1
|
Woodward ER, Lalloo F, Forde C, Pugh S, Burghel GJ, Schlecht H, Harkness EF, Howell A, Howell SJ, Gandhi A, Evans DG. Germline testing of BRCA1, BRCA2, PALB2 and CHEK2 c.1100delC in 1514 triple negative familial and isolated breast cancers from a single centre, with extended testing of ATM, RAD51C and RAD51D in over 400. J Med Genet 2024; 61:385-391. [PMID: 38123987 DOI: 10.1136/jmg-2023-109671] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Accepted: 11/14/2023] [Indexed: 12/23/2023]
Abstract
BACKGROUND The identification of germline pathogenic gene variants (PGVs) in triple negative breast cancer (TNBC) is important to inform further primary cancer risk reduction and TNBC treatment strategies. We therefore investigated the contribution of breast cancer associated PGVs to familial and isolated invasive TNBC. METHODS Outcomes of germline BRCA1, BRCA2 and CHEK2_c.1100delC testing were recorded in 1514 women (743-isolated, 771-familial), and for PALB2 in 846 women (541-isolated, 305-familial), with TNBC and smaller numbers for additional genes. Breast cancer free controls were identified from Predicting Risk Of Cancer At Screening and BRIDGES (Breast cancer RIsk after Diagnostic GEne Sequencing) studies. RESULTS BRCA1_PGVs were detected in 52 isolated (7.0%) and 195 (25.3%) familial cases (isolated-OR=58.9, 95% CI: 16.6 to 247.0), BRCA2_PGVs in 21 (2.8%) isolated and 67 (8.7%) familial cases (isolated-OR=5.0, 95% CI: 2.3 to 11.2), PALB2_PGVs in 9 (1.7%) isolated and 12 (3.9%) familial cases (isolated-OR=8.8, 95% CI: 2.5 to 30.4) and CHEK2_c.1100delC in 0 isolated and 3 (0.45%) familial cases (isolated-OR=0.0, 95% CI: 0.00 to 2.11). BRCA1_PGV detection rate was >10% for all familial TNBC age groups and significantly higher for younger diagnoses (familial: <50 years, n=165/538 (30.7%); ≥50 years, n=30/233 (12.9%); p<0.0001). Women with a G3_TNBC were more likely to have a BRCA1_PGV as compared with a BRCA2 or PALB2_PGV (p<0.0001). 0/743 isolated TNBC had the CHEK2_c.1100delC PGV and 0/305 any ATM_PGV, but 2/240 (0.83%) had a RAD51D_PGV. CONCLUSION PGVs in BRCA1 are associated with G3_TNBCs. Familial TNBCs and isolated TNBCs <30 years have a >10% likelihood of a PGV in BRCA1. BRCA1_PGVs are associated with younger age of familial TNBC. There was no evidence for any increased risk of TNBC with CHEK2 or ATM PGVs.
Collapse
Affiliation(s)
- Emma R Woodward
- Manchester Centre for Genomic Medicine, Manchester University Hospitals NHS Foundation Trust, Manchester, UK
- Division of Evolution, Infection and Genomics, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester, UK
- Manchester Breast Centre, The Christie NHS Foundation Trust, Manchester, UK
| | - Fiona Lalloo
- Manchester Centre for Genomic Medicine, Manchester University Hospitals NHS Foundation Trust, Manchester, UK
| | - Claire Forde
- Manchester Centre for Genomic Medicine, Manchester University Hospitals NHS Foundation Trust, Manchester, UK
| | - Sarah Pugh
- Manchester Centre for Genomic Medicine, Manchester University Hospitals NHS Foundation Trust, Manchester, UK
| | - George J Burghel
- Manchester Centre for Genomic Medicine, Manchester University Hospitals NHS Foundation Trust, Manchester, UK
| | - Helene Schlecht
- Manchester Centre for Genomic Medicine, Manchester University Hospitals NHS Foundation Trust, Manchester, UK
| | - Elaine F Harkness
- Division of Informatics, Imaging and Data Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester, UK
| | - Anthony Howell
- Manchester Breast Centre, The Christie NHS Foundation Trust, Manchester, UK
- Prevent Breast Cancer Unit, Wythenshawe Hospital, Manchester University NHS Foundation Trust, Manchester, UK
- Division of Cancer Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester, UK
| | - Sacha J Howell
- Manchester Breast Centre, The Christie NHS Foundation Trust, Manchester, UK
- Prevent Breast Cancer Unit, Wythenshawe Hospital, Manchester University NHS Foundation Trust, Manchester, UK
- Division of Cancer Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester, UK
| | - Ashu Gandhi
- Prevent Breast Cancer Unit, Wythenshawe Hospital, Manchester University NHS Foundation Trust, Manchester, UK
- Division of Cancer Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester, UK
| | - D Gareth Evans
- Manchester Centre for Genomic Medicine, Manchester University Hospitals NHS Foundation Trust, Manchester, UK
- Division of Evolution, Infection and Genomics, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester, UK
- Manchester Breast Centre, The Christie NHS Foundation Trust, Manchester, UK
- Division of Informatics, Imaging and Data Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester, UK
| |
Collapse
|
2
|
Morgan RD, Burghel GJ, Schlecht H, Clamp AR, Hasan J, Mitchell CL, Salih Z, Shaw J, Desai S, Jayson GC, Woodward ER, Evans DGR. Real-World Concordance between Germline and Tumour BRCA1/2 Status in Epithelial Ovarian Cancer. Cancers (Basel) 2023; 16:177. [PMID: 38201604 PMCID: PMC10778166 DOI: 10.3390/cancers16010177] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2023] [Revised: 12/22/2023] [Accepted: 12/26/2023] [Indexed: 01/12/2024] Open
Abstract
Patients diagnosed with epithelial ovarian cancer may undergo reflex tumour BRCA1/2 testing followed by germline BRCA1/2 testing in patients with a positive tumour test result. This testing model relies on tumour BRCA1/2 tests being able to detect all types of pathogenic variant. We analysed germline and tumour BRCA1/2 test results from patients treated for epithelial ovarian cancer at our specialist oncological referral centre. Tumour BRCA1/2 testing was performed using the next-generation sequencing (NGS)-based myChoice® companion diagnostic (CDx; Myriad Genetics, Inc.). Germline BRCA1/2 testing was performed in the North West Genomic Laboratory Hub using NGS and multiplex ligation-dependent probe amplification. Between 11 April 2021 and 11 October 2023, 382 patients were successfully tested for tumour BRCA1 and BRCA2 variants. Of these, 367 (96.1%) patients were tested for germline BRCA1/2 variants. In those patients who underwent tumour and germline testing, 15.3% (56/367) had a BRCA1/2 pathogenic variant (36 germline and 20 somatic). All germline BRCA1/2 pathogenic small sequencing variants were detected in tumour DNA. By contrast, 3 out of 8 germline BRCA1/2 pathogenic large rearrangements were not reported in tumour DNA. The overall concordance of germline BRCA1/2 pathogenic variants detected in germline and tumour DNA was clinically acceptable at 91.7% (33/36). The myChoice® CDx was able to detect most germline BRCA1/2 pathogenic variants in tumour DNA, although a proportion of pathogenic large rearrangements were not reported. If Myriad's myChoice® CDx is used for tumour BRCA1/2 testing, our data supports a testing strategy of germline and tumour BRCA1/2 testing in all patients diagnosed with epithelial ovarian cancer aged < 79 years old, with germline BRCA1/2 testing only necessary for patients aged ≥ 80 years old with a tumour BRCA1/2 pathogenic variant.
Collapse
Affiliation(s)
- Robert D. Morgan
- Department of Medical Oncology, The Christie NHS Foundation Trust, Wilmslow Road, Manchester M20 4BX, UK
- Division of Cancer Sciences, Faculty of Biology, Medicine and Health, School of Medical Sciences, University of Manchester, Manchester M13 9PL, UK
| | - George J. Burghel
- North West Genomic Laboratory Hub, Manchester University NHS Foundation Trust, Oxford Road, Manchester M13 9WL, UK
- Division of Evolution, Infection and Genomics, Faculty of Biology, Medicine and Health, School of Biological Sciences, University of Manchester, Manchester M13 9PL, UK
| | - Helene Schlecht
- North West Genomic Laboratory Hub, Manchester University NHS Foundation Trust, Oxford Road, Manchester M13 9WL, UK
| | - Andrew R. Clamp
- Department of Medical Oncology, The Christie NHS Foundation Trust, Wilmslow Road, Manchester M20 4BX, UK
- Division of Cancer Sciences, Faculty of Biology, Medicine and Health, School of Medical Sciences, University of Manchester, Manchester M13 9PL, UK
| | - Jurjees Hasan
- Department of Medical Oncology, The Christie NHS Foundation Trust, Wilmslow Road, Manchester M20 4BX, UK
| | - Claire L. Mitchell
- Department of Medical Oncology, The Christie NHS Foundation Trust, Wilmslow Road, Manchester M20 4BX, UK
| | - Zena Salih
- Department of Medical Oncology, The Christie NHS Foundation Trust, Wilmslow Road, Manchester M20 4BX, UK
| | - Joseph Shaw
- Department of Gynaecological Pathology, Manchester University NHS Foundation Trust, Oxford Road, Manchester M13 9WL, UK
| | - Sudha Desai
- Department of Pathology, The Christie NHS Foundation Trust, Wilmslow Road, Manchester M20 4BX, UK
| | - Gordon C. Jayson
- Department of Medical Oncology, The Christie NHS Foundation Trust, Wilmslow Road, Manchester M20 4BX, UK
- Division of Cancer Sciences, Faculty of Biology, Medicine and Health, School of Medical Sciences, University of Manchester, Manchester M13 9PL, UK
| | - Emma R. Woodward
- North West Genomic Laboratory Hub, Manchester University NHS Foundation Trust, Oxford Road, Manchester M13 9WL, UK
- Division of Evolution, Infection and Genomics, Faculty of Biology, Medicine and Health, School of Biological Sciences, University of Manchester, Manchester M13 9PL, UK
- Department of Clinical Genetics, Manchester University NHS Foundation Trust, Oxford Road, Manchester M13 9WL, UK
| | - D. Gareth R. Evans
- North West Genomic Laboratory Hub, Manchester University NHS Foundation Trust, Oxford Road, Manchester M13 9WL, UK
- Division of Evolution, Infection and Genomics, Faculty of Biology, Medicine and Health, School of Biological Sciences, University of Manchester, Manchester M13 9PL, UK
- Department of Clinical Genetics, Manchester University NHS Foundation Trust, Oxford Road, Manchester M13 9WL, UK
| |
Collapse
|
3
|
Evans DG, Burghel GJ, Schlecht H, Harkness EF, Gandhi A, Howell SJ, Howell A, Forde C, Lalloo F, Newman WG, Smith MJ, Woodward ER. Detection of pathogenic variants in breast cancer susceptibility genes in bilateral breast cancer. J Med Genet 2023; 60:974-979. [PMID: 37055167 DOI: 10.1136/jmg-2023-109196] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Accepted: 03/22/2023] [Indexed: 04/15/2023]
Abstract
PURPOSE To investigate the frequency of germline pathogenic variants (PVs) in women with bilateral breast cancer. METHODS We undertook BRCA1/2 and CHEK2 c.1100delC molecular analysis in 764 samples and a multigene panel in 156. Detection rates were assessed by age at first primary, Manchester Score, and breast pathology. Oestrogen receptor (ER) status of the contralateral versus first breast cancer was compared on 1081 patients with breast cancer with BRCA1/BRCA2 PVs. RESULTS 764 women with bilateral breast cancer have undergone testing of BRCA1/2 and CHEK2; 407 were also tested for PALB2 and 177 for ATM. Detection rates were BRCA1 11.6%, BRCA2 14.0%, CHEK2 2.4%, PALB2 1.0%, ATM 1.1% and, for a subset of mainly very early onset tumours, TP53 4.6% (9 of 195). The highest PV detection rates were for triple negative cancers for BRCA1 (26.4%), grade 3 ER+HER2 for BRCA2 (27.9%) and HER2+ for CHEK2 (8.9%). ER status of the first primary in BRCA1 and BRCA2 PV heterozygotes was strongly predictive of the ER status of the second contralateral tumour since ~90% of second tumours were ER- in BRCA1 heterozygotes, and 50% were ER- in BRCA2 heterozygotes if the first was ER-. CONCLUSION We have shown a high rate of detection of BRCA1 and BRCA2 PVs in triple negative and grade 3 ER+HER2- first primary diagnoses, respectively. High rates of HER2+ were associated with CHEK2 PVs, and women ≤30 years were associated with TP53 PVs. First primary ER status in BRCA1/2 strongly predicts the second tumour will be the same ER status even if unusual for PVs in that gene.
Collapse
Affiliation(s)
- D Gareth Evans
- Genomic Medicine, Manchester University Hospitals NHS Foundation Trust, Manchester, UK
- Genomic Medicine, Manchester Academic Health Science Centre, Manchester, UK
| | - George J Burghel
- Genomic Diagnostic Laboratory, Manchester University NHS Foundation Trust, Manchester, UK
| | - Helene Schlecht
- North West Genomic Laboratory Hub, Central Manchester University Hospitals NHS Foundation Trust, Manchester, UK
| | | | - Ashu Gandhi
- Prevent Breast Cancer Centre, Wythenshawe Hospital Manchester Universities Foundation Trust, Manchester, UK
| | - Sacha J Howell
- Genomic Medicine, Wythenshawe Hospital Manchester Universities Foundation Trust, Wythenshawe, UK
- Genomic Medicine, The Christie NHS Foundation Trust, Manchester, UK
| | - Anthony Howell
- Genomic Medicine, Prevent Breast Cancer Centre, Manchester, UK
| | - Claire Forde
- Clinical Genetics Service, Manchester Centre for Genomic Medicine, Central Manchester University Hospitals NHS Foundation Trust, Manchester, UK
| | - Fiona Lalloo
- Clinical Genetics Service, Manchester Centre for Genomic Medicine, Central Manchester University Hospitals NHS Foundation Trust, Manchester, UK
| | - William G Newman
- Genetics, Central Manchester University foundation Trust, Manchester, UK
| | | | - Emma Roisin Woodward
- Manchester Centre for Genomic Medicine, Central Manchester NHS Foundation Trust, Manchester, UK
| |
Collapse
|
4
|
Morgan RD, Burghel GJ, Flaum N, Bulman M, Smith P, Clamp AR, Hasan J, Mitchell C, Salih Z, Woodward ER, Lalloo F, Shaw J, Desai S, Crosbie EJ, Edmondson RJ, Schlecht H, Wallace AJ, Jayson GC, Evans DGR. Predicting the likelihood of a BRCA1/2 pathogenic variant being somatic by testing only tumour DNA in non-mucinous high-grade epithelial ovarian cancer. J Clin Pathol 2023; 76:684-689. [PMID: 35738887 DOI: 10.1136/jcp-2022-208369] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Accepted: 06/09/2022] [Indexed: 11/04/2022]
Abstract
AIMS Clinical guidelines recommend testing both germline and tumour DNA for BRCA1/2 pathogenic variants (PVs) in non-mucinous high-grade epithelial ovarian cancer (NMEOC). In this study, we show that some tumour BRCA1/2 PVs are highly likely to be somatic based on certain clinical and variant characteristics, meaning it may not be necessary to test all NMEOC cases for germline BRCA1/2 PVs. METHODS An observational study that included all tumour BRCA1/2 PVs detected in cases of NMEOC in the Northwest of England between July 2017 and February 2022. All tumour BRCA1/2 PVs were compared with PVs recorded in a prospectively gathered pan-cancer germline BRCA1/2 (gBRCA) testing database for the same geographical region (gBRCA1 PVs=910 and gBRCA2 PVs=922). Tumour BRCA1/2 PVs were categorised as common (≥1%), uncommon (<1%) or absent from the germline database. RESULTS One hundred and thirteen tumour BRCA1/2 PVs were detected in 111 NMEOC cases. There were 69 germline and 44 somatic variants. The mean age at diagnosis for gBRCA and somatic BRCA1/2 (sBRCA) PVs was 56.9 and 68.5 years, respectively (Student's t-test p<0.0001). All sBRCA PVs were detected in non-familial cases. All tumour BRCA1/2 PVs with a variant allele frequency (VAF) <35% in non-familial cases were somatic variants. Eighty-one per cent of germline-tumour BRCA1/2 PVs were present (common=31, uncommon=25) in the gBRCA testing database, while 89% of somatic-tumour BRCA1/2 PVs were absent (n=39). CONCLUSIONS We predict the likelihood of a tumour BRCA1/2 PV being somatic is 99.8% in non-familial cases of NMEOC diagnosed aged ≥75, where the VAF is ≤30% and there is no regional germline commonality.
Collapse
Affiliation(s)
- Robert D Morgan
- Department of Medical Oncology, The Christie NHS Foundation Trust, Manchester, UK
| | - George J Burghel
- North West Genomic Laboratory Hub, Manchester University NHS Foundation Trust, Manchester, UK
| | - Nicola Flaum
- Department of Medical Oncology, The Christie NHS Foundation Trust, Manchester, UK
- North West Genomic Laboratory Hub, Manchester University NHS Foundation Trust, Manchester, UK
- Division of Evolution, Infection and Genomics, University of Manchester, Manchester, UK
| | - Michael Bulman
- North West Genomic Laboratory Hub, Manchester University NHS Foundation Trust, Manchester, UK
| | - Philip Smith
- North West Genomic Laboratory Hub, Manchester University NHS Foundation Trust, Manchester, UK
| | - Andrew R Clamp
- Department of Medical Oncology, The Christie NHS Foundation Trust, Manchester, UK
- Division of Cancer Sciences, University of Manchester, Manchester, UK
| | - Jurjees Hasan
- Department of Medical Oncology, The Christie NHS Foundation Trust, Manchester, UK
| | - Claire Mitchell
- Department of Medical Oncology, The Christie NHS Foundation Trust, Manchester, UK
| | - Zena Salih
- Department of Medical Oncology, The Christie NHS Foundation Trust, Manchester, UK
| | - Emma R Woodward
- North West Genomic Laboratory Hub, Manchester University NHS Foundation Trust, Manchester, UK
- Department of Clinical Genetics, Manchester University NHS Foundation Trust, Manchester, UK
| | - Fiona Lalloo
- North West Genomic Laboratory Hub, Manchester University NHS Foundation Trust, Manchester, UK
- Department of Clinical Genetics, Manchester University NHS Foundation Trust, Manchester, UK
| | - Joseph Shaw
- Department of Histopathology, Manchester University NHS Foundation Trust, Manchester, UK
| | - Sudha Desai
- Department of Histopathology, The Christie NHS Foundation Trust, Manchester, UK
| | - Emma J Crosbie
- Division of Cancer Sciences, University of Manchester, Manchester, UK
- Department of Gynaecological Surgery, Manchester University NHS Foundation Trust, Manchester, UK
| | - Richard J Edmondson
- Division of Cancer Sciences, University of Manchester, Manchester, UK
- Department of Gynaecological Surgery, Manchester University NHS Foundation Trust, Manchester, UK
| | - Helene Schlecht
- North West Genomic Laboratory Hub, Manchester University NHS Foundation Trust, Manchester, UK
| | - Andrew J Wallace
- North West Genomic Laboratory Hub, Manchester University NHS Foundation Trust, Manchester, UK
| | - Gordon C Jayson
- Department of Medical Oncology, The Christie NHS Foundation Trust, Manchester, UK
- Division of Cancer Sciences, University of Manchester, Manchester, UK
| | - D Gareth R Evans
- North West Genomic Laboratory Hub, Manchester University NHS Foundation Trust, Manchester, UK
- Division of Evolution, Infection and Genomics, University of Manchester, Manchester, UK
- Department of Clinical Genetics, Manchester University NHS Foundation Trust, Manchester, UK
| |
Collapse
|
5
|
Morgan RD, Clamp AR, Barnes BM, Timms K, Schlecht H, Yarram-Smith L, Wallis Y, Valganon-Petrizan M, MacMahon S, White R, Morgan S, McKenna S, Hudson E, Tookman L, George A, Manchanda R, Sundar SS, Nicum S, Brenton JD, Kristeleit RS, Banerjee S, McNeish IA, Ledermann JA, Taylor SS, Evans DGR, Jayson GC. Homologous recombination deficiency in newly diagnosed FIGO stage III/IV high-grade epithelial ovarian cancer: a multi-national observational study. Int J Gynecol Cancer 2023; 33:1253-1259. [PMID: 37072323 DOI: 10.1136/ijgc-2022-004211] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/20/2023] Open
Abstract
OBJECTIVE Olaparib plus bevacizumab maintenance therapy improves survival outcomes in women with newly diagnosed, advanced, high-grade ovarian cancer with a deficiency in homologous recombination. We report data from the first year of routine homologous recombination deficiency testing in the National Health Service (NHS) in England, Wales, and Northern Ireland between April 2021 and April 2022. METHODS The Myriad myChoice companion diagnostic was used to test DNA extracted from formalin-fixed, paraffin-embedded tumor tissue in women with newly diagnosed International Federation of Gynecology and Obstetrics (FIGO) stage III/IV high-grade epithelial ovarian, fallopian tube, or primary peritoneal cancer. Tumors with homologous recombination deficiency were those with a BRCA1/2 mutation and/or a Genomic Instability Score (GIS) ≥42. Testing was coordinated by the NHS Genomic Laboratory Hub network. RESULTS The myChoice assay was performed on 2829 tumors. Of these, 2474 (87%) and 2178 (77%) successfully underwent BRCA1/2 and GIS testing, respectively. All complete and partial assay failures occurred due to low tumor cellularity and/or low tumor DNA yield. 385 tumors (16%) contained a BRCA1/2 mutation and 814 (37%) had a GIS ≥42. Tumors with a GIS ≥42 were more likely to be BRCA1/2 wild-type (n=510) than BRCA1/2 mutant (n=304). The distribution of GIS was bimodal, with BRCA1/2 mutant tumors having a higher mean score than BRCA1/2 wild-type tumors (61 vs 33, respectively, χ2 test p<0.0001). CONCLUSION This is the largest real-world evaluation of homologous recombination deficiency testing in newly diagnosed FIGO stage III/IV high-grade epithelial ovarian, fallopian tube, or primary peritoneal cancer. It is important to select tumor tissue with adequate tumor content and quality to reduce the risk of assay failure. The rapid uptake of testing across England, Wales, and Northern Ireland demonstrates the power of centralized NHS funding, center specialization, and the NHS Genomic Laboratory Hub network.
Collapse
Affiliation(s)
- Robert D Morgan
- The Christie NHS Foundation Trust, Manchester, UK
- Division of Cancer Sciences, School of Medical Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
| | - Andrew R Clamp
- The Christie NHS Foundation Trust, Manchester, UK
- Division of Cancer Sciences, School of Medical Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
| | - Bethany M Barnes
- Division of Cancer Sciences, School of Medical Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
| | | | - Helene Schlecht
- North West Genomic Laboratory Hub, Manchester University NHS Foundation Trust, Manchester, UK
| | | | - Yvonne Wallis
- Central and South Genomic Laboratory Hub, Birmingham Women's and Children's NHS Foundation Trust, Birmingham, UK
| | - Mikel Valganon-Petrizan
- North Thames Genomic Laboratory Hub, The Royal Marsden Hospital NHS Foundation Trust, Surrey, UK
| | - Suzanne MacMahon
- North Thames Genomic Laboratory Hub, The Royal Marsden Hospital NHS Foundation Trust, Surrey, UK
| | - Rhian White
- All Wales Genomics Laboratory, Institute of Medical Genetics, University Hospital Wales, Cardiff, UK
| | - Sian Morgan
- All Wales Genomics Laboratory, Institute of Medical Genetics, University Hospital Wales, Cardiff, UK
| | | | | | | | - Angela George
- The Royal Marsden NHS Foundation Trust, London, UK
- The Institute of Cancer Research, London, UK
| | - Ranjit Manchanda
- Barts Health NHS Trust, London, UK
- Department of Health Services Research, The Faculty of Public Health and Policy, London School of Hygiene & Tropical Medicine, London, UK
- Wolfson Institute of Population Health, Queen Mary's University of London, London, UK
| | - Sudha S Sundar
- Sandwell and West Birmingham Hospitals NHS Trust, Birmingham, UK
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
| | - Shibani Nicum
- University College London Hospitals NHS Foundation Trust, London, UK
- UCL Cancer Institute, London, UK
| | - James D Brenton
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
- CRUK Cambridge Institute, University of Cambridge, Cambridge, UK
| | | | - Susana Banerjee
- The Royal Marsden NHS Foundation Trust, London, UK
- The Institute of Cancer Research, London, UK
| | - Iain A McNeish
- Imperial College Healthcare NHS Trust, London, UK
- Ovarian Cancer Action Research Centre, Department of Surgery and Cancer, Imperial College London, London, UK
| | - Jonathan A Ledermann
- University College London Hospitals NHS Foundation Trust, London, UK
- UCL Cancer Institute, London, UK
| | - Stephen S Taylor
- Division of Cancer Sciences, School of Medical Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
| | - D Gareth R Evans
- Manchester University NHS Foundation Trust, Manchester, UK
- Division of Evolution, Infection and Genomics, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
| | - Gordon C Jayson
- The Christie NHS Foundation Trust, Manchester, UK
- Division of Cancer Sciences, School of Medical Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
| |
Collapse
|
6
|
Evans DG, Sithambaram S, van Veen EM, Burghel GJ, Schlecht H, Harkness EF, Byers H, Ellingford JM, Gandhi A, Howell SJ, Howell A, Forde C, Lalloo F, Newman WG, Smith MJ, Woodward ER. Differential involvement of germline pathogenic variants in breast cancer genes between DCIS and low-grade invasive cancers. J Med Genet 2023; 60:740-746. [PMID: 36442995 DOI: 10.1136/jmg-2022-108790] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Accepted: 11/14/2022] [Indexed: 11/29/2022]
Abstract
PURPOSE To investigate frequency of germline pathogenic variants (PVs) in women with ductal carcinoma in situ (DCIS) and grade 1 invasive breast cancer (G1BC). METHODS We undertook BRCA1/2 analysis in 311 women with DCIS and 392 with G1BC and extended panel testing (non-BRCA1/2) in 176/311 with DCIS and 156/392 with G1BC. We investigated PV detection by age at diagnosis, Manchester Score (MS), DCIS grade and receptor status. RESULTS 30/311 (9.6%) with DCIS and 16/392 with G1BC (4.1%) had a BRCA1/2 PV (p=0.003), and 24/176-(13.6%) and 7/156-(4.5%), respectively, a non-BRCA1/2 PV (p=0.004). Increasing MS was associated with increased likelihood of BRCA1/2 PV in both DCIS and G1BC, although the 10% threshold was not predictive for G1GB. 13/32 (40.6%) DCIS and 0/17 with G1BC <40 years had a non-BRCA1/2 PV (p<0.001). 0/16 DCIS G1 had a PV. For G2 and G3 DCIS, PV rates were 10/98 (BRCA1/2) and 9/90 (non-BRCA1/2), and 8/47 (BRCA1/2) and 8/45 (non-BRCA1/2), respectively. 6/9 BRCA1 and 3/26 BRCA2-associated DCIS were oestrogen receptor negative-(p=0.003). G1BC population testing showed no increased PV rate (OR=1.16, 95% CI 0.28 to 4.80). CONCLUSION DCIS is more likely to be associated with both BRCA1/2 and non-BRCA1/2 PVs than G1BC. Extended panel testing ought to be offered in young-onset DCIS where PV detection rates are highest.
Collapse
Affiliation(s)
- D Gareth Evans
- Division of Evolution and Genomic Science, The University of Manchester School of Health Sciences, Manchester, UK
| | - Siva Sithambaram
- Manchester Univerities Hospital NHS Foundation Trust, Manchester, UK
| | - Elke Maria van Veen
- Division of Evolution and Genomic Sciences, The University of Manchester, Manchester, UK
| | | | - Helene Schlecht
- North West Genomic Laboratory Hub, Central Manchester University Hospitals NHS Foundation Trust, Manchester, UK
| | - Elaine F Harkness
- Division of Evolution and Genomic Sciences, The University of Manchester, Manchester, UK
| | - Helen Byers
- Genomic Medicine, The University of Manchester School of Health Sciences, Manchester, UK
| | - Jamie M Ellingford
- Institute of Human Development, The University of Manchester School of Health Sciences, Manchester, UK
| | - Ashu Gandhi
- Prevent Breast Cancer Centre, Wythenshawe Hospital Manchester Universities Foundation Trust, Manchester, UK
| | - Sacha J Howell
- Manchester Univerities Hospital NHS Foundation Trust, Manchester, UK
- Department of Medical Oncology, The Christie NHS Foundation Trust, Manchester, UK
| | - Anthony Howell
- Manchester Foundation Trust, Prevent Breast Cancer Centre, Manchester, UK
| | - Claire Forde
- Clinical Genetics Service, Central Manchester University Hospitals NHS Foundation Trust, Manchester, UK
| | - Fiona Lalloo
- Clinical Genetics Service, Manchester Centre for Genomic Medicine, Central Manchester University Hospitals NHS Foundation Trust, Manchester, UK
| | - William G Newman
- Genetics, The University of Manchester School of Health Sciences, Manchester, UK
| | - Miriam Jane Smith
- Genetic Medicine, The University of Manchester School of Health Sciences, Manchester, UK
| | | |
Collapse
|
7
|
Strach M, Chakrabarty B, Nagaraju R, Burghel G, Schlecht H, Mullamitha S, Braun M, O'Dwyer S, Aziz O, Barriuso J. 10P Molecular mutations in appendix cancers. ESMO Open 2023. [DOI: 10.1016/j.esmoop.2023.101032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/05/2023] Open
|
8
|
Morgan RD, Burghel GJ, Flaum N, Bulman M, Smith P, Clamp AR, Hasan J, Mitchell CL, Salih Z, Woodward ER, Lalloo F, Crosbie EJ, Edmondson RJ, Schlecht H, Jayson GC, Evans DGR. Is Reflex Germline BRCA1/2 Testing Necessary in Women Diagnosed with Non-Mucinous High-Grade Epithelial Ovarian Cancer Aged 80 Years or Older? Cancers (Basel) 2023; 15:730. [PMID: 36765687 PMCID: PMC9913244 DOI: 10.3390/cancers15030730] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2022] [Revised: 01/21/2023] [Accepted: 01/23/2023] [Indexed: 01/26/2023] Open
Abstract
Women diagnosed with non-mucinous high-grade epithelial ovarian cancer (EOC) in England are often reflex-tested for germline and tumour BRCA1/2 variants. The value of germline BRCA1/2 testing in women diagnosed aged ≥80 is questionable. We performed an observational study of all women diagnosed with non-mucinous high-grade EOC who underwent germline and tumour BRCA1/2 testing by the North West of England Genomic Laboratory Hub. A subgroup of women also underwent germline testing using a panel of homologous recombination repair (HRR) genes and/or tumour testing for homologous recombination deficiency (HRD) using Myriad's myChoice® companion diagnostic. Seven-hundred-two patients successfully underwent both germline and tumour BRCA1/2 testing. Of these, 48 were diagnosed with non-mucinous high-grade EOC aged ≥80. In this age group, somatic BRCA1/2 pathogenic/likely pathogenic variants (PV/LPVs) were detected nine times more often than germline BRCA1/2 PV/LPVs. The only germline PV reported in a patient aged ≥80 was detected in germline and tumour DNA (BRCA2 c.4478_4481del). No patient aged ≥80 had a germline PV/LPVs in a non-BRCA1/2 HRR gene. Thirty-eight percent of patients aged ≥80 had a tumour positive for HRD. Our data suggest that tumour BRCA1/2 and HRD testing is adequate for patients diagnosed with non-mucinous high-grade EOC aged ≥80, with germline BRCA1/2 testing reserved for women with a tumour BRCA1/2 PV/LPVs.
Collapse
Affiliation(s)
- Robert D. Morgan
- Department of Medical Oncology, The Christie NHS Foundation Trust, Wilmslow Road, Manchester M20 4BX, UK
- Division of Cancer Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester M13 9PL, UK
| | - George J. Burghel
- Manchester Centre for Genomic Medicine, North West Genomic Laboratory Hub, Saint Mary’s Hospital, Oxford Road, Manchester M13 9WL, UK
| | - Nicola Flaum
- Department of Medical Oncology, The Christie NHS Foundation Trust, Wilmslow Road, Manchester M20 4BX, UK
- Division of Evolution and Genomic Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester M13 9PL, UK
| | - Michael Bulman
- Manchester Centre for Genomic Medicine, North West Genomic Laboratory Hub, Saint Mary’s Hospital, Oxford Road, Manchester M13 9WL, UK
| | - Philip Smith
- Manchester Centre for Genomic Medicine, North West Genomic Laboratory Hub, Saint Mary’s Hospital, Oxford Road, Manchester M13 9WL, UK
| | - Andrew R. Clamp
- Department of Medical Oncology, The Christie NHS Foundation Trust, Wilmslow Road, Manchester M20 4BX, UK
- Division of Cancer Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester M13 9PL, UK
| | - Jurjees Hasan
- Department of Medical Oncology, The Christie NHS Foundation Trust, Wilmslow Road, Manchester M20 4BX, UK
| | - Claire L. Mitchell
- Department of Medical Oncology, The Christie NHS Foundation Trust, Wilmslow Road, Manchester M20 4BX, UK
| | - Zena Salih
- Department of Medical Oncology, The Christie NHS Foundation Trust, Wilmslow Road, Manchester M20 4BX, UK
| | - Emma R. Woodward
- Division of Evolution and Genomic Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester M13 9PL, UK
- Department of Clinical Genetics, Saint Mary’s Hospital, Oxford Road, Manchester M13 9WL, UK
| | - Fiona Lalloo
- Department of Clinical Genetics, Saint Mary’s Hospital, Oxford Road, Manchester M13 9WL, UK
| | - Emma J. Crosbie
- Division of Cancer Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester M13 9PL, UK
- Department of Gynaecological Oncology, Saint Mary’s Hospital, Oxford Road, Manchester M13 9WL, UK
| | - Richard J. Edmondson
- Division of Cancer Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester M13 9PL, UK
- Department of Gynaecological Oncology, Saint Mary’s Hospital, Oxford Road, Manchester M13 9WL, UK
| | - Helene Schlecht
- Manchester Centre for Genomic Medicine, North West Genomic Laboratory Hub, Saint Mary’s Hospital, Oxford Road, Manchester M13 9WL, UK
| | - Gordon C. Jayson
- Department of Medical Oncology, The Christie NHS Foundation Trust, Wilmslow Road, Manchester M20 4BX, UK
- Division of Cancer Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester M13 9PL, UK
| | - D. Gareth R. Evans
- Manchester Centre for Genomic Medicine, North West Genomic Laboratory Hub, Saint Mary’s Hospital, Oxford Road, Manchester M13 9WL, UK
- Division of Evolution and Genomic Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester M13 9PL, UK
- Department of Clinical Genetics, Saint Mary’s Hospital, Oxford Road, Manchester M13 9WL, UK
| |
Collapse
|
9
|
Flaum N, Crosbie EJ, Edmondson R, Woodward ER, Lalloo F, Smith MJ, Schlecht H, Evans DG. High detection rate from genetic testing in BRCA-negative women with familial epithelial ovarian cancer. Genet Med 2022; 24:2578-2586. [PMID: 36169650 DOI: 10.1016/j.gim.2022.08.022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Revised: 08/23/2022] [Accepted: 08/23/2022] [Indexed: 12/14/2022] Open
Abstract
PURPOSE Epithelial ovarian cancer (EOC) is associated with pathogenic variants (PVs) in homologous recombination and/or mismatch repair genes. We aimed to review the testing of women with familial EOC at our center. METHODS Women with familial EOC (≥2 EOC in family, including index case) referred to our center between 1993 and 2021 were included. Genetic testing (BRCA/Lynch syndrome screening, exome sequencing, panel testing, 100,000 Genome Project, and NIHR BioResource genome sequencing) and clinical demographic, diagnosis, and survival data were reviewed. RESULTS Of 277, 128 (46.2%) women were BRCA heterozygotes (BRCA1: 89, BRCA2: 39). The detection rate in BRCA-negative women was 21.8%; the most commonly affected gene was BRIP1 (5.9%). The non-BRCA detection rate was significantly higher in families with 2 affected members with EOC only (22.4%) than the families with ≥3 (11.1%) affected members (odds ratio = 9.9, 95% CI = 1.6-105.2, P = .0075). Overall, 112 different PVs in 12 homologous recombination/mismatch repair genes were detected in 150 of 277 (54.2%) unrelated women. CONCLUSION This is the largest report of women with familial EOC undergoing wider testing to date. One-fifth of BRCA-negative women were heterozygous for a PV in a potentially actionable gene. Wider genetic testing of women with familial EOC is essential to optimize their treatment and prevention of disease in family members.
Collapse
Affiliation(s)
- Nicola Flaum
- Division of Evolution, Infection and Genomics, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, United Kingdom; North West Genomics Laboratory Hub, Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester University NHS Foundation Trust, Manchester Academic Health Science Centre, United Kingdom.
| | - Emma J Crosbie
- Division of Cancer Sciences, School of Medical Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Uunited Kingdom; Division of Gynaecology, St Mary's Hospital, Manchester University NHS Foundation Trust, Manchester, United Kingdom
| | - Richard Edmondson
- Division of Cancer Sciences, School of Medical Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Uunited Kingdom; Division of Gynaecology, St Mary's Hospital, Manchester University NHS Foundation Trust, Manchester, United Kingdom
| | - Emma R Woodward
- Clinical Genetics Service, Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester University NHS Foundation Trust, Manchester, United Kingdom
| | - Fiona Lalloo
- Clinical Genetics Service, Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester University NHS Foundation Trust, Manchester, United Kingdom
| | - Miriam J Smith
- Division of Evolution, Infection and Genomics, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, United Kingdom; North West Genomics Laboratory Hub, Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester University NHS Foundation Trust, Manchester Academic Health Science Centre, United Kingdom
| | - Helene Schlecht
- North West Genomics Laboratory Hub, Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester University NHS Foundation Trust, Manchester Academic Health Science Centre, United Kingdom
| | - D Gareth Evans
- Division of Evolution, Infection and Genomics, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, United Kingdom; North West Genomics Laboratory Hub, Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester University NHS Foundation Trust, Manchester Academic Health Science Centre, United Kingdom; Prevention Breast Cancer Centre and Nightingale Breast Screening Centre, University Hospital of South Manchester, Manchester, United Kingdom; The Christie NHS Foundation Trust, Manchester, United Kingdom; Manchester Breast Centre, Manchester Cancer Research Centre, University of Manchester, United Kingdom
| |
Collapse
|
10
|
Morgan R, Clamp A, Barnes B, Schlecht H, Yarram-Smith L, Wallis Y, Morgan S, Valganon M, Hudson E, McKenna S, Sundar S, Nicum S, Brenton J, Kristeleit R, Banerjee S, McNeish I, Ledermann J, Taylor S, Evans G, Jayson G. 575P Homologous recombination deficiency in newly diagnosed FIGO stage III/IV high-grade serous or endometrioid ovarian cancer: A multi-national observational study. Ann Oncol 2022. [DOI: 10.1016/j.annonc.2022.07.703] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
|
11
|
Beresford L, Murphy P, Dias S, Claxton L, Walton M, Metcalf R, Schlecht H, Ottensmeier C, Pereira M, Hodgson R. Appraising the Costs of Genomic Testing for Histology-Independent Technologies: An Illustrative Example for NTRK Fusions. Value Health 2022; 25:1133-1140. [PMID: 35779940 DOI: 10.1016/j.jval.2021.11.1359] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Revised: 11/04/2021] [Accepted: 11/14/2021] [Indexed: 06/15/2023]
Abstract
OBJECTIVES Histology-independent (HI) technologies are authorized for patients with advanced or metastatic cancer if they express a particular biomarker regardless of its position in the body. Although this represents an important advancement in cancer treatment, genomic testing to identify eligible individuals for HI technologies will require substantial investment and impact their cost-effectiveness. Estimating these costs is complicated by several issues, which affect not only the overall cost of testing but also the distribution of testing costs across tumor types. METHODS Key issues that should be considered when evaluating the cost of genomic testing to identify those eligible for HI technologies are discussed. These issues are explored in illustrative analyses where costs of genomic testing for NTRK fusions in England for recently approved HI technologies are estimated. RESULTS The prevalence of mutation, testing strategy adopted, and current testing provision affect the cost of identifying eligible patients. The illustrative analysis estimated the cost of RNA-based next-generation sequencing to identify 1 individual with an NTRK fusion ranged between £377 and £282 258. To improve cost-effectiveness, testing costs could be shared across multiple technologies. An estimated additional ∼4000 patients would need to be treated with other HI therapies for testing in patients with advanced or metastatic cancer to be cost-effective. CONCLUSIONS The cost of testing to identify individuals eligible for HI technologies affect the drug's cost-effectiveness. The cost of testing across tumor types varies owing to heterogeneity in the mutation's prevalence and current testing provision. The cost-effectiveness of HI technologies may be improved if testing costs could be shared across multiple agents.
Collapse
Affiliation(s)
- Lucy Beresford
- Centre for Reviews and Dissemination, University of York, York, England, UK.
| | - Peter Murphy
- Centre for Reviews and Dissemination, University of York, York, England, UK; Centre for Health Economics, University of York, UK
| | - Sofia Dias
- Centre for Reviews and Dissemination, University of York, York, England, UK
| | | | - Matthew Walton
- Centre for Reviews and Dissemination, University of York, York, England, UK
| | - Robert Metcalf
- Medical Oncology, The Christie Hospital, Manchester, England, UK
| | - Helene Schlecht
- Genomic Diagnostic Laboratory, Manchester Centre for Genomic Medicine, Manchester, England, UK
| | - Christian Ottensmeier
- Department of Molecular & Clinical Cancer Medicine, University of Liverpool, Liverpool, UK
| | - Marta Pereira
- Genomic Diagnostic Laboratory, Manchester Centre for Genomic Medicine, Manchester, England, UK
| | - Robert Hodgson
- Centre for Reviews and Dissemination, University of York, York, England, UK
| |
Collapse
|
12
|
Perez‐Becerril C, Wallace AJ, Schlecht H, Bowers NL, Smith PT, Gokhale C, Eaton H, Charlton C, Robinson R, Charlton RS, Evans DG, Smith MJ. Screening of potential novel candidate genes in schwannomatosis patients. Hum Mutat 2022; 43:1368-1376. [PMID: 35723634 PMCID: PMC9540472 DOI: 10.1002/humu.24424] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 06/10/2022] [Accepted: 06/15/2022] [Indexed: 01/07/2023]
Abstract
Schwannomatosis comprises a group of hereditary tumor predisposition syndromes characterized by, usually benign, multiple nerve sheath tumors, which frequently cause severe pain that does not typically respond to drug treatments. The most common schwannomatosis‐associated gene is NF2, but SMARCB1 and LZTR1 are also associated. There are still many cases in which no pathogenic variants (PVs) have been identified, suggesting the existence of as yet unidentified genetic risk factors. In this study, we performed extended genetic screening of 75 unrelated schwannomatosis patients without identified germline PVs in NF2, LZTR1, or SMARCB1. Screening of the coding region of DGCR8, COQ6, CDKN2A, and CDKN2B was carried out, based on previous reports that point to these genes as potential candidate genes for schwannomatosis. Deletions or duplications in CDKN2A, CDKN2B, and adjacent chromosome 9 region were assessed by multiplex ligation‐dependent probe amplification analysis. Sequencing analysis of a patient with multiple schwannomas and melanomas identified a novel duplication in the coding region of CDKN2A, disrupting both p14ARF and p16INK4a. Our results suggest that none of these genes are major contributors to schwannomatosis risk but the possibility remains that they may have a role in more complex mechanisms for tumor predisposition.
Collapse
Affiliation(s)
- Cristina Perez‐Becerril
- School of Biological Sciences, Division of Evolution, Infection and Genomics, Faculty of Biology, Medicine and HealthUniversity of ManchesterManchesterUK
- Manchester Centre for Genomic Medicine, St Mary's HospitalManchester University NHS Foundation TrustManchesterUK
| | - Andrew J. Wallace
- Manchester Centre for Genomic Medicine, St Mary's HospitalManchester University NHS Foundation TrustManchesterUK
| | - Helene Schlecht
- Manchester Centre for Genomic Medicine, St Mary's HospitalManchester University NHS Foundation TrustManchesterUK
| | - Naomi L. Bowers
- Manchester Centre for Genomic Medicine, St Mary's HospitalManchester University NHS Foundation TrustManchesterUK
| | - Philip T. Smith
- Manchester Centre for Genomic Medicine, St Mary's HospitalManchester University NHS Foundation TrustManchesterUK
| | - Carolyn Gokhale
- Manchester Centre for Genomic Medicine, St Mary's HospitalManchester University NHS Foundation TrustManchesterUK
| | - Helen Eaton
- Manchester Centre for Genomic Medicine, St Mary's HospitalManchester University NHS Foundation TrustManchesterUK
| | - Chris Charlton
- Manchester Centre for Genomic Medicine, St Mary's HospitalManchester University NHS Foundation TrustManchesterUK
| | - Rachel Robinson
- North East and Yorkshire Genomic Laboratory HubSt James's University HospitalLeedsUK
| | - Ruth S. Charlton
- North East and Yorkshire Genomic Laboratory HubSt James's University HospitalLeedsUK
| | - D. Gareth Evans
- School of Biological Sciences, Division of Evolution, Infection and Genomics, Faculty of Biology, Medicine and HealthUniversity of ManchesterManchesterUK
- Manchester Centre for Genomic Medicine, St Mary's HospitalManchester University NHS Foundation TrustManchesterUK
| | - Miriam J. Smith
- School of Biological Sciences, Division of Evolution, Infection and Genomics, Faculty of Biology, Medicine and HealthUniversity of ManchesterManchesterUK
- Manchester Centre for Genomic Medicine, St Mary's HospitalManchester University NHS Foundation TrustManchesterUK
| |
Collapse
|
13
|
Woodward ER, Green K, Burghel GJ, Bulman M, Clancy T, Lalloo F, Schlecht H, Wallace AJ, Evans DG. 30 year experience of index case identification and outcomes of cascade testing in high-risk breast and colorectal cancer predisposition genes. Eur J Hum Genet 2022; 30:413-419. [PMID: 34866136 PMCID: PMC8645350 DOI: 10.1038/s41431-021-01011-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Revised: 09/27/2021] [Accepted: 11/15/2021] [Indexed: 11/19/2022] Open
Abstract
It is 30 years since the first diagnostic cancer predisposition gene (CPG) test in the Manchester Centre for Genomic Medicine (MCGM), providing opportunities for cancer prevention, early detection and targeted treatments in index cases and at-risk family members. Here, we present time trends (1990-2020) of identification of index cases with a germline CPG variant and numbers of subsequent cascade tests, for 15 high-risk breast and gastro-intestinal tract cancer-associated CPGs: BRCA1, BRCA2, PALB2, PTEN, TP53, APC, BMPR1a, CDH1, MLH1, MSH2, MSH6, PMS2, SMAD4, STK11 and MUTYH. We recorded 2082 positive index case diagnostic screening tests, generating 3216 positive and 3140 negative family cascade (non-index) tests. This is equivalent to an average of 3.05 subsequent cascade tests per positive diagnostic index test, with 1.54 positive and 1.51 negative non-index tests per family. The CPGs with the highest numbers of non-index positive cases identified on cascade testing were BRCA1/2 (n = 1999) and the mismatch repair CPGs associated with Lynch Syndrome (n = 731). These data are important for service provision and health economic assessment of CPG diagnostic testing, in terms of cancer prevention and early detection strategies, and identifying those likely to benefit from targeted treatment strategies.
Collapse
Affiliation(s)
- Emma R Woodward
- Manchester Centre for Genomic Medicine, Manchester University Hospitals NHS Foundation Trust, Manchester, M13 9WL, UK
- Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester, M13 9PL, UK
| | - Kate Green
- Manchester Centre for Genomic Medicine, Manchester University Hospitals NHS Foundation Trust, Manchester, M13 9WL, UK
| | - George J Burghel
- Manchester Centre for Genomic Medicine, Manchester University Hospitals NHS Foundation Trust, Manchester, M13 9WL, UK
| | - Michael Bulman
- Manchester Centre for Genomic Medicine, Manchester University Hospitals NHS Foundation Trust, Manchester, M13 9WL, UK
| | - Tara Clancy
- Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester, M13 9PL, UK
| | - Fiona Lalloo
- Manchester Centre for Genomic Medicine, Manchester University Hospitals NHS Foundation Trust, Manchester, M13 9WL, UK
| | - Helene Schlecht
- Manchester Centre for Genomic Medicine, Manchester University Hospitals NHS Foundation Trust, Manchester, M13 9WL, UK
| | - Andrew J Wallace
- Manchester Centre for Genomic Medicine, Manchester University Hospitals NHS Foundation Trust, Manchester, M13 9WL, UK
| | - D Gareth Evans
- Manchester Centre for Genomic Medicine, Manchester University Hospitals NHS Foundation Trust, Manchester, M13 9WL, UK.
- Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester, M13 9PL, UK.
| |
Collapse
|
14
|
Berland S, Jareld J, Hickson N, Schlecht H, Houge G, Douzgou S. The blended phenotype of a germline RIT1 and a mosaic PIK3CA variant. Cold Spring Harb Mol Case Stud 2021; 7:mcs.a006121. [PMID: 34887308 PMCID: PMC8751416 DOI: 10.1101/mcs.a006121] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [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: 06/28/2021] [Accepted: 08/31/2021] [Indexed: 02/04/2023] Open
Abstract
We report a patient with a germline RIT1 and a mosaic PIK3CA variant. The diagnosis of the RASopathy was confirmed by targeted sequencing following the identification of transient cardiomyopathy in a patient with PIK3CA-related overgrowth spectrum (PROS). Our observation confirms that the PIK3CA gain-of-function (GoF) variant effects dominate those of the RASopathy, and the resulting blended phenotype mostly resembles megalencephaly-capillary malformation syndrome (MCAP PROS). There appears to be interaction between RIT1 and PI3K-AKT because the latter pathway is needed for the growth-promoting activity of the first, at least in adenocarcinomas, but the details of this interaction are not known. If so, the PIK3CA somatic variant may not be just a chance event. It could also be of etiological relevance that Rit activation mediates resistance to cellular stress—that is, promotes cell survival. This anti-apoptotic effect could also make it more likely that a cell that spontaneously acquires a PIK3CA GoF variant will survive and proliferate. We aim to encourage clinicians to investigate atypical findings in individuals with PROS. If further similar cases are reported, this would suggest that the establishment of PROS mosaicism is facilitated by the background of a RASopathy.
Collapse
Affiliation(s)
- Siren Berland
- Department of Medical Genetics, Haukeland University Hospital, N-5021, Bergen, Norway
| | - Jørgen Jareld
- Department of Paediatrics, Ålesund Hospital, Møre and Romsdal Health Trust, 6026, Ålesund, Norway
| | - Nicholas Hickson
- Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester University Hospitals NHS Foundation Trust, Manchester Academic Health Sciences Centre, Oxford Road, M13 9WL, United Kingdom
| | - Helene Schlecht
- Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester University Hospitals NHS Foundation Trust, Manchester Academic Health Sciences Centre, Oxford Road, M13 9WL, United Kingdom
| | - Gunnar Houge
- Department of Medical Genetics, Haukeland University Hospital, N-5021, Bergen, Norway.,Division of Evolution and Genomic Sciences, School of Biological Sciences, University of Manchester, Oxford Road, M13 9PL, United Kingdom
| | - Sofia Douzgou
- Department of Medical Genetics, Haukeland University Hospital, N-5021, Bergen, Norway.,Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester University Hospitals NHS Foundation Trust, Manchester Academic Health Sciences Centre, Oxford Road, M13 9WL, United Kingdom.,Division of Evolution and Genomic Sciences, School of Biological Sciences, University of Manchester, Oxford Road, M13 9PL, United Kingdom
| |
Collapse
|
15
|
Coulson-Gilmer C, Morgan RD, Nelson L, Barnes BM, Tighe A, Wardenaar R, Spierings DCJ, Schlecht H, Burghel GJ, Foijer F, Desai S, McGrail JC, Taylor SS. Replication catastrophe is responsible for intrinsic PAR glycohydrolase inhibitor-sensitivity in patient-derived ovarian cancer models. J Exp Clin Cancer Res 2021; 40:323. [PMID: 34656146 PMCID: PMC8520217 DOI: 10.1186/s13046-021-02124-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Accepted: 10/02/2021] [Indexed: 01/20/2023] Open
Abstract
BACKGROUND Patients with ovarian cancer often present at advanced stage and, following initial treatment success, develop recurrent drug-resistant disease. PARP inhibitors (PARPi) are yielding unprecedented survival benefits for women with BRCA-deficient disease. However, options remain limited for disease that is platinum-resistant and/or has inherent or acquired PARPi-resistance. PARG, the PAR glycohydrolase that counterbalances PARP activity, is an emerging target with potential to selectively kill tumour cells harbouring oncogene-induced DNA replication and metabolic vulnerabilities. Clinical development of PARG inhibitors (PARGi) will however require predictive biomarkers, in turn requiring an understanding of their mode of action. Furthermore, differential sensitivity to PARPi is key for expanding treatment options available for patients. METHODS A panel of 10 ovarian cancer cell lines and a living biobank of patient-derived ovarian cancer models (OCMs) were screened for PARGi-sensitivity using short- and long-term growth assays. PARGi-sensitivity was characterized using established markers for DNA replication stress, namely replication fibre asymmetry, RPA foci, KAP1 and Chk1 phosphorylation, and pan-nuclear γH2AX, indicating DNA replication catastrophe. Finally, gene expression in sensitive and resistant cells was also examined using NanoString or RNAseq. RESULTS PARGi sensitivity was identified in both ovarian cancer cell lines and patient-derived OCMs, with sensitivity accompanied by markers of persistent replication stress, and a pre-mitotic cell cycle block. Moreover, DNA replication genes are down-regulated in PARGi-sensitive cell lines consistent with an inherent DNA replication vulnerability. However, DNA replication gene expression did not predict PARGi-sensitivity in OCMs. The subset of patient-derived OCMs that are sensitive to single-agent PARG inhibition, includes models that are PARPi- and/or platinum-resistant, indicating that PARG inhibitors may represent an alternative treatment strategy for women with otherwise limited therapeutic options. CONCLUSIONS We discover that a subset of ovarian cancers are intrinsically sensitive to pharmacological PARG blockade, including drug-resistant disease, underpinned by a common mechanism of replication catastrophe. We explore the use of a transcript-based biomarker, and provide insight into the design of future clinical trials of PARGi in patients with ovarian cancer. However, our results highlight the complexity of developing a predictive biomarker for PARGi sensitivity.
Collapse
Affiliation(s)
- Camilla Coulson-Gilmer
- Division of Cancer Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Cancer Research Centre, Oglesby Cancer Research Building, 555 Wilmslow Road, Manchester, M20 4GJ, UK
| | - Robert D Morgan
- Division of Cancer Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Cancer Research Centre, Oglesby Cancer Research Building, 555 Wilmslow Road, Manchester, M20 4GJ, UK
- Department of Medical Oncology, The Christie NHS Foundation Trust, Wilmslow Rd, Manchester, M20 4BX, UK
| | - Louisa Nelson
- Division of Cancer Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Cancer Research Centre, Oglesby Cancer Research Building, 555 Wilmslow Road, Manchester, M20 4GJ, UK
| | - Bethany M Barnes
- Division of Cancer Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Cancer Research Centre, Oglesby Cancer Research Building, 555 Wilmslow Road, Manchester, M20 4GJ, UK
| | - Anthony Tighe
- Division of Cancer Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Cancer Research Centre, Oglesby Cancer Research Building, 555 Wilmslow Road, Manchester, M20 4GJ, UK
| | - René Wardenaar
- European Research Institute for the Biology of Ageing (ERIBA), University of Groningen, University Medical Center Groningen, Groningen, 9713, AV, The Netherlands
| | - Diana C J Spierings
- European Research Institute for the Biology of Ageing (ERIBA), University of Groningen, University Medical Center Groningen, Groningen, 9713, AV, The Netherlands
| | - Helene Schlecht
- Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester University NHS Foundation Trust, Oxford Road, Manchester, M13 9WL, UK
| | - George J Burghel
- Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester University NHS Foundation Trust, Oxford Road, Manchester, M13 9WL, UK
| | - Floris Foijer
- European Research Institute for the Biology of Ageing (ERIBA), University of Groningen, University Medical Center Groningen, Groningen, 9713, AV, The Netherlands
| | - Sudha Desai
- Department of Histopathology, The Christie NHS Foundation Trust, Wilmslow Rd, Manchester, M20 4BX, UK
| | - Joanne C McGrail
- Division of Cancer Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Cancer Research Centre, Oglesby Cancer Research Building, 555 Wilmslow Road, Manchester, M20 4GJ, UK
| | - Stephen S Taylor
- Division of Cancer Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Cancer Research Centre, Oglesby Cancer Research Building, 555 Wilmslow Road, Manchester, M20 4GJ, UK.
| |
Collapse
|
16
|
Chandrasekaran D, Sobocan M, Blyuss O, Miller RE, Evans O, Crusz SM, Mills-Baldock T, Sun L, Hammond RFL, Gaba F, Jenkins LA, Ahmed M, Kumar A, Jeyarajah A, Lawrence AC, Brockbank E, Phadnis S, Quigley M, El Khouly F, Wuntakal R, Faruqi A, Trevisan G, Casey L, Burghel GJ, Schlecht H, Bulman M, Smith P, Bowers NL, Legood R, Lockley M, Wallace A, Singh N, Evans DG, Manchanda R. Implementation of Multigene Germline and Parallel Somatic Genetic Testing in Epithelial Ovarian Cancer: SIGNPOST Study. Cancers (Basel) 2021; 13:cancers13174344. [PMID: 34503154 PMCID: PMC8431198 DOI: 10.3390/cancers13174344] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Revised: 08/09/2021] [Accepted: 08/24/2021] [Indexed: 11/16/2022] Open
Abstract
We present findings of a cancer multidisciplinary-team (MDT) coordinated mainstreaming pathway of unselected 5-panel germline BRCA1/BRCA2/RAD51C/RAD51D/BRIP1 and parallel somatic BRCA1/BRCA2 testing in all women with epithelial-OC and highlight the discordance between germline and somatic testing strategies across two cancer centres. Patients were counselled and consented by a cancer MDT member. The uptake of parallel multi-gene germline and somatic testing was 97.7%. Counselling by clinical-nurse-specialist more frequently needed >1 consultation (53.6% (30/56)) compared to a medical (15.0% (21/137)) or surgical oncologist (15.3% (17/110)) (p < 0.001). The median age was 54 (IQR = 51-62) years in germline pathogenic-variant (PV) versus 61 (IQR = 51-71) in BRCA wild-type (p = 0.001). There was no significant difference in distribution of PVs by ethnicity, stage, surgery timing or resection status. A total of 15.5% germline and 7.8% somatic BRCA1/BRCA2 PVs were identified. A total of 2.3% patients had RAD51C/RAD51D/BRIP1 PVs. A total of 11% germline PVs were large-genomic-rearrangements and missed by somatic testing. A total of 20% germline PVs are missed by somatic first BRCA-testing approach and 55.6% germline PVs missed by family history ascertainment. The somatic testing failure rate is higher (23%) for patients undergoing diagnostic biopsies. Our findings favour a prospective parallel somatic and germline panel testing approach as a clinically efficient strategy to maximise variant identification. UK Genomics test-directory criteria should be expanded to include a panel of OC genes.
Collapse
Affiliation(s)
- Dhivya Chandrasekaran
- Wolfson Institute of Population Health, Barts CRUK Cancer Centre, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, UK; (D.C.); (M.S.); (O.E.); (L.S.); (F.G.)
- Department of Gynaecological Oncology, Barts Health NHS Trust, London EC1 1BB, UK; (A.J.); (A.C.L.); (E.B.); (S.P.)
| | - Monika Sobocan
- Wolfson Institute of Population Health, Barts CRUK Cancer Centre, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, UK; (D.C.); (M.S.); (O.E.); (L.S.); (F.G.)
- Department of Gynaecological Oncology, Barts Health NHS Trust, London EC1 1BB, UK; (A.J.); (A.C.L.); (E.B.); (S.P.)
- Divison for Gynaecology and Perinatology, University Medical Centre Maribor, 2000 Maribor, Slovenia
| | - Oleg Blyuss
- School of Physics, Engineering and Computer Science, University of Hertfordshire, Hatfield AL10 9AB, UK;
- Department of Paediatrics and Paediatric Infectious Diseases, Sechenov First Moscow State Medical University, Moscow 119991, Russia
- World-Class Research Center “Digital Biodesign and Personalized Healthcare”, Sechenov First Moscow State Medical University, Moscow 119991, Russia
| | - Rowan E. Miller
- Department of Medical Oncology, Barts Health NHS Trust, London EC1A 7BE, UK; (R.E.M.); (S.M.C.)
| | - Olivia Evans
- Wolfson Institute of Population Health, Barts CRUK Cancer Centre, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, UK; (D.C.); (M.S.); (O.E.); (L.S.); (F.G.)
| | - Shanthini M. Crusz
- Department of Medical Oncology, Barts Health NHS Trust, London EC1A 7BE, UK; (R.E.M.); (S.M.C.)
| | - Tina Mills-Baldock
- Department of Medical Oncology, Barking, Havering & Redbridge University Hospitals, Essex RM7 0AG, UK; (T.M.-B.); (M.Q.); (F.E.K.)
| | - Li Sun
- Wolfson Institute of Population Health, Barts CRUK Cancer Centre, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, UK; (D.C.); (M.S.); (O.E.); (L.S.); (F.G.)
- Department of Health Services Research, Faculty of Public Health & Policy, London School of Hygiene & Tropical Medicine, London WC1H 9SH, UK;
| | - Rory F. L. Hammond
- Department of Pathology, Barts Health NHS Trust, London E1 1FR, UK; (R.F.L.H.); (A.F.); (G.T.); (L.C.); (N.S.)
| | - Faiza Gaba
- Wolfson Institute of Population Health, Barts CRUK Cancer Centre, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, UK; (D.C.); (M.S.); (O.E.); (L.S.); (F.G.)
| | - Lucy A. Jenkins
- North East Thames Regional Genetics Service, Great Ormond Street Hospital, London WC1N 3JH, UK; (L.A.J.); (M.A.); (A.K.)
| | - Munaza Ahmed
- North East Thames Regional Genetics Service, Great Ormond Street Hospital, London WC1N 3JH, UK; (L.A.J.); (M.A.); (A.K.)
| | - Ajith Kumar
- North East Thames Regional Genetics Service, Great Ormond Street Hospital, London WC1N 3JH, UK; (L.A.J.); (M.A.); (A.K.)
| | - Arjun Jeyarajah
- Department of Gynaecological Oncology, Barts Health NHS Trust, London EC1 1BB, UK; (A.J.); (A.C.L.); (E.B.); (S.P.)
| | - Alexandra C. Lawrence
- Department of Gynaecological Oncology, Barts Health NHS Trust, London EC1 1BB, UK; (A.J.); (A.C.L.); (E.B.); (S.P.)
| | - Elly Brockbank
- Department of Gynaecological Oncology, Barts Health NHS Trust, London EC1 1BB, UK; (A.J.); (A.C.L.); (E.B.); (S.P.)
| | - Saurabh Phadnis
- Department of Gynaecological Oncology, Barts Health NHS Trust, London EC1 1BB, UK; (A.J.); (A.C.L.); (E.B.); (S.P.)
| | - Mary Quigley
- Department of Medical Oncology, Barking, Havering & Redbridge University Hospitals, Essex RM7 0AG, UK; (T.M.-B.); (M.Q.); (F.E.K.)
| | - Fatima El Khouly
- Department of Medical Oncology, Barking, Havering & Redbridge University Hospitals, Essex RM7 0AG, UK; (T.M.-B.); (M.Q.); (F.E.K.)
| | - Rekha Wuntakal
- Department of Gynaecology, Barking, Havering & Redbridge University Hospitals, Essex RM7 0AG, UK;
| | - Asma Faruqi
- Department of Pathology, Barts Health NHS Trust, London E1 1FR, UK; (R.F.L.H.); (A.F.); (G.T.); (L.C.); (N.S.)
| | - Giorgia Trevisan
- Department of Pathology, Barts Health NHS Trust, London E1 1FR, UK; (R.F.L.H.); (A.F.); (G.T.); (L.C.); (N.S.)
| | - Laura Casey
- Department of Pathology, Barts Health NHS Trust, London E1 1FR, UK; (R.F.L.H.); (A.F.); (G.T.); (L.C.); (N.S.)
| | - George J. Burghel
- Manchester Centre for Genomic Medicine, Saint Marys Hospital, Manchester M13 9WL, UK; (G.J.B.); (H.S.); (M.B.); (P.S.); (N.L.B.); (A.W.); (D.G.E.)
| | - Helene Schlecht
- Manchester Centre for Genomic Medicine, Saint Marys Hospital, Manchester M13 9WL, UK; (G.J.B.); (H.S.); (M.B.); (P.S.); (N.L.B.); (A.W.); (D.G.E.)
| | - Michael Bulman
- Manchester Centre for Genomic Medicine, Saint Marys Hospital, Manchester M13 9WL, UK; (G.J.B.); (H.S.); (M.B.); (P.S.); (N.L.B.); (A.W.); (D.G.E.)
| | - Philip Smith
- Manchester Centre for Genomic Medicine, Saint Marys Hospital, Manchester M13 9WL, UK; (G.J.B.); (H.S.); (M.B.); (P.S.); (N.L.B.); (A.W.); (D.G.E.)
| | - Naomi L. Bowers
- Manchester Centre for Genomic Medicine, Saint Marys Hospital, Manchester M13 9WL, UK; (G.J.B.); (H.S.); (M.B.); (P.S.); (N.L.B.); (A.W.); (D.G.E.)
| | - Rosa Legood
- Department of Health Services Research, Faculty of Public Health & Policy, London School of Hygiene & Tropical Medicine, London WC1H 9SH, UK;
| | - Michelle Lockley
- Barts Cancer Institute, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, UK;
| | - Andrew Wallace
- Manchester Centre for Genomic Medicine, Saint Marys Hospital, Manchester M13 9WL, UK; (G.J.B.); (H.S.); (M.B.); (P.S.); (N.L.B.); (A.W.); (D.G.E.)
| | - Naveena Singh
- Department of Pathology, Barts Health NHS Trust, London E1 1FR, UK; (R.F.L.H.); (A.F.); (G.T.); (L.C.); (N.S.)
| | - D. Gareth Evans
- Manchester Centre for Genomic Medicine, Saint Marys Hospital, Manchester M13 9WL, UK; (G.J.B.); (H.S.); (M.B.); (P.S.); (N.L.B.); (A.W.); (D.G.E.)
| | - Ranjit Manchanda
- Wolfson Institute of Population Health, Barts CRUK Cancer Centre, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, UK; (D.C.); (M.S.); (O.E.); (L.S.); (F.G.)
- Department of Gynaecological Oncology, Barts Health NHS Trust, London EC1 1BB, UK; (A.J.); (A.C.L.); (E.B.); (S.P.)
- Department of Health Services Research, Faculty of Public Health & Policy, London School of Hygiene & Tropical Medicine, London WC1H 9SH, UK;
- Correspondence:
| |
Collapse
|
17
|
Bennett S, Alexander E, Fraser H, Bowers N, Wallace A, Woodward ER, Lalloo F, Quinn AM, Huang S, Schlecht H, Evans DG. Germline FFPE inherited cancer panel testing in deceased family members: implications for clinical management of unaffected relatives. Eur J Hum Genet 2021; 29:861-871. [PMID: 33654310 PMCID: PMC8110779 DOI: 10.1038/s41431-021-00817-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [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: 07/17/2020] [Revised: 01/07/2021] [Accepted: 01/23/2021] [Indexed: 01/29/2023] Open
Abstract
Where previously, germline genetic testing in deceased affected relatives was not possible due to the absence of lymphocytic DNA, the North-West-Genomic-Laboratory Hub (NWGLH) has developed and validated next-generation sequencing based gene panels utilising formalin-fixed-paraffin-embedded (FFPE) tissue DNA from deceased individuals. This technology has been utilised in the clinical setting for the management of unaffected relatives seen in the Clinical Genetics Service (CGS). Here we assess the clinical impact. At the time of data collection, the NWGLH had analysed 180 FFPE tissue samples from deceased affected individuals: 134 from breast and/or ovarian cancer cases for germline variants in the BRCA1/BRCA2 genes and 46 from colorectal, gastric, ovarian and endometrial cancer cases for germline variants in a panel of 13 genes implicated in inherited colorectal cancer and gastric cancer conditions. Successful analysis was achieved in 140/180 cases (78%). In total, 29 germline pathogenic/likely pathogenic variants were identified in autosomal dominant cancer predisposition genes where the gene was pertinent to the cancer family history (including BRCA1/BRCA2, the mismatch-repair genes and APC). Of the 180 cases, the impact of the result on clinical management of unaffected relatives was known in 143 cases. Of these, the results in 54 cases (38%) directly impacted the clinical management of relatives seen by the CGS. This included changes to risk assessments, screening recommendations and the availability of predictive genetic testing to unaffected relatives. Our data demonstrate how FFPE testing in deceased relatives is an accurate and informative tool in the clinical management of patients referred to the CGS.
Collapse
Affiliation(s)
- Sarah Bennett
- Clinical Genetics Service, Manchester Centre for Genomic Medicine, St Mary’s Hospital, Manchester University NHS Foundation Trust, Manchester, UK
| | - Elizabeth Alexander
- Clinical Genetics Service, Manchester Centre for Genomic Medicine, St Mary’s Hospital, Manchester University NHS Foundation Trust, Manchester, UK
| | - Harry Fraser
- Northern Regional Genetic Service, Genetics Health Service New Zealand, Auckland City Hospital, Auckland, New Zealand
| | - Naomi Bowers
- North West Genomic Laboratory Hub, Manchester Centre for Genomic Medicine, St Mary’s Hospital, Manchester University NHS Foundation Trust, Health Innovation Manchester, Manchester, UK
| | - Andrew Wallace
- North West Genomic Laboratory Hub, Manchester Centre for Genomic Medicine, St Mary’s Hospital, Manchester University NHS Foundation Trust, Health Innovation Manchester, Manchester, UK
| | - Emma R. Woodward
- Clinical Genetics Service, Manchester Centre for Genomic Medicine, St Mary’s Hospital, Manchester University NHS Foundation Trust, Manchester, UK ,Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Health innovation Manchester, Manchester, UK
| | - Fiona Lalloo
- Clinical Genetics Service, Manchester Centre for Genomic Medicine, St Mary’s Hospital, Manchester University NHS Foundation Trust, Manchester, UK
| | - Anne Marie Quinn
- Department of Anatomic Pathology, University Hospital Galway, Galway, Ireland
| | - Shuwen Huang
- North West Genomic Laboratory Hub, Manchester Centre for Genomic Medicine, St Mary’s Hospital, Manchester University NHS Foundation Trust, Health Innovation Manchester, Manchester, UK
| | - Helene Schlecht
- North West Genomic Laboratory Hub, Manchester Centre for Genomic Medicine, St Mary’s Hospital, Manchester University NHS Foundation Trust, Health Innovation Manchester, Manchester, UK
| | - D. Gareth Evans
- Clinical Genetics Service, Manchester Centre for Genomic Medicine, St Mary’s Hospital, Manchester University NHS Foundation Trust, Manchester, UK ,Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Health innovation Manchester, Manchester, UK
| |
Collapse
|
18
|
Barriuso J, Nagaraju RT, Belgamwar S, Chakrabarty B, Burghel GJ, Schlecht H, Foster L, Kilgour E, Wallace AJ, Braun M, Dive C, Evans DG, Bristow RG, Saunders MP, O'Dwyer ST, Aziz O. Early Adaptation of Colorectal Cancer Cells to the Peritoneal Cavity Is Associated with Activation of "Stemness" Programs and Local Inflammation. Clin Cancer Res 2021; 27:1119-1130. [PMID: 33257424 PMCID: PMC7611320 DOI: 10.1158/1078-0432.ccr-20-3320] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Revised: 10/20/2020] [Accepted: 11/24/2020] [Indexed: 11/16/2022]
Abstract
PURPOSE At diagnosis, colorectal cancer presents with synchronous peritoneal metastasis in up to 10% of patients. The peritoneum is poorly characterized with respect to its superspecialized microenvironment. Our aim was to describe the differences between peritoneal metastases and their matched primary tumors excised simultaneously at the time of surgery. Also, we tested the hypothesis of these differences being present in primary colorectal tumors and having prognostic capacity. EXPERIMENTAL DESIGN We report a comprehensive analysis of 30 samples from peritoneal metastasis with their matched colorectal cancer primaries obtained during cytoreductive surgery. We tested and validated the prognostic value of our findings in a pooled series of 660 colorectal cancer primary samples with overall survival (OS) information and 743 samples with disease-free survival (DFS) information from publicly available databases. RESULTS We identified 20 genes dysregulated in peritoneal metastasis that promote an early increasing role of "stemness" in conjunction with tumor-favorable inflammatory changes. When adjusted for age, gender, and stage, the 20-gene peritoneal signature proved to have prognostic value for both OS [adjusted HR for the high-risk group (vs. low-risk) 2.32 (95% confidence interval, CI, 1.69-3.19; P < 0.0001)] and for DFS [adjusted HR 2.08 (95% CI, 1.50-2.91; P < 0.0001)]. CONCLUSIONS Our findings indicated that the activation of "stemness" pathways and adaptation to the peritoneal-specific environment are key to early stages of peritoneal carcinomatosis. The in silico analysis suggested that this 20-gene peritoneal signature may hold prognostic information with potential for development of new precision medicine strategies in this setting.
Collapse
Affiliation(s)
- Jorge Barriuso
- Colorectal and Peritoneal Oncology Centre, The Christie NHS Foundation Trust, Manchester, England, United Kingdom.
- Division of Cancer Sciences, School of Medical Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, England, United Kingdom
- Department of Medical Oncology, The Christie NHS Foundation Trust, Manchester, England, United Kingdom
| | - Raghavendar T Nagaraju
- Colorectal and Peritoneal Oncology Centre, The Christie NHS Foundation Trust, Manchester, England, United Kingdom
- Division of Cancer Sciences, School of Medical Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, England, United Kingdom
| | - Shreya Belgamwar
- Colorectal and Peritoneal Oncology Centre, The Christie NHS Foundation Trust, Manchester, England, United Kingdom
| | - Bipasha Chakrabarty
- Colorectal and Peritoneal Oncology Centre, The Christie NHS Foundation Trust, Manchester, England, United Kingdom
- Department of Pathology, The Christie NHS Foundation Trust, Manchester, England, United Kingdom
| | - George J Burghel
- NW GLH (Manchester), Manchester Centre for Genomic Medicine, Manchester University NHS Foundation Trust, Manchester, England, United Kingdom
| | - Helene Schlecht
- NW GLH (Manchester), Manchester Centre for Genomic Medicine, Manchester University NHS Foundation Trust, Manchester, England, United Kingdom
| | - Lucy Foster
- Department of Pathology, Manchester University NHS Foundation Trust, Manchester, England, United Kingdom
| | - Elaine Kilgour
- Cancer Research UK Manchester Institute, Cancer Biomarker Centre, University of Manchester, Manchester, England, United Kingdom
| | - Andrew J Wallace
- NW GLH (Manchester), Manchester Centre for Genomic Medicine, Manchester University NHS Foundation Trust, Manchester, England, United Kingdom
| | - Michael Braun
- Colorectal and Peritoneal Oncology Centre, The Christie NHS Foundation Trust, Manchester, England, United Kingdom
- Division of Cancer Sciences, School of Medical Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, England, United Kingdom
- Department of Medical Oncology, The Christie NHS Foundation Trust, Manchester, England, United Kingdom
| | - Caroline Dive
- Cancer Research UK Manchester Institute, Cancer Biomarker Centre, University of Manchester, Manchester, England, United Kingdom
| | - D Gareth Evans
- Department of Genomic Medicine, Division of Evolution and Genomic Science, University of Manchester, England, United Kingdom
| | - Robert G Bristow
- Manchester Cancer Research Centre, CRUK Manchester Institute, University of Manchester, Manchester, England, United Kingdom
| | - Mark P Saunders
- Colorectal and Peritoneal Oncology Centre, The Christie NHS Foundation Trust, Manchester, England, United Kingdom
- Department of Clinical Oncology, The Christie NHS Foundation Trust, Manchester, England, United Kingdom
| | - Sarah T O'Dwyer
- Colorectal and Peritoneal Oncology Centre, The Christie NHS Foundation Trust, Manchester, England, United Kingdom
- Division of Cancer Sciences, School of Medical Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, England, United Kingdom
| | - Omer Aziz
- Colorectal and Peritoneal Oncology Centre, The Christie NHS Foundation Trust, Manchester, England, United Kingdom.
- Division of Cancer Sciences, School of Medical Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, England, United Kingdom
| |
Collapse
|
19
|
Flaum N, Morgan RD, Burghel GJ, Bulman M, Clamp AR, Hasan J, Mitchell CL, Badea D, Moon S, Hogg M, Hadjiyiannakis D, Clancy T, Schlecht H, Woodward ER, Crosbie EJ, Edmondson RJ, Wallace AJ, Jayson GC, Lalloo FI, Harkness EF, Evans DGR. Mainstreaming germline BRCA1/2 testing in non-mucinous epithelial ovarian cancer in the North West of England. Eur J Hum Genet 2020; 28:1541-1547. [PMID: 32651552 PMCID: PMC7575602 DOI: 10.1038/s41431-020-0692-y] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2020] [Revised: 06/14/2020] [Accepted: 06/30/2020] [Indexed: 12/24/2022] Open
Abstract
Poly(ADP-ribose) polymerase (PARP) inhibitors improve survival in BRCA-mutant high-grade serous ovarian carcinoma. As a result, germline and somatic BRCA1/2 testing has become standard practice in women diagnosed with ovarian cancer. We outline changes in testing and detection rates of germline BRCA1/2 pathogenic variants (PVs) in cases of non-mucinous epithelial ovarian cancer diagnosed during three eras, spanning 12 years, within the North West of England, and compare the uptake of cascade testing in families identified by oncology-led mainstreaming versus regional genetics clinics. Eras included: Period 1 (20% risk threshold for testing): between January 2007 and May 2013; Period 2 (10% risk threshold for testing): between June 2013 and October 2017 and; Period 3 (mainstream testing): between November 2017 and November 2019. A total of 1081 women underwent germline BRCA1/2 testing between January 2007 and November 2019 and 222 (20.5%) were found to have a PV. The monthly testing rate increased by 3.3-fold and 2.5-fold between Periods 1-2 and Periods 2-3, respectively. A similar incidence of germline BRCA1/2 PVs were detected in Period 2 (17.2%) and Period 3 (18.5%). Uptake of cascade testing from first-degree relatives was significantly lower in those women undergoing mainstream testing compared with those tested in regional genetics clinics (31.6% versus 47.3%, P = 0.038). Mainstream testing allows timely detection of germline BRCA1/2 status to select patients for PARP inhibitors, but shortfalls in the uptake of cascade testing in first-degree relatives requires optimisation to broaden benefits within families.
Collapse
Affiliation(s)
- Nicola Flaum
- The Christie NHS Foundation Trust, Manchester, UK
- Division of Cancer Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
| | - Robert D Morgan
- The Christie NHS Foundation Trust, Manchester, UK
- Division of Cancer Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
| | - George J Burghel
- St Mary's Hospital, Manchester University NHS Foundation Trust, Manchester, UK
| | - Michael Bulman
- St Mary's Hospital, Manchester University NHS Foundation Trust, Manchester, UK
| | | | | | | | - Doina Badea
- Royal Blackburn Teaching Hospital, East Lancashire Hospitals NHS Trust, Blackburn, UK
| | - Sarah Moon
- Rosemere Cancer Centre, Royal Preston Hospital, Lancashire Teaching Hospitals NHS Foundation Trust, Preston, UK
| | - Martin Hogg
- Rosemere Cancer Centre, Royal Preston Hospital, Lancashire Teaching Hospitals NHS Foundation Trust, Preston, UK
| | - Dennis Hadjiyiannakis
- Rosemere Cancer Centre, Royal Preston Hospital, Lancashire Teaching Hospitals NHS Foundation Trust, Preston, UK
| | - Tara Clancy
- St Mary's Hospital, Manchester University NHS Foundation Trust, Manchester, UK
| | - Helene Schlecht
- St Mary's Hospital, Manchester University NHS Foundation Trust, Manchester, UK
| | - Emma R Woodward
- St Mary's Hospital, Manchester University NHS Foundation Trust, Manchester, UK
| | - Emma J Crosbie
- Division of Cancer Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
- St Mary's Hospital, Manchester University NHS Foundation Trust, Manchester, UK
| | - Richard J Edmondson
- Division of Cancer Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
- St Mary's Hospital, Manchester University NHS Foundation Trust, Manchester, UK
| | - Andrew J Wallace
- St Mary's Hospital, Manchester University NHS Foundation Trust, Manchester, UK
| | - Gordon C Jayson
- The Christie NHS Foundation Trust, Manchester, UK
- Division of Cancer Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
| | - Fiona I Lalloo
- St Mary's Hospital, Manchester University NHS Foundation Trust, Manchester, UK
| | - Elaine F Harkness
- Division of Informatics, Imaging and Data Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
- Genesis Breast Cancer Prevention Centre, Manchester University NHS Foundation Trust, Manchester, UK
| | - D Gareth R Evans
- St Mary's Hospital, Manchester University NHS Foundation Trust, Manchester, UK.
- Division of Evolution and Genomic Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK.
| |
Collapse
|
20
|
Nicola PA, Rafee S, Burghel G, Wallace A, Schlecht H, Baker E, Baker K, Priest L, Carter M, Moghadam S, Rogan J, Bristow RG, Newman W, Blackhall FH, Lindsay C. Abstract 3810: Persistence of smoking signature 4 in the non-small cell lung cancer genome. Cancer Res 2020. [DOI: 10.1158/1538-7445.am2020-3810] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Introduction Lung cancer is the most common cause of cancer-related death. Carcinogenic and endogenous processes driving somatic mutation acquisition in cancer can be extracted and defined as mutational signatures using whole genome sequencing (WGS). Tobacco smoke is the main aetiological cause of lung cancer, with mutational signature 4 representing the characteristic C>A transversions produced by smoking. Whilst smoking cessation has been shown to reduce lung cancer risk in epidemiological studies, there has been little exploration into the persistence of smoking 4 in NSCLC genomes after a patient has quit smoking. We investigated the extent and persistence of signature 4 in NSCLC genomes of current, ex- and never-smokers, correlating in particular with clinical history of smoking cessation.
Methods 132 NSCLC samples were resected from 131 patients in Greater Manchester. These samples were submitted to the 100,000 Genomes Project (Genomics England). WGS was performed on tumour specimens and matched blood samples. Data generated was processed by a standard pipeline devised by Genomics England. Tumour mutational burden (TMB), mutational signatures and copy number variation (CNV) were obtained. Clinical data collected included: smoking status, date of diagnosis, TNM stage, date of relapse and date of death (where relevant). Fisher's exact tests and Kruskal-Wallis tests were used for statistical comparisons, with Kaplan-Meier plots for survival.
Results Signature 4 was associated with a smoking history in 102/119 (85.7%) NSCLCs with a detailed smoking history available. In 17/119 (14.3%) patients with a smoking history but no signature 4 NSCLC, 15/17 (88.2%) patients quit smoking a median of 22 years ago (range 0.006 - 45 years). 6/7 (85.7%) never-smoker NSCLCs were non-signature 4 NSCLCs. 60/75 (80%) ex-smokers had sufficient smoking data to assess signature 4 persistence. Signature 4 endured in the lung tissue prior to tumour diagnosis for a median of 180 months (15 years) (range 1 - 600 months). There was no association between the time of smoking cessation and the time to NSCLC diagnosis (R2=0.0009, p=0.82). Non-signature 4 NSCLCs had a more diverse signature profile (signature 4: mean 4.36, 95% CI 4.13-4.58; non-signature 4: mean 5.52, 95% CI 4.95-6.09; p=<0.0001) with a lower TMB (signature 4: median 9.76/Mb, 95% CI 9.8-12.7; non-signature 4: median 2.02/Mb, 95% CI 1.3-9.3; p=<0.0001). There was no difference in relapse-free survival between signature 4 and non-signature 4 patients with early stage disease (signature 4: median 456 days, HR 0.999, 95% CI 0.419-2.385; non-signature 4: median 319 days, HR 1.001, 95% CI 0.417-2.399).
Conclusion The genomic alterations introduced by smoking persist for many years after smoking cessation. NSCLCs arising from smoking carry a distinctive identity compared to those from never-smokers, with higher TMBs driven primarily by signature 4. Whilst survival analysis is limited in this cohort, the pervasive contributions from smoking suggest that lung cancer screening programmes should include all patients with a smoking history.
Citation Format: Pantelis A. Nicola, Shereen Rafee, George Burghel, Andrew Wallace, Helene Schlecht, Eleanor Baker, Katie Baker, Lynsey Priest, Mathew Carter, Sharzad Moghadam, Jane Rogan, Robert G. Bristow, William Newman, Fiona H. Blackhall, Colin Lindsay. Persistence of smoking signature 4 in the non-small cell lung cancer genome [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 3810.
Collapse
Affiliation(s)
| | - Shereen Rafee
- 2The Christie NHS Foundation Trust, Manchester, United Kingdom
| | - George Burghel
- 1Manchester Centre for Genomic Medicine, Manchester, United Kingdom
| | - Andrew Wallace
- 1Manchester Centre for Genomic Medicine, Manchester, United Kingdom
| | - Helene Schlecht
- 1Manchester Centre for Genomic Medicine, Manchester, United Kingdom
| | - Eleanor Baker
- 1Manchester Centre for Genomic Medicine, Manchester, United Kingdom
| | - Katie Baker
- 2The Christie NHS Foundation Trust, Manchester, United Kingdom
| | - Lynsey Priest
- 2The Christie NHS Foundation Trust, Manchester, United Kingdom
| | - Mathew Carter
- 2The Christie NHS Foundation Trust, Manchester, United Kingdom
| | - Sharzad Moghadam
- 1Manchester Centre for Genomic Medicine, Manchester, United Kingdom
| | - Jane Rogan
- 2The Christie NHS Foundation Trust, Manchester, United Kingdom
| | | | - William Newman
- 1Manchester Centre for Genomic Medicine, Manchester, United Kingdom
| | | | - Colin Lindsay
- 2The Christie NHS Foundation Trust, Manchester, United Kingdom
| |
Collapse
|
21
|
Lindsay CR, Nicola P, Jamal-Hanjani M, Wallace A, Wilson G, Burghel G, Schlecht H, Baker K, Baker E, Priest L, Rogan J, Moghadam S, Carter M, Dive C, Bristow RG, Swanton C, Newman W, Blackhall F. Abstract B49: “Triple wild-type” co-mutational profile in early-stage KRAS-mutant lung cancer. Mol Cancer Res 2020. [DOI: 10.1158/1557-3125.ras18-b49] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Introduction: Kirsten rat sarcoma viral oncogene (KRAS) is the most frequently mutated oncogene in non-small cell lung cancer (NSCLC), occurring in approximately 30% of cases. Recent work suggests KRAS -mutant (KRASm) NSCLC is a microcosm for diverse immune checkpoint inhibitor responses, partly dictated by its co-mutation with TP53 (“KP” group=~1/3 cases, “immune hot”), STK11 (“KL” group=~1/3 cases, “immune cold”) or CDKN2A (“KC” group=~1/3 cases). Here we identify and describe genomic and clinical associations of a further subset of KRASm NSCLC defined by “triple WT” status for common KRASm co-mutations.
Method: Sequencing results from 364 early-stage NSCLC cases from the Cancer Research UK TRACERx program (whole-exome sequencing) and the Genomics England 100,000 genome program (whole-genome sequencing) were analyzed for KRASm, associated co-mutations in TP53, STK11 and CDKN2A, copy number changes in the RAS-RAF-MEK-ERK axis, tumor mutational burden (TMB) and mutational signatures. Clinical demographics and factors including tumor size, nodal status and stage were ascertained and assessed for statistical associations with sequencing data using the Mann-Whitney and Fisher’s exact tests.
Results: Overall, 143/364 lung cancer cases (39%) were KRASm with 65/143 (45%) tumors identified as “KP,” 26/143 (18%) as “KL,” and 3/143 (2%) as “KC.” There were 49/143 KRASm cases (34%) with no co-mutation in TP53, STK11 or CDKN2A, defined as “triple wild-type” (triple WT). Relative to the KP, KL and KC genotypes, there was a positive association of the KRAS G12D mutation with triple WT status: 10/49 cases, 20%; KP/KL/KC: 6/94 cases, 6%; p=0.022). In the 100,000-genome cohort, TMB was similar for the triple WT and KL groups but significantly lower than that observed for KP (KP: median 10.55 mut/Mb, 95% CI 8.8-15.33; triple WT: median 6.96, 95% CI 4.87-12.53; p=0.036). Despite this lower median TMB, smoking-associated mutational signature 4 was common in triple WT tumors (triple WT: 13/14 pts, 93%; overall 76/114 pts, 67%). In the triple WT group overall, there was a reduction of >50% in cancers with copy number changes of NF1 and NRAS. There was an inverse association between pathologic stage III tumors and KRASm triple WT genotype (p=0.0014).
Conclusion: There are a significant proportion of KRASm NSCLC patients whose tumors are triple WT for TP53, STK11 and CDKN2A. Despite their high frequency of smoking-associated mutational signatures, these tumors are characterized by low TMB and are more common in early-stage disease. They also associate more commonly with KRAS G12D. Our observations suggest a discrete KRASm subset that may have implications for stratification in trials of immune checkpoint inhibitors and/or targeted therapeutics of KRASm tumors.
Citation Format: Colin R. Lindsay, Pantelis Nicola, Mariam Jamal-Hanjani, Andrew Wallace, Gareth Wilson, George Burghel, Helene Schlecht, Katie Baker, Eleanour Baker, Lynsey Priest, Jane Rogan, Sharzad Moghadam, Mathew Carter, Caroline Dive, Robert G. Bristow, Charles Swanton, William Newman, Fiona Blackhall. “Triple wild-type” co-mutational profile in early-stage KRAS-mutant lung cancer [abstract]. In: Proceedings of the AACR Special Conference on Targeting RAS-Driven Cancers; 2018 Dec 9-12; San Diego, CA. Philadelphia (PA): AACR; Mol Cancer Res 2020;18(5_Suppl):Abstract nr B49.
Collapse
Affiliation(s)
| | | | | | - Andrew Wallace
- 3Manchester Centre for Genomic Medicine, Manchester, United Kingdom,
| | | | - George Burghel
- 3Manchester Centre for Genomic Medicine, Manchester, United Kingdom,
| | - Helene Schlecht
- 3Manchester Centre for Genomic Medicine, Manchester, United Kingdom,
| | - Katie Baker
- 5Manchester Cancer Research Centre, Manchester, United Kingdom,
| | - Eleanour Baker
- 3Manchester Centre for Genomic Medicine, Manchester, United Kingdom,
| | - Lynsey Priest
- 5Manchester Cancer Research Centre, Manchester, United Kingdom,
| | - Jane Rogan
- 5Manchester Cancer Research Centre, Manchester, United Kingdom,
| | | | - Mathew Carter
- 5Manchester Cancer Research Centre, Manchester, United Kingdom,
| | - Caroline Dive
- 6Cancer Research UK Manchester Institute, Manchester, United Kingdom,
| | | | - Charles Swanton
- 7Crick Institute (on behalf of the TRACERx consortium), London, United Kingdom
| | - William Newman
- 3Manchester Centre for Genomic Medicine, Manchester, United Kingdom,
| | | |
Collapse
|
22
|
Lindsay C, Rafee S, Nicola P, Wallace A, Burghel G, Schlecht H, Baker K, Baker E, Priest L, Rogan J, Moghadam S, Carter M, Newman W, Blackhall F. MA25.08 Characterisation of Tumor Aetiology Using Mutational Signatures from the Non-Small Cell Lung Cancer Genome. J Thorac Oncol 2019. [DOI: 10.1016/j.jtho.2019.08.714] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
|
23
|
Nicola PA, Burghel G, Wallace A, Schlecht H, Baker E, Baker K, Priest L, Carter M, Moghadam S, Rogan J, Bristow RG, Newman W, Blackhall F, Lindsay CR. Abstract 1763: Tumor mutational burden, mutational signatures and copy number variation in lung cancer driven by the Ras-Raf-MEK-ERK pathway. Cancer Res 2019. [DOI: 10.1158/1538-7445.am2019-1763] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Introduction: Lung cancer is the most common cause of cancer-related death. Kirsten rat sarcoma viral oncogene (KRAS) is the most frequently mutated gene in non-small cell lung cancer (NSCLC), occurring in approximately 30% of cases. We characterised the genomic landscape of NSCLCs with an aberrant Ras-Raf-MEK-ERK pathway.
Methods: 121 Greater Manchester patients with resected NSCLC were recruited into the UK 100,000 Genomes Project (Genomics England). Whole genome sequencing (WGS) was performed on tumor specimens and matched blood samples. Data generated was processed by a standard pipeline devised by Genomics England, then mined for mutations in the Ras-Raf-MEK-ERK pathway. NF1 mutation was assessed as a positive control for RAS pathway activation. Tumor mutational burden (TMB), mutational signature profiles and copy number variation (CNV) were also obtained. Clinical characteristics including tumor size, nodal status and stage were documented. Mann-Whitney and Fisher’s exact tests were used for statistical comparisons.
Results: Cancers from 42/121 (34.7%) patients (pts) had a RAS variant, of which 40/42 (95.2%) were KRAS alterations. A single NRAS-mutant adenocarcinoma (Q61L) was identified, as was a HRAS variant, not previously observed in squamous lung cancer (Q61L). Codon 12 was the most frequently mutated KRAS site with four mutant alleles (G12C 17/40 pts, G12V 6/40, G12D 4/40, G12A 2/40). Median TMB was not significantly different between KRAS-mutant cases (8.06, range 1.84-55.2) and KRAS-wildtype samples (7.1, range 0.98-45.32) (p=0.3). Smoking-associated signature 4 was the most common mutational process (37/40 pts, median 50%, range 20-70%), appearing in a mutually exclusive fashion from the intrinsic signature 1 (3/40 pts, median 20% range 10-30%). 47/121 pts (38.8%) showed a KRAS CNV with 34/47 (72.3%) being gains. For NF1, 12/121 (9.9%) variants were identified. 6/12 (50%) were missense variants, each with a different codon affected (5/12 splice site variants, 1/12 frameshift). Median TMB was not significantly higher in NF1-mutants (NF1m: median 11.54, range 4.47-28.27; NF1 WT: median 7.1, 0.98-55.2; p=0.065) and mutational signature 4 was again the most common (11/12, median 40%, range 20-60%). 37/121(30.6%) samples showed NF1 CNV, the majority of which were surprisingly gains (25/37 pts, 67.6%). In terms of clinical outcome, neither KRAS-mutant or NF1-mutant tumors were more likely to occur in later stage III disease (KRASm: 9/30 pts, 30%, p=0.817; NF1m: 5/11 cases, 45.5%; p=0.326).
Conclusions: Approximately one half of this NSCLC cohort recruited from Greater Manchester carried a Ras-Raf-MEK-ERK pathway aberration. These KRAS-mutant tumors were often at an early stage and driven by tobacco as their main aetiological process. The mutual exclusivity of signature 4 and 1 suggests there are further complexities to be established in Ras-driven NSCLC.
Citation Format: Pantelis A. Nicola, George Burghel, Andrew Wallace, Helene Schlecht, Eleanor Baker, Katie Baker, Lynsey Priest, Mathew Carter, Sharzad Moghadam, Jane Rogan, Robert G. Bristow, William Newman, Fiona Blackhall, Colin R. Lindsay. Tumor mutational burden, mutational signatures and copy number variation in lung cancer driven by the Ras-Raf-MEK-ERK pathway [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 1763.
Collapse
Affiliation(s)
| | - George Burghel
- 1Manchester Centre for Genomic Medicine, Manchester, United Kingdom
| | - Andrew Wallace
- 1Manchester Centre for Genomic Medicine, Manchester, United Kingdom
| | - Helene Schlecht
- 1Manchester Centre for Genomic Medicine, Manchester, United Kingdom
| | - Eleanor Baker
- 1Manchester Centre for Genomic Medicine, Manchester, United Kingdom
| | - Katie Baker
- 2The Christie NHS Foundation Trust, Manchester, United Kingdom
| | - Lynsey Priest
- 2The Christie NHS Foundation Trust, Manchester, United Kingdom
| | - Mathew Carter
- 2The Christie NHS Foundation Trust, Manchester, United Kingdom
| | | | - Jane Rogan
- 2The Christie NHS Foundation Trust, Manchester, United Kingdom
| | | | - William Newman
- 1Manchester Centre for Genomic Medicine, Manchester, United Kingdom
| | - Fiona Blackhall
- 2The Christie NHS Foundation Trust, Manchester, United Kingdom
| | | |
Collapse
|
24
|
Morgan RD, Burghel GJ, Flaum N, Bulman M, Clamp AR, Hasan J, Mitchell CL, Schlecht H, Woodward ER, Lallo FI, Crosbie EJ, Edmondson RJ, Wallace AJ, Jayson GC, Evans DGR. Prevalence of germline pathogenic BRCA1/2 variants in sequential epithelial ovarian cancer cases. J Med Genet 2019; 56:301-307. [DOI: 10.1136/jmedgenet-2018-105792] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2018] [Revised: 12/14/2018] [Accepted: 01/05/2019] [Indexed: 12/29/2022]
Abstract
IntroductionPoly(ADP-ribose) polymerase inhibitors significantly improve progression-free survival in platinum-sensitive high-grade serous and endometrioid ovarian carcinoma, with greatest benefits observed in women with a pathogenic BRCA1/2 variant. Consequently, the demand for germline BRCA1/2 testing in ovarian cancer has increased substantially, leading to the screening of unselected populations of patients. We aimed to determine the prevalence of pathogenic germline BRCA1/2 variants in women diagnosed with epithelial ovarian cancer, categorised according to the established risk factors for hereditary breast and ovarian cancer syndrome and the Manchester BRCA Score, to inform risk stratification.MethodsA cohort of sequential epithelial ovarian cancer cases recruited between June 2013 and September 2018 underwent germline BRCA1/2 testing by next-generation sequencing and multiplex ligation-dependent probe amplification.ResultsFive hundred and fifty-seven patients were screened. Of these, 18% had inherited a pathogenic BRCA1/2 variant. The prevalence of pathogenic BRCA1/2 variants was >10% in women diagnosed with ovarian cancer earlier than 60 years of age (21%) and those diagnosed later than 60 years of age with a family history of breast and/or ovarian cancer (17%) or a medical history of breast cancer (34%). The prevalence of pathogenic BRCA1/2 variants was also >10% in women with a Manchester BRCA Score of ≥15 points (14%).DiscussionOur study suggests that age at diagnosis, family history of breast and/or ovarian cancer, medical history of breast cancer or a Manchester BRCA Score of ≥15 points are associated with a >10% prevalence of germline pathogenic BRCA1/2 variants in epithelial ovarian cancer.
Collapse
|
25
|
Ghosh A, Schlecht H, Heptinstall LE, Bassett JK, Cartwright E, Bhaskar SS, Urquhart J, Broomfield A, Morris AA, Jameson E, Schwahn BC, Walter JH, Douzgou S, Murphy H, Hendriksz C, Sharma R, Wilcox G, Crushell E, Monavari AA, Martin R, Doolan A, Senniappan S, Ramsden SC, Jones SA, Banka S. Diagnosing childhood-onset inborn errors of metabolism by next-generation sequencing. Arch Dis Child 2017; 102:1019-1029. [PMID: 28468868 DOI: 10.1136/archdischild-2017-312738] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/18/2017] [Revised: 03/23/2017] [Accepted: 03/26/2017] [Indexed: 11/04/2022]
Abstract
BACKGROUND Inborn errors of metabolism (IEMs) underlie a substantial proportion of paediatric disease burden but their genetic diagnosis can be challenging using the traditional approaches. METHODS We designed and validated a next-generation sequencing (NGS) panel of 226 IEM genes, created six overlapping phenotype-based subpanels and tested 102 individuals, who presented clinically with suspected childhood-onset IEMs. RESULTS In 51/102 individuals, NGS fully or partially established the molecular cause or identified other actionable diagnoses. Causal mutations were identified significantly more frequently when the biochemical phenotype suggested a specific IEM or a group of IEMs (p<0.0001), demonstrating the pivotal role of prior biochemical testing in guiding NGS analysis. The NGS panel helped to avoid further invasive, hazardous, lengthy or expensive investigations in 69% individuals (p<0.0001). Additional functional testing due to novel or unexpected findings had to be undertaken in only 3% of subjects, demonstrating that the use of NGS does not significantly increase the burden of subsequent follow-up testing. Even where a molecular diagnosis could not be achieved, NGS-based approach assisted in the management and counselling by reducing the likelihood of a high-penetrant genetic cause. CONCLUSION NGS has significant clinical utility for the diagnosis of IEMs. Biochemical testing and NGS analysis play complementary roles in the diagnosis of IEMs. Incorporating NGS into the diagnostic algorithm of IEMs can improve the accuracy of diagnosis.
Collapse
Affiliation(s)
- Arunabha Ghosh
- Manchester Centre for Genomic Medicine, St. Mary's Hospital, Central Manchester NHS Trust, Manchester Academic Health Science Centre, Manchester, UK.,Divison of Evolution and Genomic Sciences, School of Biology, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
| | - Helene Schlecht
- Manchester Centre for Genomic Medicine, St. Mary's Hospital, Central Manchester NHS Trust, Manchester Academic Health Science Centre, Manchester, UK
| | - Lesley E Heptinstall
- Manchester Centre for Genomic Medicine, St. Mary's Hospital, Central Manchester NHS Trust, Manchester Academic Health Science Centre, Manchester, UK
| | - John K Bassett
- Manchester Centre for Genomic Medicine, St. Mary's Hospital, Central Manchester NHS Trust, Manchester Academic Health Science Centre, Manchester, UK
| | - Eleanor Cartwright
- Manchester Centre for Genomic Medicine, St. Mary's Hospital, Central Manchester NHS Trust, Manchester Academic Health Science Centre, Manchester, UK
| | - Sanjeev S Bhaskar
- Manchester Centre for Genomic Medicine, St. Mary's Hospital, Central Manchester NHS Trust, Manchester Academic Health Science Centre, Manchester, UK
| | - Jill Urquhart
- Manchester Centre for Genomic Medicine, St. Mary's Hospital, Central Manchester NHS Trust, Manchester Academic Health Science Centre, Manchester, UK
| | - Alexander Broomfield
- Manchester Centre for Genomic Medicine, St. Mary's Hospital, Central Manchester NHS Trust, Manchester Academic Health Science Centre, Manchester, UK
| | - Andrew Am Morris
- Manchester Centre for Genomic Medicine, St. Mary's Hospital, Central Manchester NHS Trust, Manchester Academic Health Science Centre, Manchester, UK
| | - Elisabeth Jameson
- Manchester Centre for Genomic Medicine, St. Mary's Hospital, Central Manchester NHS Trust, Manchester Academic Health Science Centre, Manchester, UK
| | - Bernd C Schwahn
- Manchester Centre for Genomic Medicine, St. Mary's Hospital, Central Manchester NHS Trust, Manchester Academic Health Science Centre, Manchester, UK
| | - John H Walter
- Manchester Centre for Genomic Medicine, St. Mary's Hospital, Central Manchester NHS Trust, Manchester Academic Health Science Centre, Manchester, UK
| | - Sofia Douzgou
- Manchester Centre for Genomic Medicine, St. Mary's Hospital, Central Manchester NHS Trust, Manchester Academic Health Science Centre, Manchester, UK.,Divison of Evolution and Genomic Sciences, School of Biology, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
| | - Helen Murphy
- Manchester Centre for Genomic Medicine, St. Mary's Hospital, Central Manchester NHS Trust, Manchester Academic Health Science Centre, Manchester, UK
| | - Chris Hendriksz
- Adult Inherited Metabolic Disorders, The Mark Holland Metabolic Unit, Salford Royal NHS Foundation Trust, Salford, UK.,Department of Paediatrics and Child Health, Steve Biko Academic Unit, University of Pretoria, Pretoria, South Africa
| | - Reena Sharma
- Adult Inherited Metabolic Disorders, The Mark Holland Metabolic Unit, Salford Royal NHS Foundation Trust, Salford, UK
| | - Gisela Wilcox
- Adult Inherited Metabolic Disorders, The Mark Holland Metabolic Unit, Salford Royal NHS Foundation Trust, Salford, UK
| | - Ellen Crushell
- National Centre for Inherited Metabolic Disorders, Temple Street Children's University Hospital, Dublin, Ireland
| | - Ardeshir A Monavari
- National Centre for Inherited Metabolic Disorders, Temple Street Children's University Hospital, Dublin, Ireland
| | - Richard Martin
- Institute of Human Genetics, The International Centre For Life, Newcastle, UK
| | - Anne Doolan
- Cork University Maternity Hospital, Cork, Ireland
| | - Senthil Senniappan
- Department of Endocrinology, Alder Hey Children's Hospital, Liverpool, UK
| | - Simon C Ramsden
- Manchester Centre for Genomic Medicine, St. Mary's Hospital, Central Manchester NHS Trust, Manchester Academic Health Science Centre, Manchester, UK
| | - Simon A Jones
- Manchester Centre for Genomic Medicine, St. Mary's Hospital, Central Manchester NHS Trust, Manchester Academic Health Science Centre, Manchester, UK.,Divison of Evolution and Genomic Sciences, School of Biology, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
| | - Siddharth Banka
- Manchester Centre for Genomic Medicine, St. Mary's Hospital, Central Manchester NHS Trust, Manchester Academic Health Science Centre, Manchester, UK.,Divison of Evolution and Genomic Sciences, School of Biology, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
| |
Collapse
|
26
|
Sipos P, Rens W, Schlecht H, Fan X, Wareing M, Baker P, Davidge S, Crocker I. Fetal Endothelial Colony Forming Cells Assist Vasculogenesis in the Pregnant Uterus. FASEB J 2012. [DOI: 10.1096/fasebj.26.1_supplement.1126.4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Peter Sipos
- Maternal and Fetal Health Research CentreUniversity of ManchesterManchesterUnited Kingdom
| | - Willem Rens
- Department of Veterinary MedicineUniversity of CambridgeCambridgeUnited Kingdom
| | - Helene Schlecht
- Department of GeneticsUniversity of ManchesterManchesterUnited Kingdom
| | - Xiaho Fan
- Deparment of Peadiatrics and PharmacologyUniversity of AlbertaEdmontonABCanada
| | - Mark Wareing
- Maternal and Fetal Health Research CentreUniversity of ManchesterManchesterUnited Kingdom
| | - Philip Baker
- Department of Obstetrics and GyneacologyUniversity of AlbertaEdmontonABCanada
| | - Sandra Davidge
- Department of Obstetrics and GyneacologyUniversity of AlbertaEdmontonABCanada
| | - Ian Crocker
- Maternal and Fetal Health Research CentreUniversity of ManchesterManchesterUnited Kingdom
| |
Collapse
|
27
|
Schlecht H. Trichozephaliasis und okkultes Blut. Dtsch Med Wochenschr 2009. [DOI: 10.1055/s-0028-1134886] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
|
28
|
|
29
|
|
30
|
|
31
|
Liivak K, Tobi S, Schlecht H, Tillmann V. Incidence of classical 21-hydroxylase deficiency and distribution of CYP21A2 mutations in Estonia. Horm Res 2008; 69:227-32. [PMID: 18204270 DOI: 10.1159/000113023] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2006] [Accepted: 06/07/2007] [Indexed: 12/13/2022]
Abstract
AIMS To determine the incidence of classical 21-hydroxylase deficiency (21-OHD) in Estonia from 1978 to 2004, and describe their phenotype and genotype. METHODS All Estonian endocrinologists informed us about their patients with 21-OHD. The diagnosis was confirmed in 20 patients, who were all screened for 8 common mutations of the CYP21A2 gene. RESULTS The 27-year period incidence was 1:25,500. The incidence from 1992 was 1:16,100, which more accurately reflects the real situation in Estonia. The salt-wasting form (SW) was diagnosed in 14 (7 males) and the simple virilizing form in 6 patients (1 male). The median age at diagnosis of the SW form was 30 days in males and 2 days in females. The investigation of 34 unrelated alleles showed that a common deletion/conversion was the most frequent mutation in our group (7/34). Six other mutations were present: p.Ile172Asn (5/34), 8-bp deletion (3/34), intron-2 splice mutation (3/34), p.Arg356Trp (3/34), p.Gln318X (3/34) and a small conversion (2/34). Mutations in 8 alleles remained uncertain. CONCLUSIONS The incidence of classical 21-OHD in Estonia in 1992-2004 was 1:16,100. The genotype of our patients is similar to those from other Caucasian populations. The relatively late age at diagnosis and the skewed female:male ratio supports the need for newborn screening for 21-OHD.
Collapse
Affiliation(s)
- Kaur Liivak
- Department of Paediatrics, University of Tartu, Tartu, Estonia
| | | | | | | |
Collapse
|
32
|
Tucker P, Laemle L, Munson A, Kanekar S, Oliver ER, Brown N, Schlecht H, Vetter M, Glaser T. The eyeless mouse mutation (ey1) removes an alternative start codon from the Rx/rax homeobox gene. Genesis 2001; 31:43-53. [PMID: 11668677 DOI: 10.1002/gene.10003] [Citation(s) in RCA: 66] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The eyeless inbred mouse strain ZRDCT has long served as a spontaneous model for human anophthalmia and the evolutionary reduction of eyes that has occurred in some naturally blind mammals. ZRDCT mice have orbits but lack eyes and optic tracts and have hypothalamic abnormalities. Segregation data suggest that a small number of interacting genes are responsible, including at least one major recessive locus, ey1. Although predicted since the 1940s, these loci were never identified. We mapped ey1 to chromosome 18 using an F2 genome scan and there found a Met10-->Leu mutation in Rx/rax, a homeobox gene that is expressed in the anterior headfold, developing retina, pineal, and hypothalamus and is translated via a leaky scanning mechanism. The mutation affects a conserved AUG codon that functions as an alternative translation initiation site and consequently reduces the abundance of Rx protein. In contrast to a targeted Rx null allele, which causes anophthalmia, central nervous system defects, and neonatal death, the hypomorphic M10L allele is fully viable.
Collapse
Affiliation(s)
- P Tucker
- Museum of Zoology and Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan, USA
| | | | | | | | | | | | | | | | | |
Collapse
|
33
|
Glawisxhnig E, Swoboda R, Schlecht H. [Occurrence of porcine dermatosis vegetans in Austria]. Dtsch Tierarztl Wochenschr 1974; 81:5-9. [PMID: 4591465] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
|
34
|
Glawischnig VE, Köhler H, Swoboda R, Schlecht H, Kaun R. [Vaccination studies in the so-called enzootic pneumonia of the swine using a SEP-formalin-vaccine]. Dtsch Tierarztl Wochenschr 1973; 80:271-4 concl. [PMID: 4578370] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
|
35
|
Glawischnig VE, Köhler H, Swoboda R, Schlecht H, Kaun R. [Vaccination studies in the so-called enzootic pneumonia of the swine using an SEP-formalin vaccine]. Dtsch Tierarztl Wochenschr 1973; 80:245-9 contd. [PMID: 4578284] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
|
36
|
Schlecht H. [Carbon monoxide poisoning in swine]. Wien Tierarztl Monatsschr 1971; 58:263-4. [PMID: 5108815] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
|
37
|
|
38
|
Schlecht H. Umstimmung durch Klima und Wetter. Dtsch Med Wochenschr 1933. [DOI: 10.1055/s-0028-1131570] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
|
39
|
|
40
|
|
41
|
|
42
|
Schittenhelm A, Schlecht H. Erfahrungen über die Malaria und ihre Behandlung. Dtsch Med Wochenschr 1918. [DOI: 10.1055/s-0028-1134333] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
|
43
|
Schlecht H, Schwenker G. Über lokale Eosinophilie in den Bronchien und in der Lunge beim anaphylaktischen Meerschweinchen. Naunyn Schmiedebergs Arch Pharmacol 1912. [DOI: 10.1007/bf01863371] [Citation(s) in RCA: 29] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
|
44
|
|