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He SY, Li YC, Wang Y, Peng HL, Zhou CL, Zhang CM, Chen SL, Yin JF, Lin M. Fecal gene detection based on next generation sequencing for colorectal cancer diagnosis. World J Gastroenterol 2022; 28:2920-2936. [PMID: 35978873 PMCID: PMC9280739 DOI: 10.3748/wjg.v28.i25.2920] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/16/2022] [Revised: 03/18/2022] [Accepted: 05/28/2022] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Colorectal cancer (CRC) is one of the most common malignancies worldwide. Given its insidious onset, the condition often already progresses to advanced stage when symptoms occur. Thus, early diagnosis is of great significance for timely clinical intervention, efficacy enhancement, and prognostic improvement. Featuring high throughput, fastness, and rich information, next generation sequencing (NGS) can greatly shorten the detection time, which is a widely used detection technique at present.
AIM To screen specific genes or gene combinations in fecal DNA that are suitable for diagnosis and prognostic prediction of CRC, and to establish a technological platform for CRC screening, diagnosis, and efficacy monitoring through fecal DNA detection.
METHODS NGS was used to sequence the stool DNA of patients with CRC, which were then compared with the genetic testing results of the stool samples of normal controls and patients with benign intestinal disease, as well as the tumor tissues of CRC patients. Specific genes or gene combinations in fecal DNA suitable for diagnosis and prognostic prediction of CRC were screened, and their significances in diagnosing CRC and predicting patients' prognosis were comprehensively evaluated.
RESULTS High mutation frequencies of TP53, APC, and KRAS were detected in the stools and tumor tissues of CRC patients prior to surgery. Contrastively, no pathogenic mutations of the above three genes were noted in the postoperative stools, the normal controls, or the benign intestinal disease group. This indicates that tumor-specific DNA was detectable in the preoperative stools of CRC patients. The preoperative fecal expression of tumor-associated genes can reflect the gene mutations in tumor tissues to some extent. Compared to the postoperative stools and the stools in the two control groups, the pathogenic mutation frequencies of TP53 and KRAS were significantly higher for the preoperative stools (χ2 = 7.328, P < 0.05; χ2 = 4.219, P < 0.05), suggesting that fecal TP53 and KRAS genes can be used for CRC screening, diagnosis, and prognostic prediction. No significant difference in the pathogenic mutation frequency of the APC gene was found from the postoperative stools or the two control groups (χ2 = 0.878, P > 0.05), so further analysis with larger sample size is required. Among CRC patients, the pathogenic mutation sites of TP53 occurred in 16 of 27 preoperative stools, with a true positive rate of 59.26%, while the pathogenic mutation sites of KRAS occurred in 10 stools, with a true positive rate of 37.04%. The sensitivity and negative predictive values of the combined genetic testing of TP53 and KRAS were 66.67% (18/27) and 68.97%, respectively, both of which were higher than those of TP53 or KRAS mutation detection alone, suggesting that the combined genetic testing can improve the CRC detection rate. The mutation sites TP53 exon 4 A84G and EGFR exon 20 I821T (mutation start and stop positions were both 7579436 for the former, while 55249164 for the latter) were found in the preoperative stools and tumor tissues. These "undetected" mutation sites may be new types of mutations occurring during the CRC carcinogenesis and progression, which needs to be confirmed through further research. Some mutations of "unknown clinical significance" were found in such genes as TP53, PTEN, KRAS, BRAF, AKT1, and PIK3CA, whose clinical values is worthy of further exploration.
CONCLUSION NGS-based fecal genetic testing can be used as a complementary technique for the CRC diagnosis. Fecal TP53 and KRAS can be used as specific genes for the screening, diagnosis, prognostic prediction, and recurrence monitoring of CRC. Moreover, the combined testing of TP53 and KRAS genes can improve the CRC detection rate.
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Affiliation(s)
- Si-Yu He
- Department of Clinical Laboratory, Taizhou People's Hospital (Postgraduate Training Base of Dalian Medical University), Taizhou 225300, Jiangsu Province, China
- Department of Clinical Laboratory, The First People's Hospital of Tianmen City, Tianmen 431700, Hubei Province, China
| | - Ying-Chun Li
- Department of General Surgery, Taizhou People's Hospital (Postgraduate Training Base of Dalian Medical University), Taizhou 225300, Jiangsu Province, China
| | - Yong Wang
- Department of General Surgery, Taizhou People's Hospital (Postgraduate Training Base of Dalian Medical University), Taizhou 225300, Jiangsu Province, China
| | - Hai-Lin Peng
- Department of Clinical Laboratory, Taizhou People's Hospital (Postgraduate Training Base of Dalian Medical University), Taizhou 225300, Jiangsu Province, China
| | - Cheng-Lin Zhou
- Department of Clinical Laboratory, Taizhou People's Hospital (Postgraduate Training Base of Dalian Medical University), Taizhou 225300, Jiangsu Province, China
| | - Chuan-Meng Zhang
- Central Laboratory, Taizhou People's Hospital (Postgraduate training base of Dalian Medical University), Taizhou 225300, Jiangsu Province, China
| | - Sheng-Lan Chen
- Department of Laboratory, Taizhou Genewill Medical Laboratory Company Limited, Taizhou 225300, Jiangsu Province, China
| | - Jian-Feng Yin
- Department of Laboratory, Jiangsu CoWin Biotech Co., Ltd., Taizhou 225300, Jiangsu Province, China
| | - Mei Lin
- Department of Clinical Laboratory, Taizhou People's Hospital (Postgraduate Training Base of Dalian Medical University), Taizhou 225300, Jiangsu Province, China
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Murphy A, Solomons J, Risby P, Gabriel J, Bedenham T, Johnson M, Atkinson N, Bailey AA, Bird‐Lieberman E, Leedham SJ, East JE, Biswas S. Germline variant testing in serrated polyposis syndrome. J Gastroenterol Hepatol 2022; 37:861-869. [PMID: 35128723 PMCID: PMC9305167 DOI: 10.1111/jgh.15791] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Revised: 12/13/2021] [Accepted: 01/12/2022] [Indexed: 12/09/2022]
Abstract
BACKGROUND AND AIM Serrated polyposis syndrome (SPS) is now known to be the commonest polyposis syndrome. Previous analyses for germline variants have shown no consistent positive findings. To exclude other polyposis syndromes, 2019 British Society of Gastroenterology (BSG) guidelines advise gene panel testing if the patient is under 50 years, there are multiple affected individuals within a family, or there is dysplasia within any of the polyps. METHODS A database of SPS patients was established at the Oxford University Hospitals NHS Foundation Trust. Patients were referred for genetic assessment based on personal and family history and patient preference. The majority were tested for a hereditary colorectal cancer panel including MUTYH, APC, PTEN, SMAD4, BMPR1A, STK11, NTLH1, POLD1, POLE, GREM1 (40-kb duplication), PMS2, and Lynch syndrome mismatch repair genes. RESULTS One hundred and seventy-three patients were diagnosed with SPS based on World Health Organization 2019 criteria between February 2010 and December 2020. The mean age of diagnosis was 54.2 ± 16.8 years. Seventy-three patients underwent genetic testing and 15/73 (20.5%) were found to have germline variants, of which 7/73 (9.6%) had a pathogenic variant (MUTYH n = 2, SMAD4 n = 1, CHEK2 n = 2, POLD1 n = 1, and RNF43 n = 1). Only 60% (9/15) of these patients would have been recommended for gene panel testing according to current BSG guidelines. CONCLUSIONS A total of 20.5% of SPS patients tested were affected by heterozygous germline variants, including previously unreported associations with CHEK2 and POLD1. This led to a change in management in seven patients (9.6%). Current recommendations may miss SPS associated with germline variants, which is more common than previously anticipated.
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Affiliation(s)
- Aisling Murphy
- Translational Gastroenterology Unit, Oxford NIHR Biomedical Research CentreUniversity of OxfordOxfordUK
| | - Joyce Solomons
- Oxford Centre for Genomic Medicine, Nuffield Orthopaedic CentreOxford University Hospitals NHS Foundation TrustOxfordUK
| | - Peter Risby
- Oxford Centre for Genomic Medicine, Nuffield Orthopaedic CentreOxford University Hospitals NHS Foundation TrustOxfordUK
| | - Jessica Gabriel
- Oxford Regional Genetics Laboratories, Churchill HospitalOxford University Hospitals NHS Foundation TrustOxfordUK
| | - Tina Bedenham
- Oxford Regional Genetics Laboratories, Churchill HospitalOxford University Hospitals NHS Foundation TrustOxfordUK
| | - Michael Johnson
- Translational Gastroenterology Unit, Oxford NIHR Biomedical Research CentreUniversity of OxfordOxfordUK
| | - Nathan Atkinson
- New Zealand Familial Gastrointestinal Cancer RegistryAuckland City HospitalAucklandNew Zealand
| | - Adam A Bailey
- Translational Gastroenterology Unit, Oxford NIHR Biomedical Research CentreUniversity of OxfordOxfordUK
| | - Elizabeth Bird‐Lieberman
- Translational Gastroenterology Unit, Oxford NIHR Biomedical Research CentreUniversity of OxfordOxfordUK
| | - Simon J Leedham
- Translational Gastroenterology Unit, Oxford NIHR Biomedical Research CentreUniversity of OxfordOxfordUK,Intestinal Stem Cell Biology Lab, Wellcome Centre for Human GeneticsUniversity of OxfordOxfordUK
| | - James E East
- Translational Gastroenterology Unit, Oxford NIHR Biomedical Research CentreUniversity of OxfordOxfordUK
| | - Sujata Biswas
- Translational Gastroenterology Unit, Oxford NIHR Biomedical Research CentreUniversity of OxfordOxfordUK,Gastroenterology DepartmentBuckinghamshire Healthcare NHS TrustUK
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Abu-Ghazaleh N, Kaushik V, Gorelik A, Jenkins M, Macrae F. Worldwide prevalence of Lynch syndrome in patients with colorectal cancer: Systematic review and meta-analysis. Genet Med 2022; 24:971-985. [PMID: 35177335 DOI: 10.1016/j.gim.2022.01.014] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Revised: 01/20/2022] [Accepted: 01/21/2022] [Indexed: 10/19/2022] Open
Abstract
PURPOSE Lynch syndrome (LS) is the most common hereditary colorectal cancer (CRC) syndrome, with an estimated prevalence of 2% to 3% of CRC. A prevalence study is needed to provide accurate estimates of the true prevalence of LS. METHODS MEDLINE (Ovid), Embase, and Web of Science were searched. Prevalence was calculated by random effects meta-analysis models. I2 score was used to assess heterogeneity across studies. Meta-regression was performed for between-study variance. RESULTS A total of 51 studies were included in this review. The overall pooled yield of LS screening was 2.2% based on all methods of detection. Studies performing germline tests on all participants with CRC reported higher prevalence (5.1%) as opposed to studies only performing germline tests on participants with tumors with mismatch repair deficiency (1.6%) or microsatellite instability (1.1%). Selected cohorts of CRC had a higher prevalence of germline LS diagnoses. CONCLUSION LS prevalence across multiple ethnic, geographic, and clinical populations is remarkably similar. Universal germline testing of patients presenting with cancer identifies that most CRCs are attributed to LS. Young patients presenting with CRC and those who fulfill criteria for a familial risk provide the highest returns for LS identification. Our study supports the universal germline CRC screening for LS.
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Affiliation(s)
- Nadine Abu-Ghazaleh
- Department of Medicine, University of Melbourne, Parkville, Victoria, Australia; Department of Colorectal Cancer and Genetics, Royal Melbourne Hospital, Parkville, Victoria, Australia.
| | - Varun Kaushik
- Department of Medicine, University of Melbourne, Parkville, Victoria, Australia; Department of Colorectal Cancer and Genetics, Royal Melbourne Hospital, Parkville, Victoria, Australia
| | - Alexandra Gorelik
- Department of Colorectal Cancer and Genetics, Royal Melbourne Hospital, Parkville, Victoria, Australia; Monash Department of Clinical Epidemiology, Cabrini Institute, Malvern, Victoria, Australia
| | - Mark Jenkins
- Department of Medicine, University of Melbourne, Parkville, Victoria, Australia; School of Population and Global Health, University of Melbourne, Parkville, Victoria, Australia
| | - Finlay Macrae
- Department of Medicine, University of Melbourne, Parkville, Victoria, Australia; Department of Colorectal Cancer and Genetics, Royal Melbourne Hospital, Parkville, Victoria, Australia
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Olkinuora AP, Peltomäki PT, Aaltonen LA, Rajamäki K. From APC to the genetics of hereditary and familial colon cancer syndromes. Hum Mol Genet 2021; 30:R206-R224. [PMID: 34329396 PMCID: PMC8490010 DOI: 10.1093/hmg/ddab208] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Revised: 07/01/2021] [Accepted: 07/05/2021] [Indexed: 11/12/2022] Open
Abstract
Hereditary colorectal cancer (CRC) syndromes attributable to high penetrance mutations represent 9-26% of young-onset CRC cases. The clinical significance of many of these mutations is understood well enough to be used in diagnostics and as an aid in patient care. However, despite the advances made in the field, a significant proportion of familial and early-onset cases remains molecularly uncharacterized and extensive work is still needed to fully understand the genetic nature of CRC susceptibility. With the emergence of next-generation sequencing and associated methods, several predisposition loci have been unraveled, but validation is incomplete. Individuals with cancer-predisposing mutations are currently enrolled in life-long surveillance, but with the development of new treatments, such as cancer vaccinations, this might change in the not so distant future for at least some individuals. For individuals without a known cause for their disease susceptibility, prevention and therapy options are less precise. Herein, we review the progress achieved in the last three decades with a focus on how CRC predisposition genes were discovered. Furthermore, we discuss the clinical implications of these discoveries and anticipate what to expect in the next decade.
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Affiliation(s)
- Alisa P Olkinuora
- Department of Medical and Clinical Genetics, Medicum, University of Helsinki, 00014 Helsinki, Finland
- iCAN Digital Precision Cancer Medicine Flagship, University of Helsinki, 00014 Helsinki, Finland
| | - Päivi T Peltomäki
- Department of Medical and Clinical Genetics, Medicum, University of Helsinki, 00014 Helsinki, Finland
- iCAN Digital Precision Cancer Medicine Flagship, University of Helsinki, 00014 Helsinki, Finland
| | - Lauri A Aaltonen
- Department of Medical and Clinical Genetics, Medicum, University of Helsinki, 00014 Helsinki, Finland
- iCAN Digital Precision Cancer Medicine Flagship, University of Helsinki, 00014 Helsinki, Finland
- Applied Tumor Genomics Research Program, Research Programs Unit, University of Helsinki, 00014 Helsinki, Finland
| | - Kristiina Rajamäki
- Department of Medical and Clinical Genetics, Medicum, University of Helsinki, 00014 Helsinki, Finland
- Applied Tumor Genomics Research Program, Research Programs Unit, University of Helsinki, 00014 Helsinki, Finland
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5
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Salo-Mullen EE, Maio A, Mukherjee S, Bandlamudi C, Shia J, Kemel Y, Cadoo KA, Liu Y, Carlo M, Ranganathan M, Kane S, Srinivasan P, Chavan SS, Donoghue MTA, Bourque C, Sheehan M, Tejada PR, Patel Z, Arnold AG, Kennedy JA, Amoroso K, Breen K, Catchings A, Sacca R, Marcell V, Markowitz AJ, Latham A, Walsh M, Misyura M, Ceyhan-Birsoy O, Solit DB, Berger MF, Robson ME, Taylor BS, Offit K, Mandelker D, Stadler ZK. Prevalence and Characterization of Biallelic and Monoallelic NTHL1 and MSH3 Variant Carriers From a Pan-Cancer Patient Population. JCO Precis Oncol 2021; 5:PO.20.00443. [PMID: 34250384 PMCID: PMC8232072 DOI: 10.1200/po.20.00443] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Revised: 01/11/2021] [Accepted: 01/27/2021] [Indexed: 01/03/2023] Open
Abstract
NTHL1 and MSH3 have been implicated as autosomal recessive cancer predisposition genes. Although individuals with biallelic NTHL1 and MSH3 pathogenic variants (PVs) have increased cancer and polyposis risk, risks for monoallelic carriers are uncertain. We sought to assess the prevalence and characterize NTHL1 and MSH3 from a large pan-cancer patient population. MATERIALS AND METHODS Patients with pan-cancer (n = 11,081) underwent matched tumor-normal sequencing with consent for germline analysis. Medical records and tumors were reviewed and analyzed. Prevalence of PVs was compared with reference controls (Genome Aggregation Database). RESULTS NTHL1-PVs were identified in 40 patients including 39 monoallelic carriers (39/11,081 = 0.35%) and one with biallelic variants (1/11,081 = 0.009%) and a diagnosis of isolated early-onset breast cancer. NTHL1-associated mutational signature 30 was identified in the tumors of the biallelic patient and two carriers. Colonic polyposis was not identified in any NTHL1 patient. MSH3-PVs were identified in 13 patients, including 12 monoallelic carriers (12/11,081 = 0.11%) and one with biallelic MSH3 variants (1/11,081 = 0.009%) and diagnoses of later-onset cancers, attenuated polyposis, and abnormal MSH3-protein expression. Of the 12 MSH3 carriers, two had early-onset cancer diagnoses with tumor loss of heterozygosity of the wild-type MSH3 allele. Ancestry-specific burden tests demonstrated that NTHL1 and MSH3 prevalence was not significantly different in this pan-cancer population versus controls. CONCLUSION NTHL1 and MSH3 germline alterations were not enriched in this pan-cancer patient population. However, tumor-specific findings, such as mutational signature 30 and loss of heterozygosity of the wild-type allele, suggest the potential contribution of monoallelic variants to tumorigenesis in a subset of patients.
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Affiliation(s)
- Erin E. Salo-Mullen
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Anna Maio
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Semanti Mukherjee
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Chaitanya Bandlamudi
- Marie-Josee and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Jinru Shia
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Yelena Kemel
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Karen A. Cadoo
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Ying Liu
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Maria Carlo
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Megha Ranganathan
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Sarah Kane
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Preethi Srinivasan
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Shweta S. Chavan
- Marie-Josee and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Mark T. A. Donoghue
- Marie-Josee and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Caitlin Bourque
- Marie-Josee and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Margaret Sheehan
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | | | - Zalak Patel
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Angela G. Arnold
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Jennifer A. Kennedy
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Kimberly Amoroso
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Kelsey Breen
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Amanda Catchings
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Rosalba Sacca
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Vanessa Marcell
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Arnold J. Markowitz
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Alicia Latham
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Michael Walsh
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Maksym Misyura
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Ozge Ceyhan-Birsoy
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - David B. Solit
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
- Marie-Josee and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Michael F. Berger
- Marie-Josee and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Mark E. Robson
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Barry S. Taylor
- Marie-Josee and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Kenneth Offit
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Diana Mandelker
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Zsofia K. Stadler
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
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Kunnackal John G, Das Villgran V, Caufield-Noll C, Giardiello FM. Comparison of universal screening in major lynch-associated tumors: a systematic review of literature. Fam Cancer 2021; 21:57-67. [PMID: 33426601 DOI: 10.1007/s10689-020-00226-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Accepted: 12/23/2020] [Indexed: 01/13/2023]
Abstract
Lynch syndrome (LS) is associated with an increased lifetime risk of several cancers including colorectal (CRC), endometrial (EC), ovarian (OC), urinary (UT) and sebaceous tumors (ST). The benefit for universal screening in CRC and EC is well known. However, this benefit in other major lynch-associated tumors is unclear. We performed a systematic review of all published articles in the MEDLINE database between 2005 to 2017 to identify studies performing universal screening for LS in unselected CRC, EC, OC, UT and ST. All cases with MSI-H (instability in two or more markers) or missing one or more proteins on IHC testing were considered screening positive. Cases with MLH1 promoter hypermethylation or BRAF mutation positive were considered to have somatic mutations. A total of 3788 articles were identified in MEDLINE yielding 129 study arms from 113 studies. The overall pooled yield of universal LS screening and germline mismatch gene mutation was significantly different across the major LS-associated tumors (Mann Whitney test, p < 0.001). The pooled screening yield was highest in ST [52.5% (355/676), 95% CI 48.74-56.26%] followed by EC [22.65% (1142/5041), 95% CI 21.54-23.86%], CRC [11.9% (5649/47,545), 95% CI 11.61-12.19%], OC [11.29% (320/2833), 95% CI 10.13-12.47%] and UT [11.2% (31/276), 95% CI 7.48-14.92%]. ST also had the highest pooled germline positivity for mismatch repair gene mutation [18.8%, 33/176, 95%CI 13.03-24.57], followed by EC [2.6% (97/3765), 95% CI 2.09-3.11], CRC [1.8% (682/37,220), 95% CI 1.66-1.94%], UT [1.8%(3/164), 95% CI - 0.24-3.83%] and OC [0.83%(25/2983), 95% CI 0.48-1.12%]. LS screening in EC yielded significantly higher somatic mutations compared to CRC [pooled percentage 16.94% [(538/3176), 95%CI 15.60-18.20%] vs. 5.23% [(1639/26,152), 95% CI 4.93-5.47%], Mann Whitney test, p < 0.0001. Universal LS testing should be routinely performed in OC, UT and STs in addition to CRC and EC. Our findings also support consideration for IHC and somatic mutation testing before germline testing in EC due to higher prevalence of somatic mutations as well as germline testing in all patients with ST. Our results have implications for future design of LS screening programs and further studies are needed to assess the cost effectiveness and burden on genetic counselling services with expanded universal testing for LS.
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Affiliation(s)
- George Kunnackal John
- Clinical Assistant Professor, Division of Gastroenterology and Hepatology, University of Maryland School of Medicine, 511 Idlewild Ave, Easton, MD, 21601, USA.
| | - Vipin Das Villgran
- Pulmonary and Critical Care Fellow, Allegheny Health Network, Pittsburgh, PA, 15212, USA
| | | | - Francis M Giardiello
- Division of Gastroenterology and Hepatology, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
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Dhooge M, Baert-Desurmont S, Corsini C, Caron O, Andrieu N, Berthet P, Bonadona V, Cohen-Haguenauer O, De Pauw A, Delnatte C, Dussart S, Lasset C, Leroux D, Maugard C, Moretta-Serra J, Popovici C, Buecher B, Colas C, Noguès C. National recommendations of the French Genetics and Cancer Group - Unicancer on the modalities of multi-genes panel analyses in hereditary predispositions to tumors of the digestive tract. Eur J Med Genet 2020; 63:104080. [PMID: 33039684 DOI: 10.1016/j.ejmg.2020.104080] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Revised: 09/29/2020] [Accepted: 09/29/2020] [Indexed: 12/13/2022]
Abstract
In case of suspected hereditary predisposition to digestive cancers, next-generation sequencing can analyze simultaneously several genes associated with an increased risk of developing these tumors. Thus, "Gastro Intestinal" (GI) gene panels are commonly used in French molecular genetic laboratories. Lack of international recommendations led to disparities in the composition of these panels and in the management of patients. To harmonize practices, the Genetics and Cancer Group (GGC)-Unicancer set up a working group who carried out a review of the literature for 31 genes of interest in this context and established a list of genes for which the estimated risks associated with pathogenic variant seemed sufficiently reliable and high for clinical use. Pancreatic cancer susceptibility genes have been excluded. This expertise defined a panel of 14 genes of confirmed clinical interest and relevant for genetic counseling: APC, BMPR1A, CDH1, EPCAM, MLH1, MSH2, MSH6, MUTYH, PMS2, POLD1, POLE, PTEN, SMAD4 and STK11. The reasons for the exclusion of the others 23 genes have been discussed. The paucity of estimates of the associated tumor risks led to the exclusion of genes, in particular CTNNA1, MSH3 and NTHL1, despite their implication in the molecular pathways involved in the pathophysiology of GI cancers. A regular update of the literature is planned to up-grade this panel of genes in case of new data on candidate genes. Genetic and epidemiological studies and international collaborations are needed to better estimate the risks associated with the pathogenic variants of these genes either selected or not in the current panel.
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Affiliation(s)
- Marion Dhooge
- APHP.Centre (Cochin Hospital), Paris University, Paris, France.
| | - Stéphanie Baert-Desurmont
- Normandie Univ, UNIROUEN, Inserm U1245 and Rouen University Hospital, Department of Genetics, Normandy Center for Genomic and Personalized Medicine, Rouen, France
| | - Carole Corsini
- Arnaud de Villeneuve University Hospital, Montpellier, France
| | - Olivier Caron
- Gustave-Roussy University Hospital, Villejuif, France
| | - Nadine Andrieu
- Institut Curie, PSL Research University, Department of Tumor Biology, Paris, France; Unité Inserm, Institut Curie, Paris, France
| | | | | | | | - Antoine De Pauw
- Institut Curie, PSL Research University, Department of Tumor Biology, Paris, France
| | | | | | | | - Dominique Leroux
- Grenoble University Hospital, Couple-Enfant Hospital, Grenoble, France
| | | | - Jessica Moretta-Serra
- Institut Paoli-Calmettes, Department of Clinical Cancer Genetics, Aix Marseille Univ, INSERM, IRD, SESSTIM, Marseille, France
| | - Cornel Popovici
- Institut Paoli-Calmettes, Department of Clinical Cancer Genetics, Aix Marseille Univ, INSERM, IRD, SESSTIM, Marseille, France
| | - Bruno Buecher
- Institut Curie, PSL Research University, Department of Tumor Biology, Paris, France
| | - Chrystelle Colas
- Institut Curie, PSL Research University, Department of Tumor Biology, Paris, France
| | - Catherine Noguès
- Institut Paoli-Calmettes, Department of Clinical Cancer Genetics, Aix Marseille Univ, INSERM, IRD, SESSTIM, Marseille, France
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8
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Worldwide variation in lynch syndrome screening: case for universal screening in low colorectal cancer prevalence areas. Fam Cancer 2020; 20:145-156. [PMID: 32914371 DOI: 10.1007/s10689-020-00206-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Accepted: 09/01/2020] [Indexed: 02/07/2023]
Abstract
To perform a systematic assessment of universal Lynch syndrome (LS) screening yield in colorectal cancer (CRC) patients around the world. Universal screening for LS is recommended in all CRC patients. However, the variation in yield of LS screening in the setting of significant global variation in CRC prevalence is unknown. A systematic review of articles in the MEDLINE database was performed to identify studies performing universal screening for LS. All cases with microsatellite instability (MSI-H) or missing one or more proteins on immunohistochemistry (IHC) were considered screening positive. The overall pooled yield of universal LS screening in 97 study arms from 89 identified studies was 11.9% (5649/47545) and the overall pooled percentage of confirmed LS patients was 1.8% (682/37220). LS screening positivity varied significantly based on geographic region (Kruskal Wallis test, p < 0.001) and reported 5-year CRC prevalence in the country (Fisher's exact, p < 0.001). Significant inverse correlation was found between LS screening positivity and 5-year CRC prevalence (Pearson correlation, r = - 0.56, p < 0.001). The overall yield of LS screening was 15.00% (382/2553) and rate of confirmed LS was 7.7% (113/1475) in LS screening done in patients ≤ 50 years (16 studies). There is significant geographic variation in LS screening positivity with higher yield in countries with lower prevalence of CRC. Our results highlight the importance of universal LS screening in younger patients and low CRC prevalence countries.
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9
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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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10
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Rau TT, Dawson H, Hartmann A, Rüschoff J. [Hereditary colorectal cancer : An update on genetics and entities in terms of differential diagnosis]. DER PATHOLOGE 2019; 38:156-163. [PMID: 28474162 DOI: 10.1007/s00292-017-0294-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
The pathologist can contribute to recognizing hereditary causes of colorectal cancer via morphology. By identifying so-called index patients, it is possible to take preventive measures in affected families. The precise definition of the clinical presentation and the histopathological phenotype help to narrow the spectrum of expected genetic alterations. Novelties within Lynch syndrome include the recognition of EPCAM as a fifth gene locus, as well as the newly defined Lynch-like syndrome with evidence of somatic mismatch repair (MMR) mutations. With regard to polyposis-associated syndromes, the spectrum of polyps, whether serrated, hamartomatous or classic adenoma, is of crucial importance. The resulting differential diagnosis includes (attenuated) familial adenomatous polyposis ([a]FAP), MUTYH-associated polyposis (MAP), polymerase proofreading-associated polyposis (PPAP), phosphatase and tensin homolog (PTEN) hamartoma tumor syndrome (PHTS), Peutz-Jeghers syndrome and juvenile polyposis, each with a specific genetic background.
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Affiliation(s)
- T T Rau
- Institut für Pathologie, Universität Bern, Murtenstrasse 31, 3008, Bern, Schweiz.
| | - H Dawson
- Institut für Pathologie, Universität Bern, Murtenstrasse 31, 3008, Bern, Schweiz
| | - A Hartmann
- Pathologisches Institut, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Deutschland
| | - J Rüschoff
- Pathologie Nordhessen, Kassel, Deutschland
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11
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Figueiredo J, Melo S, Carneiro P, Moreira AM, Fernandes MS, Ribeiro AS, Guilford P, Paredes J, Seruca R. Clinical spectrum and pleiotropic nature of CDH1 germline mutations. J Med Genet 2019; 56:199-208. [PMID: 30661051 PMCID: PMC6581119 DOI: 10.1136/jmedgenet-2018-105807] [Citation(s) in RCA: 63] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Revised: 12/05/2018] [Accepted: 12/10/2018] [Indexed: 12/12/2022]
Abstract
CDH1 encodes E-cadherin, a key protein in adherens junctions. Given that E-cadherin is involved in major cellular processes such as embryogenesis and maintenance of tissue architecture, it is no surprise that deleterious effects arise from its loss of function. E-cadherin is recognised as a tumour suppressor gene, and it is well established that CDH1 genetic alterations cause diffuse gastric cancer and lobular breast cancer—the foremost manifestations of the hereditary diffuse gastric cancer syndrome. However, in the last decade, evidence has emerged demonstrating that CDH1 mutations can be associated with lobular breast cancer and/or several congenital abnormalities, without any personal or family history of diffuse gastric cancer. To date, no genotype–phenotype correlations have been observed. Remarkably, there are reports of mutations affecting the same nucleotide but inducing distinct clinical outcomes. In this review, we bring together a comprehensive analysis of CDH1-associated disorders and germline alterations found in each trait, providing important insights into the biological mechanisms underlying E-cadherin’s pleiotropic effects. Ultimately, this knowledge will impact genetic counselling and will be relevant to the assessment of risk of cancer development or congenital malformations in CDH1 mutation carriers.
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Affiliation(s)
- Joana Figueiredo
- Epithelial Interactions in Cancer Department, Instituto de Investigação e Inovação em Saúde (i3S), Porto, Portugal.,Epithelial Interactions in Cancer, Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), Porto, Portugal
| | - Soraia Melo
- Epithelial Interactions in Cancer Department, Instituto de Investigação e Inovação em Saúde (i3S), Porto, Portugal.,Epithelial Interactions in Cancer, Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), Porto, Portugal.,Medical Faculty of the University of Porto, Porto, Portugal
| | - Patrícia Carneiro
- Epithelial Interactions in Cancer Department, Instituto de Investigação e Inovação em Saúde (i3S), Porto, Portugal.,Epithelial Interactions in Cancer, Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), Porto, Portugal
| | - Ana Margarida Moreira
- Epithelial Interactions in Cancer Department, Instituto de Investigação e Inovação em Saúde (i3S), Porto, Portugal.,Medical Faculty of the University of Porto, Porto, Portugal.,Epithelial Interactions in Cancer, Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), Porto, Portugal
| | - Maria Sofia Fernandes
- Epithelial Interactions in Cancer Department, Instituto de Investigação e Inovação em Saúde (i3S), Porto, Portugal.,Epithelial Interactions in Cancer, Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), Porto, Portugal.,Institute for Systems and Robotics (ISR/IST), LARSyS, Bioengineering Department, Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal
| | - Ana Sofia Ribeiro
- Epithelial Interactions in Cancer Department, Instituto de Investigação e Inovação em Saúde (i3S), Porto, Portugal.,Epithelial Interactions in Cancer, Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), Porto, Portugal
| | - Parry Guilford
- Cancer Genetics Laboratory, Centre for Translational Cancer Research (Te Aho Matatū), Department of Biochemistry, University of Otago, Dunedin, New Zealand
| | - Joana Paredes
- Epithelial Interactions in Cancer Department, Instituto de Investigação e Inovação em Saúde (i3S), Porto, Portugal.,Medical Faculty of the University of Porto, Porto, Portugal.,Epithelial Interactions in Cancer, Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), Porto, Portugal
| | - Raquel Seruca
- Epithelial Interactions in Cancer Department, Instituto de Investigação e Inovação em Saúde (i3S), Porto, Portugal.,Medical Faculty of the University of Porto, Porto, Portugal.,Epithelial Interactions in Cancer, Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), Porto, Portugal
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12
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Katz G, Pitts PJ. Implications of CRISPR-Based Germline Engineering for Cancer Survivors. Ther Innov Regul Sci 2018; 51:672-682. [PMID: 30227096 DOI: 10.1177/2168479017723401] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Cancer survivors can carry germline mutations that will be transmitted to their progeny. Today, many of these mutations have been identified and can be tracked. With the recent development of genome-editing technologies and CRISPR (clustered regularly interspaced short palindromic repeats), the possibility of genetically modifying the human germline-gametes and embryos-has never been closer. This perspective has sparked a controversy within the scientific community with reactions ranging from calls for a ban on germline modification to cautious approval of further research. This Editorial analyzes the possible adoption of CRISPR-based germline engineering to prevent the spread of cancer predispositions in the human population. We discuss whether the genomic edition of human sperm and eggs would contribute to rectifying or altering the heritable genome. We anticipate the emergence of a new form of liberal eugenics fueled by a logic of offer and demand from stakeholders such as cancer survivors and their relatives and offspring, but also from fertility clinics, biotech firms, insurers, and clinicians. From a regulatory perspective, validating the clinical safety and utility of CRISPR-based germline engineering is an essential step. However, with time, gradually perfecting the technology and assessing the economic benefits for stakeholders could soften society's resistance and align opinions in support of genomic decontamination of human germlines. This progressive shift would be justified in the name of cancer prevention as well as a moral obligation to facilitate the conception of cancer-free children at a cost that is acceptable to individuals and health systems.
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Affiliation(s)
- Gregory Katz
- 1 Chaired Professor of Innovation Management & Healthcare Performance, School of Medicine, Paris-Descartes University, Paris, France
| | - Peter J Pitts
- 2 President of the Center for Medicine in the Public Interest, Former Associate Commissioner, United States Food and Drug Administration, New York, NY, USA
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13
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Abstract
Lynch Syndrome (LS) is the most common dominantly inherited colorectal cancer (CRC) predisposition and is caused by a heterozygous germline defect in one of the DNA mismatch repair (MMR) genes MLH1, MSH2, MSH6, or PMS2. High microsatellite instability (MSI-H) and loss of MMR protein expression in tumours reflecting a defective MMR are indicators for LS, as well as a positive family history of early onset CRC. MSH2 and MSH6 form a major functional heterodimer, and MSH3 is an alternative binding partner for MSH2. So far, the role of germline MSH3 variants remains unclear, as to our knowledge heterozygous truncating variants are not regarded causative for LS, but were detected in patients with CRC, and recently biallelic MSH3 defects have been identified in two patients with adenomatous polyposis. By gene screening we investigated the role of MSH3 in 11 LS patients with truncating MSH6 germline variants and an unexplained MSH2 protein loss in their corresponding MSI-H tumours. We report the first two LS patients harbouring heterozygous germline variants c.1035del and c.2732T>G in MSH3 coincidentally with truncating variants in MSH6. In the patient with truncating germline variants in MSH3 and MSH6, two additional somatic second hits in both genes abrogate all binding partners for the MSH2 protein which might subsequently be degraded. The clinical relevance of MSH3 germline variants is currently under re-evaluation, and heterozygous MSH3 defects alone do not seem to induce a LS phenotype, but might aggravate the MSH6 phenotype in affected family members.
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14
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Abstract
With the increased use of modern next generation sequencing technologies in routine molecular pathology practice, the proportion of cancer cases with a definite or probable hereditary background seems to be steadily increasing. Currently, it is assumed that ≥10% of all malignancies develop in the setting of germline predisposition. Diagnosis and recognition of cancer predisposition syndromes relies not rarely on distinctive histopathological features that proved to be highly valuable and reproducible in uncovering those diseases that would otherwise have gone undetected by clinicians as being hereditary in nature. This is especially true in case of new mutations without suspicious family history. Example of such entities are fumarate hydratase-deficient renal cell carcinoma (RCC), succinate dehydrogenase-deficient RCC, hereditary gastrointestinal stromal tumor syndromes and many other diseases. It is remarkable that many of these inherited cancer syndromes do present as unifocal disease with highly variable age of onset so that many of them are misinterpreted as sporadic on clinical grounds. Availability of specialized cancer screening programs and disease-specific follow-up schemes for several hereditary cancer syndromes encourages the recognition of such disorders, so that "at risk patients" can be enrolled in such programs for early detection and timely intervention/ treatment of these malignancies which are in the majority of cases aggressive. In several conditions, as in familial adenomatous polyposis coli (FAP), well established prophylactic surgical interventions may be adopted to prevent the disease manifestations, highlighting the importance of the timely recognition of these potentially life-limiting neoplasms. In this review, the clinicopathological, demographic and histological features that are considered highly suggestive of a hereditary basis of "a neoplasm under consideration" are highlighted and discussed briefly. The details of some of these entities are in addition dealt with in reviews devoted to them in this special issue.
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Affiliation(s)
- Abbas Agaimy
- Institute of Pathology, Friedrich-Alexander-University Erlangen-Nürnberg, University Hospital, Erlangen, Germany.
| | - Arndt Hartmann
- Institute of Pathology, Friedrich-Alexander-University Erlangen-Nürnberg, University Hospital, Erlangen, Germany
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15
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Lorans M, Dow E, Macrae FA, Winship IM, Buchanan DD. Update on Hereditary Colorectal Cancer: Improving the Clinical Utility of Multigene Panel Testing. Clin Colorectal Cancer 2018; 17:e293-e305. [PMID: 29454559 DOI: 10.1016/j.clcc.2018.01.001] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2017] [Revised: 12/17/2017] [Accepted: 01/09/2018] [Indexed: 12/30/2022]
Abstract
Colorectal cancer (CRC), one of the most common cancers, is a major public health issue globally, especially in Westernized countries. Up to 35% of CRCs are thought to be due to heritable factors, but currently only 5% to 10% of CRCs are attributable to high-risk mutations in known CRC susceptibility genes, predominantly the mismatch repair genes (Lynch syndrome) and adenomatous polyposis coli gene (APC; familial adenomatous polyposis). In this era of precision medicine, high-risk mutation carriers, when identified, can be offered various risk management options that prevent cancers and improve survival, including risk-reducing medication, screening for early detection, and surgery. The practice of clinical genetics is currently transitioning from phenotype-directed single gene testing to multigene panels, now offered by numerous providers. For CRC, the genes included across these panels vary, ranging from well established, clinically actionable susceptibility genes with quantified magnitude of risk, to genes that lack extensive validation or have less evidence of association with CRC and, therefore, have minimal clinical utility. The current lack of consensus regarding inclusion of genes in CRC panels presents challenges in patient counseling and management, particularly when a variant in a less validated gene is identified. Furthermore, there remain considerable challenges regarding variant interpretation even for the well established CRC susceptibility genes. Ironically though, only through more widespread testing and the accumulation of large international data sets will sufficient information be generated to (i) enable well powered studies to determine if a gene is associated with CRC susceptibility, (ii) to develop better models for variant interpretation and (iii) to facilitate clinical translation.
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Affiliation(s)
- Marie Lorans
- Colorectal Oncogenomics Group, Department of Clinical Pathology, The University of Melbourne, Parkville, Victoria, Australia
| | - Eryn Dow
- Genetic Medicine and Family Cancer Clinic, Royal Melbourne Hospital, Parkville, Victoria, Australia
| | - Finlay A Macrae
- Genetic Medicine and Family Cancer Clinic, Royal Melbourne Hospital, Parkville, Victoria, Australia; Department of Medicine, The University of Melbourne, Parkville, Victoria, Australia; Colorectal Medicine and Genetics, Royal Melbourne Hospital, Parkville, Victoria, Australia
| | - Ingrid M Winship
- Genetic Medicine and Family Cancer Clinic, Royal Melbourne Hospital, Parkville, Victoria, Australia; Department of Medicine, The University of Melbourne, Parkville, Victoria, Australia
| | - Daniel D Buchanan
- Colorectal Oncogenomics Group, Department of Clinical Pathology, The University of Melbourne, Parkville, Victoria, Australia; Genetic Medicine and Family Cancer Clinic, Royal Melbourne Hospital, Parkville, Victoria, Australia; Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Carlton, Victoria, Australia; University of Melbourne Centre for Cancer Research, Victorian Comprehensive Cancer Centre, Parkville, Victoria, Australia.
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16
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Rohlin A, Rambech E, Kvist A, Törngren T, Eiengård F, Lundstam U, Zagoras T, Gebre-Medhin S, Borg Å, Björk J, Nilbert M, Nordling M. Expanding the genotype-phenotype spectrum in hereditary colorectal cancer by gene panel testing. Fam Cancer 2017; 16:195-203. [PMID: 27696107 PMCID: PMC5357488 DOI: 10.1007/s10689-016-9934-0] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Hereditary syndromes causing colorectal cancer include both polyposis and non-polyposis syndromes. Overlapping phenotypes between the syndromes have been recognized and this make targeted molecular testing for single genes less favorable, instead there is a gaining interest for multi-gene panel-based approaches detecting both SNVs, indels and CNVs in the same assay. We applied a panel including 19 CRC susceptibility genes to 91 individuals of six phenotypic subgroups. Targeted NGS-based sequencing of the whole gene regions including introns of the 19 genes was used. The individuals had a family history of CRC or had a phenotype consistent with a known CRC syndrome. The purpose of the study was to demonstrate the diagnostic difficulties linked to genotype-phenotype diversity and the benefits of using a gene panel. Pathogenicity classification was carried out on 46 detected variants. In total we detected sixteen pathogenic or likely pathogenic variants and 30 variants of unknown clinical significance. Four of the pathogenic or likely pathogenic variants were found in BMPR1A in patients with unexplained familial adenomatous polyposis or atypical adenomatous polyposis, which extends the genotype-phenotype spectrum for this gene. Nine patients had more than one variant remaining after the filtration, including three with truncating mutations in BMPR1A, PMS2 and AXIN2. CNVs were found in three patients, in upstream regions of SMAD4, MSH3 and CTNNB1, and one additional individual harbored a 24.2 kb duplication in CDH1 intron1.
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Affiliation(s)
- Anna Rohlin
- Department of Molecular and Clinical Genetics, Institute of Biomedicine, Sahlgrenska Academy at University of Gothenburg, Gothenburg, Sweden.
| | - Eva Rambech
- Division of Oncology and Pathology Department of Clinical Sciences Lund, Lund University, Medicon Village, 22381, Lund, Sweden
| | - Anders Kvist
- Division of Oncology and Pathology Department of Clinical Sciences Lund, Lund University, Medicon Village, 22381, Lund, Sweden
| | - Therese Törngren
- Division of Oncology and Pathology Department of Clinical Sciences Lund, Lund University, Medicon Village, 22381, Lund, Sweden
| | - Frida Eiengård
- Department of Molecular and Clinical Genetics, Institute of Biomedicine, Sahlgrenska Academy at University of Gothenburg, Gothenburg, Sweden
| | - Ulf Lundstam
- Department of Surgery, Sahlgrenska Academy at University of Gothenburg, Sahlgrenska University Hospital/Östra, 416 85, Gothenburg, Sweden
| | - Theofanis Zagoras
- Department of Molecular and Clinical Genetics, Institute of Biomedicine, Sahlgrenska Academy at University of Gothenburg, Gothenburg, Sweden
| | - Samuel Gebre-Medhin
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden
- Department of Clinical Genetics, Office for Medical Services, Division of Laboratory Medicine, Lund, Sweden
| | - Åke Borg
- Division of Oncology and Pathology Department of Clinical Sciences Lund, Lund University, Medicon Village, 22381, Lund, Sweden
| | - Jan Björk
- The Swedish Polyposis Registry, Department of Medicine, Karolinska Institute, Stockholm, Sweden
| | - Mef Nilbert
- Division of Oncology and Pathology Department of Clinical Sciences Lund, Lund University, Medicon Village, 22381, Lund, Sweden
- The HNPCC-register, Hvidovre University Hospital, Copenhagen University, Hvidovre, Denmark
| | - Margareta Nordling
- Department of Molecular and Clinical Genetics, Institute of Biomedicine, Sahlgrenska Academy at University of Gothenburg, Gothenburg, Sweden
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17
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Trippel M, Imboden S, Papadia A, Mueller MD, Mertineit N, Härmä K, Nicolae A, Vassella E, Rau TT. Intestinal differentiated mucinous adenocarcinoma of the endometrium with sporadic MSI high status: a case report. Diagn Pathol 2017; 12:39. [PMID: 28494767 PMCID: PMC5427532 DOI: 10.1186/s13000-017-0629-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2016] [Accepted: 04/21/2017] [Indexed: 11/27/2022] Open
Abstract
Background Intestinal differentiation of primary mucinous adenocarcinoma of the uterine corpus is exceedingly rare in comparison to the approximately 25% rate in endocervical and ovarian mucinous carcinoma. Additionally, little is known about the related genetic and epigenetic alterations, even though large-scale molecular characterisation of the different types of endometrial cancer took place in the TCGA project along the entities defined by the recent WHO classification. Case presentation We present a 62-year-old patient harbouring a primary mucinous carcinoma of the uterine corpus with a morphological resemblance to mucinous colorectal adenocarcinoma. The intestinal differentiation was substantiated by CDX2 and CK20 positivity in the absence of PAX8, p16, WT1, p53, ER, PgR, AFP, SALL4 and Glypican3. A high MSI status with MLH1 hypermethylation was revealed by molecular testing. Conclusion Intestinal differentiation of mucinous adenocarcinoma of the endometrium is a unique observation. Besides morphology, it obviously can share molecular features of sporadic MSI colorectal cancers. It can be speculated that either CDX2 positive morula formation or intestinal metaplasia of the endometrium as rare conditions might be the origin of carcinogenesis for this type II endometrial cancer. Both conditions were not detectable in this case. Of note, categorising endometrial cancers in genetic subgroups like MSI high cancers alone might lead to the integration of likewise morphologically different tumours like the case presented here with intestinal differentiation. Hence, careful genotype-phenotype correlations are warranted for studies of mucinous adenocarcinoma of the endometrium. Electronic supplementary material The online version of this article (doi:10.1186/s13000-017-0629-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Mafalda Trippel
- Institute of Pathology, University of Bern, Murtenstr. 31, 3008, Bern, CH, Switzerland
| | - Sara Imboden
- Department of Obstetrics and Gynaecology, Inselspital, University of Bern, Bern, Switzerland
| | - Andrea Papadia
- Department of Obstetrics and Gynaecology, Inselspital, University of Bern, Bern, Switzerland
| | - Michael D Mueller
- Department of Obstetrics and Gynaecology, Inselspital, University of Bern, Bern, Switzerland
| | - Nando Mertineit
- Department of Radiology, Inselspital, University of Bern, Bern, Switzerland
| | - Kirsi Härmä
- Department of Radiology, Inselspital, University of Bern, Bern, Switzerland
| | - Alina Nicolae
- Institute of Pathology, University of Bern, Murtenstr. 31, 3008, Bern, CH, Switzerland
| | - Erik Vassella
- Institute of Pathology, University of Bern, Murtenstr. 31, 3008, Bern, CH, Switzerland
| | - Tilman T Rau
- Institute of Pathology, University of Bern, Murtenstr. 31, 3008, Bern, CH, Switzerland.
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18
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Rau T. [Pathogenetic aspects in precursor lesions of gastrointestinal tumors]. DER PATHOLOGE 2016; 37:186-190. [PMID: 27638535 DOI: 10.1007/s00292-016-0220-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The pathogenesis of precursor lesions of gastrointestinal tumors is manifested in many ways. In the esophagus an aberrant genetic expression of intestinal transcription factors, such as CDX2 is initiated by local environment factors. During the subsequent dysplasia to carcinoma sequence, chromosomal gain and loss of genes occurs. A 4-color fluorescence in situ hybridization (FISH) assay can be applied in dysplasia as well as in Barrett's adenocarcinoma to define prognostic marker combinations. In the gastric carcinogenesis sequence the gene expression of CDX1 is regulatively dependent on an interplay between inflammation and promotor methylation. In the colon sessile serrated adenomas show a sequence with initial BRAF mutation and late onset of MLH1 promotor hypermethylation with consecutive potential cancer progression. This event is accompanied by an increase of intraepithelial lymphocytes, which is an easy to use tool for routine diagnostics using H&E sections. Next generation sequencing (NGS) investigations of germline mutations in colorectal cancer revealed a spectrum of mutations with low penetration in the field of mismatch repair proteins as well as the APC gene. An individual risk stratification for penetration of these germline mutations is necessary. In conclusion, genetics, phenotypes and terminology of gastrointestinal precursor lesions are unified to a mutually influencing concept within medicine.
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Affiliation(s)
- T Rau
- Pathologisches Institut, Universitätsklinikum Erlangen, Erlangen, Deutschland. .,Institut für Pathologie, Universität Bern, Murtenstr. 31, 3010, Bern, Schweiz.
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19
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Jones S, Anagnostou V, Lytle K, Parpart-Li S, Nesselbush M, Riley DR, Shukla M, Chesnick B, Kadan M, Papp E, Galens KG, Murphy D, Zhang T, Kann L, Sausen M, Angiuoli SV, Diaz LA, Velculescu VE. Personalized genomic analyses for cancer mutation discovery and interpretation. Sci Transl Med 2016; 7:283ra53. [PMID: 25877891 DOI: 10.1126/scitranslmed.aaa7161] [Citation(s) in RCA: 307] [Impact Index Per Article: 38.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Massively parallel sequencing approaches are beginning to be used clinically to characterize individual patient tumors and to select therapies based on the identified mutations. A major question in these analyses is the extent to which these methods identify clinically actionable alterations and whether the examination of the tumor tissue alone is sufficient or whether matched normal DNA should also be analyzed to accurately identify tumor-specific (somatic) alterations. To address these issues, we comprehensively evaluated 815 tumor-normal paired samples from patients of 15 tumor types. We identified genomic alterations using next-generation sequencing of whole exomes or 111 targeted genes that were validated with sensitivities >95% and >99%, respectively, and specificities >99.99%. These analyses revealed an average of 140 and 4.3 somatic mutations per exome and targeted analysis, respectively. More than 75% of cases had somatic alterations in genes associated with known therapies or current clinical trials. Analyses of matched normal DNA identified germline alterations in cancer-predisposing genes in 3% of patients with apparently sporadic cancers. In contrast, a tumor-only sequencing approach could not definitively identify germline changes in cancer-predisposing genes and led to additional false-positive findings comprising 31% and 65% of alterations identified in targeted and exome analyses, respectively, including in potentially actionable genes. These data suggest that matched tumor-normal sequencing analyses are essential for precise identification and interpretation of somatic and germline alterations and have important implications for the diagnostic and therapeutic management of cancer patients.
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Affiliation(s)
- Siân Jones
- Personal Genome Diagnostics, Baltimore, MD 21224, USA
| | - Valsamo Anagnostou
- The Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Karli Lytle
- Personal Genome Diagnostics, Baltimore, MD 21224, USA
| | | | | | - David R Riley
- Personal Genome Diagnostics, Baltimore, MD 21224, USA
| | - Manish Shukla
- Personal Genome Diagnostics, Baltimore, MD 21224, USA
| | | | - Maura Kadan
- Personal Genome Diagnostics, Baltimore, MD 21224, USA
| | - Eniko Papp
- The Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | | | - Derek Murphy
- Personal Genome Diagnostics, Baltimore, MD 21224, USA
| | - Theresa Zhang
- Personal Genome Diagnostics, Baltimore, MD 21224, USA
| | - Lisa Kann
- Personal Genome Diagnostics, Baltimore, MD 21224, USA
| | - Mark Sausen
- Personal Genome Diagnostics, Baltimore, MD 21224, USA
| | | | - Luis A Diaz
- The Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Victor E Velculescu
- The Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA.
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Kotoula V, Lyberopoulou A, Papadopoulou K, Charalambous E, Alexopoulou Z, Gakou C, Lakis S, Tsolaki E, Lilakos K, Fountzilas G. Evaluation of two highly-multiplexed custom panels for massively parallel semiconductor sequencing on paraffin DNA. PLoS One 2015; 10:e0128818. [PMID: 26039550 PMCID: PMC4454570 DOI: 10.1371/journal.pone.0128818] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2015] [Accepted: 04/30/2015] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND AIM Massively parallel sequencing (MPS) holds promise for expanding cancer translational research and diagnostics. As yet, it has been applied on paraffin DNA (FFPE) with commercially available highly multiplexed gene panels (100s of DNA targets), while custom panels of low multiplexing are used for re-sequencing. Here, we evaluated the performance of two highly multiplexed custom panels on FFPE DNA. METHODS Two custom multiplex amplification panels (B, 373 amplicons; T, 286 amplicons) were coupled with semiconductor sequencing on DNA samples from FFPE breast tumors and matched peripheral blood samples (n samples: 316; n libraries: 332). The two panels shared 37% DNA targets (common or shifted amplicons). Panel performance was evaluated in paired sample groups and quartets of libraries, where possible. RESULTS Amplicon read ratios yielded similar patterns per gene with the same panel in FFPE and blood samples; however, performance of common amplicons differed between panels (p<0.001). FFPE genotypes were compared for 1267 coding and non-coding variant replicates, 999 out of which (78.8%) were concordant in different paired sample combinations. Variant frequency was highly reproducible (Spearman's rho 0.959). Repeatedly discordant variants were of high coverage / low frequency (p<0.001). Genotype concordance was (a) high, for intra-run duplicates with the same panel (mean±SD: 97.2±4.7, 95%CI: 94.8-99.7, p<0.001); (b) modest, when the same DNA was analyzed with different panels (mean±SD: 81.1±20.3, 95%CI: 66.1-95.1, p = 0.004); and (c) low, when different DNA samples from the same tumor were compared with the same panel (mean±SD: 59.9±24.0; 95%CI: 43.3-76.5; p = 0.282). Low coverage / low frequency variants were validated with Sanger sequencing even in samples with unfavourable DNA quality. CONCLUSIONS Custom MPS may yield novel information on genomic alterations, provided that data evaluation is adjusted to tumor tissue FFPE DNA. To this scope, eligibility of all amplicons along with variant coverage and frequency need to be assessed.
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Affiliation(s)
- Vassiliki Kotoula
- Laboratory of Molecular Oncology, Hellenic Foundation for Cancer Research, Aristotle University of Thessaloniki School of Medicine, Thessaloniki, Greece
- Department of Pathology, Aristotle University of Thessaloniki School of Medicine, Thessaloniki, Greece
- * E-mail:
| | - Aggeliki Lyberopoulou
- Laboratory of Molecular Oncology, Hellenic Foundation for Cancer Research, Aristotle University of Thessaloniki School of Medicine, Thessaloniki, Greece
| | - Kyriaki Papadopoulou
- Laboratory of Molecular Oncology, Hellenic Foundation for Cancer Research, Aristotle University of Thessaloniki School of Medicine, Thessaloniki, Greece
| | - Elpida Charalambous
- Laboratory of Molecular Oncology, Hellenic Foundation for Cancer Research, Aristotle University of Thessaloniki School of Medicine, Thessaloniki, Greece
| | | | - Chryssa Gakou
- Laboratory of Molecular Oncology, Hellenic Foundation for Cancer Research, Aristotle University of Thessaloniki School of Medicine, Thessaloniki, Greece
| | - Sotiris Lakis
- Laboratory of Molecular Oncology, Hellenic Foundation for Cancer Research, Aristotle University of Thessaloniki School of Medicine, Thessaloniki, Greece
| | - Eleftheria Tsolaki
- Laboratory of Molecular Oncology, Hellenic Foundation for Cancer Research, Aristotle University of Thessaloniki School of Medicine, Thessaloniki, Greece
| | - Konstantinos Lilakos
- Department of Haematology, “Laikon” General Hospital, University of Athens Medical School, Athens, Greece
| | - George Fountzilas
- Laboratory of Molecular Oncology, Hellenic Foundation for Cancer Research, Aristotle University of Thessaloniki School of Medicine, Thessaloniki, Greece
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