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Kerkhof J, Rastin C, Levy MA, Relator R, McConkey H, Demain L, Dominguez-Garrido E, Kaat LD, Houge SD, DuPont BR, Fee T, Fletcher RS, Gokhale D, Haukanes BI, Henneman P, Hilton S, Hilton BA, Jenkinson S, Lee JA, Louie RJ, Motazacker MM, Rzasa J, Stevenson RE, Plomp A, van der Laan L, van der Smagt J, Walden KK, Banka S, Mannens M, Skinner SA, Friez MJ, Campbell C, Tedder ML, Alders M, Sadikovic B. Diagnostic utility and reporting recommendations for clinical DNA methylation episignature testing in genetically undiagnosed rare diseases. Genet Med 2024; 26:101075. [PMID: 38251460 DOI: 10.1016/j.gim.2024.101075] [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: 08/29/2023] [Revised: 01/09/2024] [Accepted: 01/12/2024] [Indexed: 01/23/2024] Open
Abstract
PURPOSE This study aims to assess the diagnostic utility and provide reporting recommendations for clinical DNA methylation episignature testing based on the cohort of patients tested through the EpiSign Clinical Testing Network. METHODS The EpiSign assay utilized unsupervised clustering techniques and a support vector machine-based classification algorithm to compare each patient's genome-wide DNA methylation profile with the EpiSign Knowledge Database, yielding the result that was reported. An international working group, representing distinct EpiSign Clinical Testing Network health jurisdictions, collaborated to establish recommendations for interpretation and reporting of episignature testing. RESULTS Among 2399 cases analyzed, 1667 cases underwent a comprehensive screen of validated episignatures, imprinting, and promoter regions, resulting in 18.7% (312/1667) positive reports. The remaining 732 referrals underwent targeted episignature analysis for assessment of sequence or copy-number variants (CNVs) of uncertain significance or for assessment of clinical diagnoses without confirmed molecular findings, and 32.4% (237/732) were positive. Cases with detailed clinical information were highlighted to describe various utility scenarios for episignature testing. CONCLUSION Clinical DNA methylation testing including episignatures, imprinting, and promoter analysis provided by an integrated network of clinical laboratories enables test standardization and demonstrates significant diagnostic yield and clinical utility beyond DNA sequence analysis in rare diseases.
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Affiliation(s)
- Jennifer Kerkhof
- Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, ON, Canada
| | - Cassandra Rastin
- Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, ON, Canada
| | - Michael A Levy
- Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, ON, Canada
| | - Raissa Relator
- Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, ON, Canada
| | - Haley McConkey
- Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, ON, Canada
| | - Leigh Demain
- Manchester Centre for Genomic Medicine, Manchester University NHS Foundation Trust, Manchester, United Kingdom
| | | | - Laura Donker Kaat
- Department of Clinical Genetics, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Sofia Douzgou Houge
- Haukeland University Hospital, Centre for Medical Genetics and Molecular Medicine, Bergen, Norway
| | | | | | | | - David Gokhale
- Manchester Centre for Genomic Medicine, Manchester University NHS Foundation Trust, Manchester, United Kingdom
| | - Bjørn Ivar Haukanes
- Haukeland University Hospital, Centre for Medical Genetics and Molecular Medicine, Bergen, Norway
| | - Peter Henneman
- Amsterdam University Medical Center, University of Amsterdam, Department of Human Genetics, Amsterdam Reproduction and Development Research Institute, Amsterdam, The Netherlands
| | - Sarah Hilton
- Manchester Centre for Genomic Medicine, Manchester University NHS Foundation Trust, Manchester, United Kingdom
| | | | - Sarah Jenkinson
- Manchester Centre for Genomic Medicine, Manchester University NHS Foundation Trust, Manchester, United Kingdom
| | | | | | - M Mahdi Motazacker
- Amsterdam University Medical Center, University of Amsterdam, Department of Human Genetics, Amsterdam Reproduction and Development Research Institute, Amsterdam, The Netherlands
| | - Jessica Rzasa
- Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, ON, Canada
| | | | - Astrid Plomp
- Department of Clinical Genetics, AMC, Amsterdam, The Netherlands
| | - Liselot van der Laan
- Amsterdam University Medical Center, University of Amsterdam, Department of Human Genetics, Amsterdam Reproduction and Development Research Institute, Amsterdam, The Netherlands
| | - Jasper van der Smagt
- Department of Genetics, Utrecht University Medical Center, Utrecht, The Netherlands
| | | | - Siddharth Banka
- Manchester Centre for Genomic Medicine, Manchester University NHS Foundation Trust, Manchester, United Kingdom; Division of Evolution, Infection and Genomic Sciences, School of Biological Sciences, University of Manchester, Manchester, United Kingdom
| | - Marcel Mannens
- Amsterdam University Medical Center, University of Amsterdam, Department of Human Genetics, Amsterdam Reproduction and Development Research Institute, Amsterdam, The Netherlands
| | | | | | - Christopher Campbell
- Manchester Centre for Genomic Medicine, Manchester University NHS Foundation Trust, Manchester, United Kingdom
| | | | - Marielle Alders
- Amsterdam University Medical Center, University of Amsterdam, Department of Human Genetics, Amsterdam Reproduction and Development Research Institute, Amsterdam, The Netherlands
| | - Bekim Sadikovic
- Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, ON, Canada; Department of Pathology and Laboratory Medicine, Western University, London, ON, Canada.
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Dayimu A, Gupta A, Matin RN, Nobes J, Board R, Payne M, Rao A, Fusi A, Danson S, Eccles B, Carser J, Brown CO, Steven N, Bhattacharyya M, Brown E, Gonzalez M, Highley M, Pickering L, Kumar S, Waterston A, Burghel G, Demain L, Baker E, Wulff J, Qian W, Twelves S, Middleton M, Corrie P. A randomised phase 2 study of intermittent versus continuous dosing of dabrafenib plus trametinib in patients with BRAF V600 mutant advanced melanoma (INTERIM). Eur J Cancer 2024; 196:113455. [PMID: 38029480 DOI: 10.1016/j.ejca.2023.113455] [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: 09/05/2023] [Revised: 11/07/2023] [Accepted: 11/15/2023] [Indexed: 12/01/2023]
Abstract
BACKGROUND BRAF+MEK inhibitors extend life expectancy of patients with BRAFV600 mutant advanced melanoma. Acquired resistance limits duration of benefit, but preclinical and case studies suggest intermittent dosing could overcome this limitation. INTERIM was a phase 2 trial evaluating an intermittent dosing regimen. METHODS Patients with BRAFV600 mutant advanced melanoma due to start dabrafenib+trametinib were randomised to receive either continuous (CONT), or intermittent (INT; dabrafenib d1-21, trametinib d1-14 every 28 days) dosing. A composite primary endpoint included progression-free survival (PFS) and quality of life (QoL). Secondary endpoints included response rate (ORR), overall survival (OS) and adverse events (AEs). Mutant BRAFV600E ctDNA was measured by droplet digital PCR (ddPCR), using mutant allele frequency of > 1 % as the detection threshold. RESULTS 79 patients (39 INT, 40 CONT) were recruited; median age 67 years, 65 % AJCC (7th ed) stage IV M1c, 29 % had brain metastases. With 19 months median follow-up, INT was inferior in all efficacy measures: median PFS 8.5 vs 10.7mo (HR 1.39, 95 %CI 0.79-2.45, p = 0.255); median OS 18.1mo vs not reached (HR 1.69, 95 %CI 0.87-3.28, p = 0.121), ORR 57 % vs 77 %. INT patients experienced fewer treatment-related AEs (76 % vs 88 %), but more grade > 3 AEs (53 % vs 42 %). QoL favoured CONT. Detection of BRAFV600E ctDNA prior to treatment correlated with worse OS (HR 2.55, 95 %CI 1.25-5.21, p = 0.01) in both arms. A change to undetected during treatment did not significantly predict better OS. CONCLUSION INTERIM findings are consistent with other recent clinical trials reporting that intermittent dosing does not improve efficacy of BRAF+MEK inhibitors.
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Affiliation(s)
- Alimu Dayimu
- Clinical Trials Unit, Department of Oncology, University of Cambridge, Cambridge, UK
| | | | - Rubeta N Matin
- Department of Dermatology, Churchill Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Jenny Nobes
- Department of Oncology, Norfolk and Norwich University Hospital NHS Foundation Trust, Norfolk, UK
| | - Ruth Board
- Department of Oncology, Lancashire Teaching Hospitals NHS Trust, Preston, UK
| | - Miranda Payne
- Oxford Cancer and Haematology Centre, Oxford University Hospitals NHS Foundation Trust, Churchill Hospital, Oxford, UK
| | - Ankit Rao
- Department of Oncology, Nottingham University Hospitals NHS Trust, Nottingham, UK
| | - Alberto Fusi
- Department of Medical Oncology, St George's University Hospitals NHS Foundation Trust, London, UK
| | - Sarah Danson
- Division of Clinical Medicine, The University of Sheffield, Sheffield, UK; Sheffield Teaching Hospital NHS Foundation Trust, Sheffield, UK
| | - Bryony Eccles
- Department of Medical Oncology, University Hospitals Dorset NHS Foundation Trust, Poole, UK
| | - Judith Carser
- Department of Oncology, Belfast Health and Social Care Trust, Belfast, UK
| | | | - Neil Steven
- Department of Oncology, University Hospitals Birmingham NHS Foundation Trust, Birmingham, UK
| | | | - Ewan Brown
- Western General Hospital, Lothian NHS Board, Edinburgh, UK
| | - Michael Gonzalez
- Department of Oncology, Imperial College Healthcare NHS Trust, London, UK
| | - Martin Highley
- Oncology Centre, Derriford Hospital, University Hospitals Plymouth NHS Trust, Plymouth, UK
| | - Lisa Pickering
- Skin and Renal Units, Royal Marsden NHS Foundation Trust, London, UK
| | - Satish Kumar
- Velindre Cancer Centre, Velindre University NHS Trust, Cardiff, UK
| | | | - George Burghel
- Manchester Centre for Genomic Medicine, Manchester University NHS Foundation Trust, Manchester, UK
| | - Leigh Demain
- Manchester Centre for Genomic Medicine, Manchester University NHS Foundation Trust, Manchester, UK
| | - Eleanor Baker
- Manchester Centre for Genomic Medicine, Manchester University NHS Foundation Trust, Manchester, UK
| | - Jerome Wulff
- Cambridge Clinical Trials Unit, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Wendi Qian
- Clinical Trials Unit, Department of Oncology, University of Cambridge, Cambridge, UK; Cambridge Clinical Trials Unit, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Sophie Twelves
- Cambridge Clinical Trials Unit, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Mark Middleton
- Oxford Cancer and Haematology Centre, Oxford University Hospitals NHS Foundation Trust, Churchill Hospital, Oxford, UK; Department of Oncology, University of Oxford, Oxford, UK
| | - Pippa Corrie
- Oncology Department, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK.
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LaFlamme CW, Rastin C, Sengupta S, Pennington HE, Russ-Hall SJ, Schneider AL, Bonkowski ES, Almanza Fuerte EP, Galey M, Goffena J, Gibson SB, Allan TJ, Nyaga DM, Lieffering N, Hebbar M, Walker EV, Darnell D, Olsen SR, Kolekar P, Djekidel N, Rosikiewicz W, McConkey H, Kerkhof J, Levy MA, Relator R, Lev D, Lerman-Sagie T, Park KL, Alders M, Cappuccio G, Chatron N, Demain L, Genevieve D, Lesca G, Roscioli T, Sanlaville D, Tedder ML, Hubshman MW, Ketkar S, Dai H, Worley KC, Rosenfeld JA, Chao HT, Neale G, Carvill GL, Wang Z, Berkovic SF, Sadleir LG, Miller DE, Scheffer IE, Sadikovic B, Mefford HC. Diagnostic Utility of Genome-wide DNA Methylation Analysis in Genetically Unsolved Developmental and Epileptic Encephalopathies and Refinement of a CHD2 Episignature. medRxiv 2023:2023.10.11.23296741. [PMID: 37873138 PMCID: PMC10592992 DOI: 10.1101/2023.10.11.23296741] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
Sequence-based genetic testing currently identifies causative genetic variants in ∼50% of individuals with developmental and epileptic encephalopathies (DEEs). Aberrant changes in DNA methylation are implicated in various neurodevelopmental disorders but remain unstudied in DEEs. Rare epigenetic variations ("epivariants") can drive disease by modulating gene expression at single loci, whereas genome-wide DNA methylation changes can result in distinct "episignature" biomarkers for monogenic disorders in a growing number of rare diseases. Here, we interrogate the diagnostic utility of genome-wide DNA methylation array analysis on peripheral blood samples from 516 individuals with genetically unsolved DEEs who had previously undergone extensive genetic testing. We identified rare differentially methylated regions (DMRs) and explanatory episignatures to discover causative and candidate genetic etiologies in 10 individuals. We then used long-read sequencing to identify DNA variants underlying rare DMRs, including one balanced translocation, three CG-rich repeat expansions, and two copy number variants. We also identify pathogenic sequence variants associated with episignatures; some had been missed by previous exome sequencing. Although most DEE genes lack known episignatures, the increase in diagnostic yield for DNA methylation analysis in DEEs is comparable to the added yield of genome sequencing. Finally, we refine an episignature for CHD2 using an 850K methylation array which was further refined at higher CpG resolution using bisulfite sequencing to investigate potential insights into CHD2 pathophysiology. Our study demonstrates the diagnostic yield of genome-wide DNA methylation analysis to identify causal and candidate genetic causes as ∼2% (10/516) for unsolved DEE cases.
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Faridi R, Rehman AU, Morell RJ, Friedman PL, Demain L, Zahra S, Khan AA, Tohlob D, Assir MZ, Beaman G, Khan SN, Newman WG, Riazuddin S, Friedman TB. Mutations of SGO2 and CLDN14 collectively cause coincidental Perrault syndrome. Clin Genet 2017; 91:328-332. [PMID: 27629923 PMCID: PMC5272805 DOI: 10.1111/cge.12867] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [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: 07/20/2016] [Revised: 08/31/2016] [Accepted: 09/03/2016] [Indexed: 01/27/2023]
Abstract
Perrault syndrome (PS) is a genetically heterogeneous disorder characterized by primary ovarian insufficiency (POI) in females and sensorineural hearing loss in males and females. In many PS subjects, causative variants have not been found in the five reported PS genes. The objective of this study was to identify the genetic cause of PS in an extended consanguineous family with six deaf individuals. Whole exome sequencing (WES) was completed on four affected members of a large family, and variants and co-segregation was confirmed by Sanger sequencing. All hearing impaired individuals, including the proband, are homozygous for a pathogenic variant of CLDN14, but this only explains the deafness. The PS proband is also homozygous for a frameshift variant (c.1453_1454delGA, p.(Glu485Lysfs*5)) in exon 7 of SGO2 encoding shugoshin 2, which is the likely cause of her concurrent ovarian insufficiency. In mouse, Sgol2a encoding shugoshin-like 2a is necessary during meiosis in both sexes to maintain the integrity of the cohesin complex that tethers sister chromatids. Human SGO2 has not previously been implicated in any disorder, but in this case of POI and perhaps others, it is a candidate for unexplained infertility.
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Affiliation(s)
- Rabia Faridi
- Laboratory of Molecular Genetics, National Institute on Deafness and Other Communication Disorders, National Institutes of Health, Bethesda, MD 20892
- National Centre of Excellence in Molecular Biology, University of the Punjab, Lahore 54550, Pakistan
| | - Atteeq U. Rehman
- Laboratory of Molecular Genetics, National Institute on Deafness and Other Communication Disorders, National Institutes of Health, Bethesda, MD 20892
| | - Robert J. Morell
- Genomics and Computational Biology Core, NIDCD, NIH, Bethesda, MD 20892, USA
| | | | - Leigh Demain
- Manchester Centre for Genomic Medicine, University of Manchester and Central Manchester University Hospitals, NHS Foundation Trust, Manchester, M13 9WL, UK
| | - Sana Zahra
- National Centre of Excellence in Molecular Biology, University of the Punjab, Lahore 54550, Pakistan
| | - Asma Ali Khan
- National Centre of Excellence in Molecular Biology, University of the Punjab, Lahore 54550, Pakistan
| | - Dalia Tohlob
- Manchester Centre for Genomic Medicine, University of Manchester and Central Manchester University Hospitals, NHS Foundation Trust, Manchester, M13 9WL, UK
- Clinical Pathology Department, Faculty of Medicine, Mansoura University, Egypt
| | - Muhammad Zaman Assir
- Allama Iqbal Medical College, University of Health Sciences, Lahore, Pakistan
- Shaheed Zulfiqar Ali Bhutto Medical University, Pakistan, Institute of Medical Sciences, Islamabad, Pakistan
| | - Glenda Beaman
- Manchester Centre for Genomic Medicine, University of Manchester and Central Manchester University Hospitals, NHS Foundation Trust, Manchester, M13 9WL, UK
| | - Shaheen N. Khan
- National Centre of Excellence in Molecular Biology, University of the Punjab, Lahore 54550, Pakistan
| | - William G. Newman
- Manchester Centre for Genomic Medicine, University of Manchester and Central Manchester University Hospitals, NHS Foundation Trust, Manchester, M13 9WL, UK
| | - Sheikh Riazuddin
- Allama Iqbal Medical Research Centre, Jinnah Hospital Complex, Lahore 54550, Pakistan
| | - Thomas B. Friedman
- Laboratory of Molecular Genetics, National Institute on Deafness and Other Communication Disorders, National Institutes of Health, Bethesda, MD 20892
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