-0017-7] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Quantitative cosegregation analysis can help evaluate the pathogenicity of genetic variants. However, genetics professionals without statistical training often use simple methods, reporting only qualitative findings. We evaluate the potential utility of quantitative cosegregation in the clinical setting by comparing three methods. One thousand pedigrees each were simulated for benign and pathogenic variants in BRCA1 and MLH1 using United States historical demographic data to produce pedigrees similar to those seen in the clinic. These pedigrees were analyzed using two robust methods, full likelihood Bayes factors (FLB) and cosegregation likelihood ratios (CSLR), and a simpler method, counting meioses. Both FLB and CSLR outperform counting meioses when dealing with pathogenic variants, though counting meioses is not far behind. For benign variants, FLB and CSLR greatly outperform as counting meioses is unable to generate evidence for benign variants. Comparing FLB and CSLR, we find that the two methods perform similarly, indicating that quantitative results from either of these methods could be combined in multifactorial calculations. Combining quantitative information will be important as isolated use of cosegregation in single families will yield classification for less than 1% of variants. To encourage wider use of robust cosegregation analysis, we present a website ( http://www.analyze.myvariant.org ) which implements the CSLR, FLB, and Counting Meioses methods for ATM, BRCA1, BRCA2, CHEK2, MEN1, MLH1, MSH2, MSH6, and PMS2. We also present an R package, CoSeg, which performs the CSLR analysis on any gene with user supplied parameters. Future variant classification guidelines should allow nuanced inclusion of cosegregation evidence against pathogenicity.
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Affiliation(s)
- John Michael O Rañola
- Department of Laboratory Medicine, University of Washington, Seattle, WA, 98105, USA.
| | - Quanhui Liu
- Department of Bioengineering, University of Washington, Seattle, WA, 98105, USA
| | - Elisabeth A Rosenthal
- Department of Medicine, Division of Medical Genetics, University of Washington, Seattle, WA, 98105, USA
| | - Brian H Shirts
- Department of Laboratory Medicine, University of Washington, Seattle, WA, 98105, USA
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21
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Rosenthal EA, Ranola JMO, Shirts BH. Power of pedigree likelihood analysis in extended pedigrees to classify rare variants of uncertain significance in cancer risk genes. Fam Cancer 2018; 16:611-620. [PMID: 28534081 DOI: 10.1007/s10689-017-9989-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Rare and private variants of uncertain significance (VUS) are routinely identified in clinical panel, exome, and genome sequencing. We investigated the power of single family co-segregation analysis to aid classification of VUS. We simulated thousands of pedigrees using demographics in China and the United States, segregating benign and pathogenic variants. Genotypes and phenotypes were simulated using penetrance models for Lynch syndrome and breast/ovarian cancer. We calculated LOD scores adjusted for proband ascertainment (LODadj), to determine power to yield quantitative evidence for, or against, pathogenicity of the VUS. Power to classify VUS was higher for Chinese than United States pedigrees. The number of affected individuals explained the most variation in LODadj (21-38%). The distance to the furthest affected relative (FAR) from the proband explained 1-7% of the variation for the benign VUS and Lynch associated cancers. Minimum age of onset (MAO) explained 5-13% of the variation in families with pathogenic breast/ovarian cancer variants. Random removal of 50% of the phenotype/genotype data reduced power and the variation in LODadj was best explained by FAR followed by the number of affected individuals and MAO when the founder was only two generations from the proband. Power to classify benign variants was ~2x power to classify pathogenic variants. Affecteds-only analysis resulted in virtually no power to correctly classify benign variants and reduced power to classify pathogenic variants. These results can be used to guide recruitment efforts to classify rare and private VUS.
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Affiliation(s)
- Elisabeth A Rosenthal
- Division of Medical Genetics, School of Medicine, University of Washington, Seattle, WA, USA.
| | - John Michael O Ranola
- Department of Laboratory Medicine, University of Washington Medical Center, Seattle, WA, USA
| | - Brian H Shirts
- Department of Laboratory Medicine, University of Washington Medical Center, Seattle, WA, USA
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22
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Shirts BH, Konnick EQ, Upham S, Walsh T, Ranola JMO, Jacobson AL, King MC, Pearlman R, Hampel H, Pritchard CC. Using Somatic Mutations from Tumors to Classify Variants in Mismatch Repair Genes. Am J Hum Genet 2018; 103:19-29. [PMID: 29887214 DOI: 10.1016/j.ajhg.2018.05.001] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2018] [Accepted: 05/01/2018] [Indexed: 01/28/2023] Open
Abstract
Present guidelines for classification of constitutional variants do not incorporate inferences from mutations seen in tumors, even when these are associated with a specific molecular phenotype. When somatic mutations and constitutional mutations lead to the same molecular phenotype, as for the mismatch repair genes, information from somatic mutations may enable interpretation of previously unclassified variants. To test this idea, we first estimated likelihoods that somatic variants in MLH1, MSH2, MSH6, and PMS2 drive microsatellite instability and characteristic IHC staining patterns by calculating likelihoods of high versus low normalized variant read fractions of 153 mutations known to be pathogenic versus those of 760 intronic passenger mutations from 174 paired tumor-normal samples. Mutations that explained the tumor mismatch repair phenotype had likelihood ratio for high variant read fraction of 1.56 (95% CI 1.42-1.71) at sites with no loss of heterozygosity and of 26.5 (95% CI 13.2-53.0) at sites with loss of heterozygosity. Next, we applied these ratios to 165 missense, synonymous, and splice variants observed in tumors, combining in a Bayesian analysis the likelihood ratio corresponding with the adjusted variant read fraction with pretest probabilities derived from published analyses and public databases. We suggest classifications for 86 of 165 variants: 7 benign, 31 likely benign, 22 likely pathogenic, and 26 pathogenic. These results illustrate that for mismatch repair genes, characterization of tumor mutations permits tumor mutation data to inform constitutional variant classification. We suggest modifications to incorporate molecular phenotype in future variant classification guidelines.
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Affiliation(s)
- Brian H Shirts
- Department of Laboratory Medicine, University of Washington, Seattle, WA 98195, USA.
| | - Eric Q Konnick
- Department of Laboratory Medicine, University of Washington, Seattle, WA 98195, USA
| | - Sarah Upham
- Department of Laboratory Medicine, University of Washington, Seattle, WA 98195, USA
| | - Tom Walsh
- Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, WA 98195, USA
| | | | - Angela L Jacobson
- Department of Laboratory Medicine, University of Washington, Seattle, WA 98195, USA
| | - Mary-Claire King
- Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, WA 98195, USA
| | - Rachel Pearlman
- Department of Internal Medicine, Division of Human Genetics, The Ohio State University Comprehensive Cancer Center, Columbus, OH 43221, USA
| | - Heather Hampel
- Department of Internal Medicine, Division of Human Genetics, The Ohio State University Comprehensive Cancer Center, Columbus, OH 43221, USA
| | - Colin C Pritchard
- Department of Laboratory Medicine, University of Washington, Seattle, WA 98195, USA
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23
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Köger N, Paulsen L, López-Kostner F, Della Valle A, Vaccaro CA, Palmero EI, Alvarez K, Sarroca C, Neffa F, Kalfayan PG, Gonzalez ML, Rossi BM, Reis RM, Brieger A, Zeuzem S, Hinrichsen I, Dominguez-Valentin M, Plotz G. Evaluation of MLH1 variants of unclear significance. Genes Chromosomes Cancer 2018. [PMID: 29520894 DOI: 10.1002/gcc.22536] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Inactivating mutations in the MLH1 gene cause the cancer predisposition Lynch syndrome, but for small coding genetic variants it is mostly unclear if they are inactivating or not. Nine such MLH1 variants have been identified in South American colorectal cancer (CRC) patients (p.Tyr97Asp, p.His112Gln, p.Pro141Ala, p.Arg265Pro, p.Asn338Ser, p.Ile501del, p.Arg575Lys, p.Lys618del, p.Leu676Pro), and evidence of pathogenicity or neutrality was not available for the majority of these variants. We therefore performed biochemical laboratory testing of the variant proteins and compared the results to protein in silico predictions on structure and conservation. Additionally, we collected all available clinical information of the families to come to a conclusion concerning their pathogenic potential and facilitate clinical diagnosis in the affected families. We provide evidence that four of the alterations are causative for Lynch syndrome, four are likely neutral and one shows compromised activity which can currently not be classified with respect to its pathogenic potential. The work demonstrates that biochemical testing, corroborated by congruent evolutionary and structural information, can serve to reliably classify uncertain variants when other data are insufficient.
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Affiliation(s)
- Nicole Köger
- Biomedizinisches Forschungslabor, Medizinische Klinik 1, Universitätsklinik Frankfurt, Frankfurt, Germany
| | - Lea Paulsen
- Biomedizinisches Forschungslabor, Medizinische Klinik 1, Universitätsklinik Frankfurt, Frankfurt, Germany
| | | | - Adriana Della Valle
- Hospital Fuerzas Armadas, Grupo Colaborativo Uruguayo, Investigación de Afecciones Oncológicas Hereditarias (GCU), Montevideo, Uruguay
| | | | - Edenir Inêz Palmero
- Barretos Cancer Hospital, Molecular Oncology Research Center, Barretos, São Paulo, Brazil.,Barretos School of Health Sciences-FACISB, Barretos, São Paulo, Brazil
| | - Karin Alvarez
- Laboratorio de Oncología y Genética Molecular, Clínica Los Condes, Santiago, Chile
| | - Carlos Sarroca
- Hospital Fuerzas Armadas, Grupo Colaborativo Uruguayo, Investigación de Afecciones Oncológicas Hereditarias (GCU), Montevideo, Uruguay
| | - Florencia Neffa
- Hospital Fuerzas Armadas, Grupo Colaborativo Uruguayo, Investigación de Afecciones Oncológicas Hereditarias (GCU), Montevideo, Uruguay
| | | | - Maria Laura Gonzalez
- Hereditary Cancer Program (PROCANHE), Hospital Italiano, Buenos Aires, Argentina
| | | | - Rui Manuel Reis
- Biomedizinisches Forschungslabor, Medizinische Klinik 1, Universitätsklinik Frankfurt, Frankfurt, Germany.,Life and Health Sciences Q5 753 Research Institute (ICVS), Health Sciences School, University of Minho, Braga, 754, Portugal.,ICVS/3B's-PT Government Associate Laboratory, Braga, Guimarães, 755, Portugal
| | - Angela Brieger
- Biomedizinisches Forschungslabor, Medizinische Klinik 1, Universitätsklinik Frankfurt, Frankfurt, Germany
| | - Stefan Zeuzem
- Biomedizinisches Forschungslabor, Medizinische Klinik 1, Universitätsklinik Frankfurt, Frankfurt, Germany
| | - Inga Hinrichsen
- Biomedizinisches Forschungslabor, Medizinische Klinik 1, Universitätsklinik Frankfurt, Frankfurt, Germany
| | - Mev Dominguez-Valentin
- Department of Tumor Biology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
| | - Guido Plotz
- Biomedizinisches Forschungslabor, Medizinische Klinik 1, Universitätsklinik Frankfurt, Frankfurt, Germany
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24
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Chandonia JM, Adhikari A, Carraro M, Chhibber A, Cutting GR, Fu Y, Gasparini A, Jones DT, Kramer A, Kundu K, Lam HYK, Leonardi E, Moult J, Pal LR, Searls DB, Shah S, Sunyaev S, Tosatto SCE, Yin Y, Buckley BA. Lessons from the CAGI-4 Hopkins clinical panel challenge. Hum Mutat 2017; 38:1155-1168. [PMID: 28397312 DOI: 10.1002/humu.23225] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2017] [Revised: 03/24/2017] [Accepted: 03/29/2017] [Indexed: 12/17/2022]
Abstract
The CAGI-4 Hopkins clinical panel challenge was an attempt to assess state-of-the-art methods for clinical phenotype prediction from DNA sequence. Participants were provided with exonic sequences of 83 genes for 106 patients from the Johns Hopkins DNA Diagnostic Laboratory. Five groups participated in the challenge, predicting both the probability that each patient had each of the 14 possible classes of disease, as well as one or more causal variants. In cases where the Hopkins laboratory reported a variant, at least one predictor correctly identified the disease class in 36 of the 43 patients (84%). Even in cases where the Hopkins laboratory did not find a variant, at least one predictor correctly identified the class in 39 of the 63 patients (62%). Each prediction group correctly diagnosed at least one patient that was not successfully diagnosed by any other group. We discuss the causal variant predictions by different groups and their implications for further development of methods to assess variants of unknown significance. Our results suggest that clinically relevant variants may be missed when physicians order small panels targeted on a specific phenotype. We also quantify the false-positive rate of DNA-guided analysis in the absence of prior phenotypic indication.
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Affiliation(s)
- John-Marc Chandonia
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California
| | - Aashish Adhikari
- Department of Plant and Microbial Biology, University of California, Berkeley, California
| | - Marco Carraro
- Department of Biomedical Sciences, University of Padova, Padova, Italy
| | | | - Garry R Cutting
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Yao Fu
- Roche Sequencing Solutions, Belmont, California
| | - Alessandra Gasparini
- Department of Biomedical Sciences, University of Padova, Padova, Italy.,Department of Women's and Children's Health, University of Padova, Padova, Italy
| | - David T Jones
- Department of Computer Science, University College London, London, United Kingdom
| | | | - Kunal Kundu
- Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, Maryland.,Computational Biology, Bioinformatics and Genomics, Biological Sciences Graduate Program, University of Maryland, College Park, Maryland
| | | | - Emanuela Leonardi
- Department of Women's and Children's Health, University of Padova, Padova, Italy
| | - John Moult
- Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, Maryland.,Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland
| | - Lipika R Pal
- Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, Maryland
| | | | - Sohela Shah
- Qiagen Bioinformatics, Redwood City, California
| | - Shamil Sunyaev
- Division of Genetics, Department of Medicine, Brigham & Women's Hospital, Harvard Medical School, Boston, Massachusetts.,Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts
| | - Silvio C E Tosatto
- Department of Biomedical Sciences, University of Padova, Padova, Italy.,CNR Institute of Neuroscience, Padova, Italy
| | - Yizhou Yin
- Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, Maryland.,Computational Biology, Bioinformatics and Genomics, Biological Sciences Graduate Program, University of Maryland, College Park, Maryland
| | - Bethany A Buckley
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland
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