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Evans DG, Lalloo F, Ryan NA, Bowers N, Green K, Woodward ER, Clancy T, Bolton J, McVey RJ, Wallace AJ, Newton K, Hill J, McMahon R, Crosbie EJ. Advances in genetic technologies result in improved diagnosis of mismatch repair deficiency in colorectal and endometrial cancers. J Med Genet 2021; 59:328-334. [PMID: 33452216 PMCID: PMC8961751 DOI: 10.1136/jmedgenet-2020-107542] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2020] [Revised: 12/17/2020] [Accepted: 12/23/2020] [Indexed: 11/04/2022]
Abstract
Background Testing cancers for mismatch repair deficiency (dMMR) by immunohistochemistry (IHC) is a quick and inexpensive means of triaging individuals for germline Lynch syndrome testing. The aim of this study was to evaluate tumour dMMR and the prevalence of Lynch syndrome in patients referred to the Manchester Centre for Genomic Medicine, which serves a population of 5.6 million. Methods Tumour testing used IHC for MMR proteins with targeted BRAF and MLH1 promotor methylation testing followed by germline mutation and somatic testing as appropriate. Results In total, 3694 index tumours were tested by IHC (2204 colorectal cancers (CRCs), 739 endometrial cancers (ECs) and 761 other), of which 672/3694 (18.2%) had protein loss, including 348 (9.4%) with MLH1 loss. MLH1 loss was significantly higher for 739 ECs (15%) vs 2204 CRCs (10%) (p=0.0003) and was explained entirely by higher rates of somatic MLH1 promoter hypermethylation (87% vs 41%, p<0.0001). Overall, 65/134 (48.5%) patients with MLH1 loss and no MLH1 hypermethylation or BRAF c.1799T>A had constitutional MLH1 pathogenic variants. Of 456 patients with tumours showing loss of MSH2/MSH6, 216 (47.3%) had germline pathogenic variants in either gene. Isolated PMS2 loss was most suggestive of a germline MMR variant in 19/26 (73%). Of those with no germline pathogenic variant, somatic testing identified likely causal variants in 34/48 (71%) with MLH1 loss and in MSH2/MSH6 in 40/47 (85%) with MSH2/MSH6 loss. Conclusions Reflex testing of EC/CRC leads to uncertain diagnoses in many individuals with dMMR following IHC but without germline pathogenic variants or MLH1 hypermethylation. Tumour mutation testing is effective at decreasing this by identifying somatic dMMR in >75% of cases.
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Affiliation(s)
- D Gareth Evans
- Division of Evolution and Genomic Medicine, The University of Manchester, Manchester, UK.,Clinical Genetics Service, Manchester Centre for Genomic Medicine, North-West Genomics Laboratory Hub, Manchester University NHS Foundation Trust, Manchester, Greater Manchester, UK
| | - Fiona Lalloo
- Clinical Genetics Service, Manchester Centre for Genomic Medicine, North-West Genomics Laboratory Hub, Manchester University NHS Foundation Trust, Manchester, Greater Manchester, UK
| | - Neil Aj Ryan
- Division of Cancer Sciences, The University of Manchester, Manchester, UK.,Department of Obstetrics and Gynaecology, Manchester University NHS Foundation Trust, Manchester, Greater Manchester, UK
| | - Naomi Bowers
- Clinical Genetics Service, Manchester Centre for Genomic Medicine, North-West Genomics Laboratory Hub, Manchester University NHS Foundation Trust, Manchester, Greater Manchester, UK
| | - Kate Green
- Clinical Genetics Service, Manchester Centre for Genomic Medicine, North-West Genomics Laboratory Hub, Manchester University NHS Foundation Trust, Manchester, Greater Manchester, UK
| | - Emma R Woodward
- Division of Evolution and Genomic Medicine, The University of Manchester, Manchester, UK.,Clinical Genetics Service, Manchester Centre for Genomic Medicine, North-West Genomics Laboratory Hub, Manchester University NHS Foundation Trust, Manchester, Greater Manchester, UK
| | - Tara Clancy
- Clinical Genetics Service, Manchester Centre for Genomic Medicine, North-West Genomics Laboratory Hub, Manchester University NHS Foundation Trust, Manchester, Greater Manchester, UK
| | - James Bolton
- Department of Pathology, Manchester University NHS Foundation Trust, Manchester, Greater Manchester, UK
| | - Rhona J McVey
- Department of Pathology, Manchester University NHS Foundation Trust, Manchester, Greater Manchester, UK
| | - Andrew J Wallace
- Clinical Genetics Service, Manchester Centre for Genomic Medicine, North-West Genomics Laboratory Hub, Manchester University NHS Foundation Trust, Manchester, Greater Manchester, UK
| | - Katy Newton
- Department of Surgery, Manchester University NHS Foundation Trust, Manchester, Greater Manchester, UK
| | - James Hill
- Department of Surgery, Manchester University NHS Foundation Trust, Manchester, Greater Manchester, UK
| | - Raymond McMahon
- Department of Pathology, Manchester University NHS Foundation Trust, Manchester, Greater Manchester, UK
| | - Emma J Crosbie
- Division of Cancer Sciences, The University of Manchester, Manchester, UK .,Department of Obstetrics and Gynaecology, Manchester University NHS Foundation Trust, Manchester, Greater Manchester, UK
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Bafligil C, Thompson DJ, Lophatananon A, Smith MJ, Ryan NA, Naqvi A, Evans DG, Crosbie EJ. Association between genetic polymorphisms and endometrial cancer risk: a systematic review. J Med Genet 2020; 57:591-600. [PMID: 32066633 PMCID: PMC7476276 DOI: 10.1136/jmedgenet-2019-106529] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2019] [Revised: 11/24/2019] [Accepted: 12/15/2019] [Indexed: 12/21/2022]
Abstract
Introduction Endometrial cancer is one of the most commonly diagnosed cancers in women. Although there is a hereditary component to endometrial cancer, most cases are thought to be sporadic and lifestyle related. The aim of this study was to systematically review prospective and retrospective case–control studies, meta-analyses and genome-wide association studies to identify genomic variants that may be associated with endometrial cancer risk. Methods We searched MEDLINE, Embase and CINAHL from 2007 to 2019 without restrictions. We followed PRISMA 2009 guidelines. The search yielded 3015 hits in total. Following duplicate exclusion, 2674 abstracts were screened and 453 full-texts evaluated based on our pre-defined screening criteria. 149 articles were eligible for inclusion. Results We found that single nucleotide polymorphisms (SNPs) in HNF1B, KLF, EIF2AK, CYP19A1, SOX4 and MYC were strongly associated with incident endometrial cancer. Nineteen variants were reported with genome-wide significance and a further five with suggestive significance. No convincing evidence was found for the widely studied MDM2 variant rs2279744. Publication bias and false discovery rates were noted throughout the literature. Conclusion Endometrial cancer risk may be influenced by SNPs in genes involved in cell survival, oestrogen metabolism and transcriptional control. Larger cohorts are needed to identify more variants with genome-wide significance.
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Affiliation(s)
- Cemsel Bafligil
- Division of Cancer Sciences, University of Manchester, Manchester, UK
| | - Deborah J Thompson
- Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | | | - Miriam J Smith
- Division of Evolution and Genomic Sciences, University of Manchester, Manchester, UK
| | - Neil Aj Ryan
- Division of Cancer Sciences, University of Manchester, Manchester, UK
| | - Anie Naqvi
- University of Manchester Medical School, Manchester, UK
| | - D Gareth Evans
- Division of Evolution and Genomic Sciences, University of Manchester, Manchester, UK
| | - Emma J Crosbie
- Division of Cancer Sciences, University of Manchester, Manchester, UK .,Department of Obstetrics and Gynaecology, Manchester University NHS Foundation Trust, Manchester, UK
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