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Stockley TL, Lo B, Box A, Gomez Corredor A, DeCoteau J, Desmeules P, Feilotter H, Grafodatskaya D, Hawkins C, Huang WY, Izevbaye I, Lepine G, Papadakis AI, Park PC, Sheffield BS, Tran-Thanh D, Yip S, Sound Tsao M. Consensus Recommendations to Optimize the Detection and Reporting of NTRK Gene Fusions by RNA-Based Next-Generation Sequencing. Curr Oncol 2023; 30:3989-3997. [PMID: 37185415 PMCID: PMC10136625 DOI: 10.3390/curroncol30040302] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2023] [Revised: 03/21/2023] [Accepted: 03/27/2023] [Indexed: 04/03/2023] Open
Abstract
The detection of gene fusions by RNA-based next-generation sequencing (NGS) is an emerging method in clinical genetic laboratories for oncology biomarker testing to direct targeted therapy selections. A recent Canadian study (CANTRK study) comparing the detection of NTRK gene fusions on different NGS assays to determine subjects’ eligibility for tyrosine kinase TRK inhibitor therapy identified the need for recommendations for best practices for laboratory testing to optimize RNA-based NGS gene fusion detection. To develop consensus recommendations, representatives from 17 Canadian genetic laboratories participated in working group discussions and the completion of survey questions about RNA-based NGS. Consensus recommendations are presented for pre-analytic, analytic and reporting aspects of gene fusion detection by RNA-based NGS.
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2
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Stockley TL, Lo B, Box A, Corredor AG, DeCoteau J, Desmeules P, Feilotter H, Grafodatskaya D, Greer W, Hawkins C, Huang WY, Izevbaye I, Lépine G, Martins Filho SN, Papadakis AI, Park PC, Riviere JB, Sheffield BS, Spatz A, Spriggs E, Tran-Thanh D, Yip S, Zhang T, Torlakovic E, Tsao MS. CANTRK: A Canadian Ring Study to Optimize Detection of NTRK Gene Fusions by Next-Generation RNA Sequencing. J Mol Diagn 2023; 25:168-174. [PMID: 36586421 DOI: 10.1016/j.jmoldx.2022.12.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Revised: 11/01/2022] [Accepted: 12/06/2022] [Indexed: 12/29/2022] Open
Abstract
The Canadian NTRK (CANTRK) study is an interlaboratory comparison ring study to optimize testing for neurotrophic receptor tyrosine kinase (NTRK) fusions in Canadian laboratories. Sixteen diagnostic laboratories used next-generation sequencing (NGS) for NTRK1, NTRK2, or NTRK3 fusions. Each laboratory received 12 formalin-fixed, paraffin-embedded tumor samples with unique NTRK fusions and two control non-NTRK fusion samples (one ALK and one ROS1). Laboratories used validated protocols for NGS fusion detection. Panels included Oncomine Comprehensive Assay v3, Oncomine Focus Assay, Oncomine Precision Assay, AmpliSeq for Illumina Focus, TruSight RNA Pan-Cancer Panel, FusionPlex Lung, and QIAseq Multimodal Lung. One sample was withdrawn from analysis because of sample quality issues. Of the remaining 13 samples, 6 of 11 NTRK fusions and both control fusions were detected by all laboratories. Two fusions, WNK2::NTRK2 and STRN3::NTRK2, were not detected by 10 laboratories using the Oncomine Comprehensive or Focus panels, due to absence of WNK2 and STRN3 in panel designs. Two fusions, TPM3::NTRK1 and LMNA::NTRK1, were challenging to detect on the AmpliSeq for Illumina Focus panel because of bioinformatics issues. One ETV6::NTRK3 fusion at low levels was not detected by two laboratories using the TruSight Pan-Cancer Panel. Panels detecting all fusions included FusionPlex Lung, Oncomine Precision, and QIAseq Multimodal Lung. The CANTRK study showed competency in detection of NTRK fusions by NGS across different panels in 16 Canadian laboratories and identified key test issues as targets for improvements.
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Affiliation(s)
- Tracy L Stockley
- Laboratory Medicine Program, University Health Network, Toronto, Ontario, Canada; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada; Advanced Molecular Diagnostics Laboratory, Princess Margaret Cancer Centre, Toronto, Ontario, Canada.
| | - Bryan Lo
- Department of Pathology and Laboratory Medicine, The Ottawa Hospital, Ottawa, Ontario, Canada
| | - Adrian Box
- Alberta Precision Labs, Calgary, Alberta, Canada
| | | | - John DeCoteau
- Department of Pathology and Laboratory Medicine, College of Medicine, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Patrice Desmeules
- IUCPQ-UL, Quebec Heart and Lung Institute, Quebec City, Quebec, Canada
| | - Harriet Feilotter
- Kingston Health Sciences Centre, Kingston, Ontario, Canada; Department of Pathology and Molecular Medicine, Queen's University, Kingston, Ontario, Canada
| | - Daria Grafodatskaya
- Hamilton Health Sciences Centre, Hamilton, Ontario, Canada; Department of Pathology and Molecular Medicine, McMaster University, Hamilton, Ontario, Canada
| | - Wenda Greer
- Nova Scotia Health Authority, Halifax, Nova Scotia, Canada
| | - Cynthia Hawkins
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada; The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Weei Yuarn Huang
- Nova Scotia Health Authority, Halifax, Nova Scotia, Canada; Sunnybrook Health Sciences Centre, Toronto, Ontario, Canada
| | - Iyare Izevbaye
- Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, Alberta, Canada
| | | | - Sebastiao N Martins Filho
- Laboratory Medicine Program, University Health Network, Toronto, Ontario, Canada; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada; Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, Alberta, Canada
| | | | - Paul C Park
- Shared Health Manitoba, Winnipeg, Manitoba, Canada
| | | | | | - Alan Spatz
- Lady Davis Institute, Jewish General Hospital, Montreal, Quebec, Canada
| | | | - Danh Tran-Thanh
- CHUM-Centre Hospitalier de l'Université de Montréal, Montreal, Quebec, Canada
| | - Stephen Yip
- BC Cancer, Vancouver, British Columbia, Canada; Department of Pathology and Laboratory Medicine, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Tong Zhang
- Advanced Molecular Diagnostics Laboratory, Princess Margaret Cancer Centre, Toronto, Ontario, Canada
| | - Emina Torlakovic
- Department of Pathology and Laboratory Medicine, College of Medicine, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Ming Sound Tsao
- Laboratory Medicine Program, University Health Network, Toronto, Ontario, Canada; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
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3
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Schenkel LC, Mathew J, Hirte H, Provias J, Paré G, Chong M, Grafodatskaya D, McCready E. Evaluation of DNA Methylation Array for Glioma Tumor Profiling and Description of a Novel Epi-Signature to Distinguish IDH1/IDH2 Mutant and Wild-Type Tumors. Genes (Basel) 2022; 13:2075. [PMID: 36360312 PMCID: PMC9690723 DOI: 10.3390/genes13112075] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Revised: 10/17/2022] [Accepted: 10/27/2022] [Indexed: 09/15/2023] Open
Abstract
UNLABELLED Molecular biomarkers, such as IDH1/IDH2 mutations and 1p19q co-deletion, are included in the histopathological and clinical criteria currently used to diagnose and classify gliomas. IDH1/IDH2 mutation is a common feature of gliomas and is associated with a glioma-CpG island methylator phenotype (CIMP). Aberrant genomic methylation patterns can also be used to extrapolate information about copy number variation in a tumor. This project's goal was to assess the feasibility of DNA methylation array for the simultaneous detection of glioma biomarkers as a more effective testing strategy compared to existing single analyte tests. METHODS Whole-genome methylation array (WGMA) testing was performed using 48 glioma DNA samples to detect methylation aberrations and chromosomal gains and losses. The analyzed samples include 39 tumors in the discovery cohort and 9 tumors in the replication cohort. Methylation profiles for each sample were correlated with IDH1 p.R132G mutation, immunohistochemistry (IHC), and previous 1p19q clinical testing to assess the sensitivity and specificity of the WGMA assay for the detection of these variants. RESULTS We developed a DNA methylation signature to specifically distinguish a IDH1/IDH2 mutant tumor from normal samples. This signature is composed of 11 CpG sites that were significantly hypermethylated in the IDH1/IDH2 mutant group. Copy number analysis using WGMA data was able to identify five of five positive samples for 1p19q co-deletion and was concordant for all negative samples. CONCLUSIONS The DNA methylation signature presented here has the potential to refine the utility of WGMA to predict IDH1/IDH2 mutation status of gliomas, thus improving diagnostic yield and efficiency of laboratory testing compared to single analyte IDH1/IDH2 or 1p19q tests.
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Affiliation(s)
- Laila C. Schenkel
- Faculty of Health Sciences, Department of Pathology and Molecular Medicine, McMaster University, 1280 Main Street West, Hamilton, ON L8S 4K1, Canada
| | - Joseph Mathew
- Faculty of Health Sciences, Department of Pathology and Molecular Medicine, McMaster University, 1280 Main Street West, Hamilton, ON L8S 4K1, Canada
| | - Hal Hirte
- Faculty of Health Sciences, Department of Oncology, McMaster University, 699 Concession Street, Hamilton, ON L8V 5C2, Canada
| | - John Provias
- Faculty of Health Sciences, Department of Pathology and Molecular Medicine, McMaster University, 1280 Main Street West, Hamilton, ON L8S 4K1, Canada
- Hamilton Regional Laboratory Medicine Program, Hamilton Health Sciences and St. Joseph’s Healthcare Hamilton, 50 Charlton Avenue East, Hamilton, ON L8N 4A6, Canada
| | - Guillaume Paré
- Faculty of Health Sciences, Department of Pathology and Molecular Medicine, McMaster University, 1280 Main Street West, Hamilton, ON L8S 4K1, Canada
- Hamilton Regional Laboratory Medicine Program, Hamilton Health Sciences and St. Joseph’s Healthcare Hamilton, 50 Charlton Avenue East, Hamilton, ON L8N 4A6, Canada
- Population Health Research Institute, 237 Barton Street East, Hamilton, ON L8L 2X2, Canada
- Faculty of Health Sciences, Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON L8S 4K1, Canada
| | - Michael Chong
- Faculty of Health Sciences, Department of Pathology and Molecular Medicine, McMaster University, 1280 Main Street West, Hamilton, ON L8S 4K1, Canada
- Population Health Research Institute, 237 Barton Street East, Hamilton, ON L8L 2X2, Canada
- Faculty of Health Sciences, Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON L8S 4K1, Canada
| | - Daria Grafodatskaya
- Faculty of Health Sciences, Department of Pathology and Molecular Medicine, McMaster University, 1280 Main Street West, Hamilton, ON L8S 4K1, Canada
- Hamilton Regional Laboratory Medicine Program, Hamilton Health Sciences and St. Joseph’s Healthcare Hamilton, 50 Charlton Avenue East, Hamilton, ON L8N 4A6, Canada
| | - Elizabeth McCready
- Faculty of Health Sciences, Department of Pathology and Molecular Medicine, McMaster University, 1280 Main Street West, Hamilton, ON L8S 4K1, Canada
- Hamilton Regional Laboratory Medicine Program, Hamilton Health Sciences and St. Joseph’s Healthcare Hamilton, 50 Charlton Avenue East, Hamilton, ON L8N 4A6, Canada
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4
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Grafodatskaya D, O'Rielly DD, Bedard K, Butcher DT, Howlett CJ, Lytwyn A, McCready E, Parboosingh J, Spriggs EL, Vaags AK, Stockley TL. Practice guidelines for BRCA1/2 tumour testing in ovarian cancer. J Med Genet 2022; 59:727-736. [PMID: 35393334 PMCID: PMC9340048 DOI: 10.1136/jmedgenet-2021-108238] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [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: 09/23/2021] [Accepted: 02/24/2022] [Indexed: 12/26/2022]
Abstract
The purpose of this document is to provide pre-analytical, analytical and post-analytical considerations and recommendations to Canadian clinical laboratories developing, validating and offering next-generation sequencing (NGS)-based BRCA1 and BRCA2 (BRCA1/2) tumour testing in ovarian cancers. This document was drafted by the members of the Canadian College of Medical Geneticists (CCMG) somatic BRCA Ad Hoc Working Group, and representatives from the Canadian Association of Pathologists. The document was circulated to the CCMG members for comment. Following incorporation of feedback, this document has been approved by the CCMG board of directors. The CCMG is a Canadian organisation responsible for certifying medical geneticists and clinical laboratory geneticists, and for establishing professional and ethical standards for clinical genetics services in Canada. The current CCMG Practice Guidelines were developed as a resource for clinical laboratories in Canada; however, they are not inclusive of all information laboratories should consider in the validation and use of NGS for BRCA1/2 tumour testing in ovarian cancers.
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Affiliation(s)
- Daria Grafodatskaya
- Department of Pathology and Molecular Medicine, McMaster University, Hamilton, Ontario, Canada.,Hamilton Regional Laboratory Medicine Program, Hamilton Health Sciences, Hamilton, Ontario, Canada
| | - Darren D O'Rielly
- Division of BioMedical Sciences, Faculty of Medicine, Memorial University of Newfoundland, St. John's, Newfoundland, Canada.,Centre for Translational Genomes & Division of Genetics, Eastern Regional Health Authority, St. John's, Newfoundland, Canada
| | - Karine Bedard
- Département de Pathologie et Biologie cellulaire, Université de Montréal, Montreal, Québec, Canada.,Laboratoire de Diagnostic Moléculaire, Centre hospitalier de l'Université de Montréal, Montreal, Québec, Canada
| | - Darci T Butcher
- Department of Pathology and Molecular Medicine, McMaster University, Hamilton, Ontario, Canada.,Hamilton Regional Laboratory Medicine Program, Hamilton Health Sciences, Hamilton, Ontario, Canada
| | - Christopher J Howlett
- Department of Pathology and Laboratory Medicine, Schulich School of Medicine & Dentistry, Wester University, London, Ontario, Canada
| | - Alice Lytwyn
- Department of Pathology and Molecular Medicine, McMaster University, Hamilton, Ontario, Canada.,Hamilton Regional Laboratory Medicine Program, Hamilton Health Sciences, Hamilton, Ontario, Canada
| | - Elizabeth McCready
- Department of Pathology and Molecular Medicine, McMaster University, Hamilton, Ontario, Canada.,Hamilton Regional Laboratory Medicine Program, Hamilton Health Sciences, Hamilton, Ontario, Canada
| | - Jillian Parboosingh
- Department of Medical Genetics, Alberta Children's Hospital Research Institute for Child and Maternal Health, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada.,Genetics and Genomics, Alberta Precision Laboratories, Calgary, Alberta, Canada
| | - Elizabeth L Spriggs
- Genomics, Diagnostic Services, Shared Health Manitoba, Winnipeg, Manitoba, Canada.,Department of Biochemistry and Medical Genetics, Max Rady College of Medicine, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Andrea K Vaags
- Laboratory Medicine and Genetics, Trillium Health Partners, Mississauga, Ontario, Canada.,Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Tracy L Stockley
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada .,Department of Clinical Laboratory Genetics, Laboratory Medicine Program, University Health Network, Toronto, Ontario, Canada
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5
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Bartlett J, Amemiya Y, Arts H, Bayani J, Eng B, Grafodatskaya D, Kamel Reid S, Lariviere M, Lo B, McClure R, Mittal V, Sadikovic B, Sadis S, Seth A, Smith J, Zhang X, Feilotter H. Multisite verification of the accuracy of a multi-gene next generation sequencing panel for detection of mutations and copy number alterations in solid tumours. PLoS One 2021; 16:e0258188. [PMID: 34597339 PMCID: PMC8486135 DOI: 10.1371/journal.pone.0258188] [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] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Accepted: 09/22/2021] [Indexed: 11/29/2022] Open
Abstract
Molecular variants including single nucleotide variants (SNVs), copy number variants (CNVs) and fusions can be detected in the clinical setting using deep targeted sequencing. These assays support low limits of detection using little genomic input material. They are gaining in popularity in clinical laboratories, where sample volumes are limited, and low variant allele fractions may be present. However, data on reproducibility between laboratories is limited. Using a ring study, we evaluated the performance of 7 Ontario laboratories using targeted sequencing panels. All laboratories analysed a series of control and clinical samples for SNVs/CNVs and gene fusions. High concordance was observed across laboratories for measured CNVs and SNVs. Over 97% of SNV calls in clinical samples were detected by all laboratories. Whilst only a single CNV was detected in the clinical samples tested, all laboratories were able to reproducibly report both the variant and copy number. Concordance for information derived from RNA was lower than observed for DNA, due largely to decreased quality metrics associated with the RNA components of the assay, suggesting that the RNA portions of comprehensive NGS assays may be more vulnerable to variations in approach and workflow. Overall the results of this study support the use of the OFA for targeted sequencing for testing of clinical samples and suggest specific internal quality metrics that can be reliable indicators of assay failure. While we believe this evidence can be interpreted to support deep targeted sequencing in general, additional studies should be performed to confirm this.
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Affiliation(s)
- John Bartlett
- Diagnostic Development, Ontario Institute for Cancer Research, Toronto, Ontario, Canada
- Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
- Edinburgh Cancer Research Centre, Edinburgh, United Kingdom
| | - Yutaka Amemiya
- SRI Genomics Laboratory and Department of Laboratory Medicine and Molecular Diagnostics, Sunnybrook Health Sciences Centre, University of Toronto, Ontario, Canada
| | - Heleen Arts
- Department of Pathology and Molecular Medicine, McMaster University, Hamilton, Ontario, Canada
| | - Jane Bayani
- Diagnostic Development, Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Barry Eng
- Department of Pathology and Molecular Medicine, McMaster University, Hamilton, Ontario, Canada
- Hamilton Regional Laboratory Medicine Program, Hamilton Health Sciences, Hamilton, Ontario, Canada
| | - Daria Grafodatskaya
- Department of Pathology and Molecular Medicine, McMaster University, Hamilton, Ontario, Canada
- Hamilton Regional Laboratory Medicine Program, Hamilton Health Sciences, Hamilton, Ontario, Canada
| | - Suzanne Kamel Reid
- Department of Clinical Laboratory Genetics, The University Health Network, Toronto, Ontario, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Mathieu Lariviere
- Thermo Fisher Scientific, South San Francisco, CA, United States of America
| | - Bryan Lo
- Dept of Pathology and Laboratory Medicine, The Ottawa Hospital, Ottawa, Ontario, Canada
| | - Rebecca McClure
- Health Sciences North/Horizon Sante-Nord, Sudbury, Ontario, Canada
| | - Vinay Mittal
- Thermo Fisher Scientific, South San Francisco, CA, United States of America
| | - Bekim Sadikovic
- Molecular Diagnostics Laboratoroy, Victoria Hospital, London Health Sciences Centre, London, Ontario, Canada
- Department of Pathology and Laboratory Medicine, Western University, London, Ontario, Canada
| | - Seth Sadis
- Thermo Fisher Scientific, South San Francisco, CA, United States of America
| | - Arun Seth
- SRI Genomics Laboratory and Department of Laboratory Medicine and Molecular Diagnostics, Sunnybrook Health Sciences Centre, University of Toronto, Ontario, Canada
| | - Jeff Smith
- Thermo Fisher Scientific, South San Francisco, CA, United States of America
| | - Xiao Zhang
- Department of Pathology and Molecular Medicine, Queen’s University, Kingston, Ontario, Canada
| | - Harriet Feilotter
- Department of Pathology and Molecular Medicine, Queen’s University, Kingston, Ontario, Canada
- Laboratory Genetics, Kingston Health Sciences Center, Kingston Ontario, Canada
- * E-mail:
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6
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Selvarajah S, Plante S, Speevak M, Vaags A, Hamelinck D, Butcher M, McCready E, Grafodatskaya D, Blais N, Tran-Thanh D, Weng X, Nassabein R, Greer W, Walton RN, Lo B, Demetrick D, Santos S, Sadikovic B, Zhang X, Zhang T, Spence T, Stockley T, Feilotter H, Joubert P. A Pan-Canadian Validation Study for the Detection of EGFR T790M Mutation Using Circulating Tumor DNA From Peripheral Blood. JTO Clin Res Rep 2021; 2:100212. [PMID: 34590051 PMCID: PMC8474449 DOI: 10.1016/j.jtocrr.2021.100212] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Revised: 06/23/2021] [Accepted: 07/08/2021] [Indexed: 11/19/2022] Open
Abstract
INTRODUCTION Genotyping circulating tumor DNA (ctDNA) is a promising noninvasive clinical tool to identify the EGFR T790M resistance mutation in patients with advanced NSCLC with resistance to EGFR inhibitors. To facilitate standardization and clinical adoption of ctDNA testing across Canada, we developed a 2-phase multicenter study to standardize T790M mutation detection using plasma ctDNA testing. METHODS In phase 1, commercial reference standards were distributed to participating clinical laboratories, to use their existing platforms for mutation detection. Baseline performance characteristics were established using known and blinded engineered plasma samples spiked with predetermined concentrations of T790M, L858R, and exon 19 deletion variants. In phase II, peripheral blood collected from local patients with known EGFR activating mutations and progressing on treatment were assayed for the presence of EGFR variants and concordance with a clinically validated test at the reference laboratory. RESULTS All laboratories in phase 1 detected the variants at 0.5 % and 5.0 % allele frequencies, with no false positives. In phase 2, the concordance with the reference laboratory for detection of both the primary and resistance mutation was high, with next-generation sequencing and droplet digital polymerase chain reaction exhibiting the best overall concordance. Data also suggested that the ability to detect mutations at clinically relevant limits of detection is generally not platform-specific, but rather impacted by laboratory-specific practices. CONCLUSIONS Discrepancies among sending laboratories using the same assay suggest that laboratory-specific practices may impact performance. In addition, a negative or inconclusive ctDNA test should be followed by tumor testing when possible.
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Affiliation(s)
- Shamini Selvarajah
- Department of Laboratory Medicine and Genetics, Trillium Health Partners, Mississauga, Ontario, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Sophie Plante
- Institut Universitaire de Cardiologie et de Pneumologie de Québec-Université Laval, Québec, Quebec, Canada
| | - Marsha Speevak
- Department of Laboratory Medicine and Genetics, Trillium Health Partners, Mississauga, Ontario, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Andrea Vaags
- Department of Laboratory Medicine and Genetics, Trillium Health Partners, Mississauga, Ontario, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Darren Hamelinck
- Department of Laboratory Medicine and Genetics, Trillium Health Partners, Mississauga, Ontario, Canada
| | - Martin Butcher
- Department of Oncology, McMaster University, Hamilton, Ontario, Canada
| | - Elizabeth McCready
- Department of Pathology and Molecular Medicine, McMaster University, Hamilton, Ontario, Canada
- Hamilton Regional Laboratory Medicine Program, Hamilton Health Sciences, Hamilton, Ontario, Canada
| | - Daria Grafodatskaya
- Department of Pathology and Molecular Medicine, McMaster University, Hamilton, Ontario, Canada
- Hamilton Regional Laboratory Medicine Program, Hamilton Health Sciences, Hamilton, Ontario, Canada
| | - Normand Blais
- Centre Hospitalier de l’Université de Montréal, Montréal, Quebec, Canada
| | - Danh Tran-Thanh
- Centre Hospitalier de l’Université de Montréal, Montréal, Quebec, Canada
| | - Xiaoduan Weng
- Centre Hospitalier de l’Université de Montréal, Montréal, Quebec, Canada
| | - Rami Nassabein
- Centre Hospitalier de l’Université de Montréal, Montréal, Quebec, Canada
| | - Wenda Greer
- Queen Elizabeth II Health Sciences Center, Department of Pathology, Faculty of Medicine, Dalhousie University, Halifax, Nova Scotia, Canada
| | | | - Bryan Lo
- Department of Pathology and Laboratory Medicine, The Ottawa Hospital, Ottawa, Ontario, Canada
| | - Doug Demetrick
- Department of Pathology and Laboratory Medicine, University of Calgary, Calgary, Alberta, Canada
- Department of Oncology, University of Calgary, Calgary, Alberta, Canada
- Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, Alberta, Canada
- Department of Medical Genetics, University of Calgary, Calgary, Alberta, Canada
| | - Stephanie Santos
- Molecular Genetics Laboratory, Molecular Diagnostics Division, London Health Sciences Centre, London, Ontario, Canada
| | - Bekim Sadikovic
- Molecular Genetics Laboratory, Molecular Diagnostics Division, London Health Sciences Centre, London, Ontario, Canada
- Department of Pathology and Laboratory Medicine, Western University, London, Ontario, Canada
- Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, Ontario, Canada
| | - Xiao Zhang
- Laboratory Genetics, Kingston Health Sciences Center, Kingston, Ontario, Canada
| | - Tong Zhang
- Department of Clinical Laboratory Genetics, University Health Network, Toronto, Ontario, Canada
| | - Tara Spence
- Department of Pathology and Molecular Medicine, Queen’s University, Kingston, Ontario, Canada
| | - Tracy Stockley
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
- Department of Clinical Laboratory Genetics, University Health Network, Toronto, Ontario, Canada
| | - Harriet Feilotter
- Laboratory Genetics, Kingston Health Sciences Center, Kingston, Ontario, Canada
- Department of Pathology and Molecular Medicine, Queen’s University, Kingston, Ontario, Canada
| | - Philippe Joubert
- Institut Universitaire de Cardiologie et de Pneumologie de Québec-Université Laval, Québec, Quebec, Canada
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7
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Selvarajah S, Plante S, Speevak M, Vaags A, Mccready E, Grafodatskaya D, Blais N, Tran-Thanh D, Greer W, Lo B, Demetrick D, Sadikovic B, Walton R, Stockley T, Feilotter H, Joubert P. FP07.08 A Pan-Canadian Validation Study for the Detection of EGFR-T790M Mutations Using Circulating Tumour DNA (ctDNA) from Blood. J Thorac Oncol 2021. [DOI: 10.1016/j.jtho.2021.01.108] [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: 11/28/2022]
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8
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Siu MT, Goodman SJ, Yellan I, Butcher DT, Jangjoo M, Grafodatskaya D, Rajendram R, Lou Y, Zhang R, Zhao C, Nicolson R, Georgiades S, Szatmari P, Scherer SW, Roberts W, Anagnostou E, Weksberg R. DNA Methylation of the Oxytocin Receptor Across Neurodevelopmental Disorders. J Autism Dev Disord 2021; 51:3610-3623. [PMID: 33394241 DOI: 10.1007/s10803-020-04792-x] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/09/2020] [Indexed: 12/24/2022]
Abstract
Many neurodevelopmental disorders (NDDs) share common learning and behavioural impairments, as well as features such as dysregulation of the oxytocin hormone. Here, we examined DNA methylation (DNAm) in the 1st intron of the oxytocin receptor gene, OXTR, in patients with autism spectrum (ASD), attention deficit and hyperactivity (ADHD) and obsessive compulsive (OCD) disorders. DNAm of OXTR was assessed for cohorts of ASD (blood), ADHD (saliva), OCD (saliva), which uncovered sex-specific DNAm differences compared to neurotypical, tissue-matched controls. Individuals with ASD or ADHD exhibiting extreme DNAm values had lower IQ and more social problems, respectively, than those with DNAm within normative ranges. This suggests that OXTR DNAm patterns are altered across NDDs and may be correlated with common clinical outcomes.
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Affiliation(s)
- Michelle T Siu
- Department of Medical Genetics, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada.,Alberta Children's Hospital Research Institute, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada.,Genetics and Genome Biology, Hospital for Sick Children, Toronto, ON, Canada
| | - Sarah J Goodman
- Genetics and Genome Biology, Hospital for Sick Children, Toronto, ON, Canada
| | - Isaac Yellan
- Genetics and Genome Biology, Hospital for Sick Children, Toronto, ON, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Darci T Butcher
- Genetics and Genome Biology, Hospital for Sick Children, Toronto, ON, Canada.,Department of Pathology and Molecular Medicine, McMaster University, Hamilton, ON, Canada
| | - Maryam Jangjoo
- Genetics and Genome Biology, Hospital for Sick Children, Toronto, ON, Canada
| | - Daria Grafodatskaya
- Department of Pathology and Molecular Medicine, McMaster University, Hamilton, ON, Canada
| | - Rageen Rajendram
- Genetics and Genome Biology, Hospital for Sick Children, Toronto, ON, Canada
| | - Youliang Lou
- Genetics and Genome Biology, Hospital for Sick Children, Toronto, ON, Canada
| | - Rujun Zhang
- Genetics and Genome Biology, Hospital for Sick Children, Toronto, ON, Canada
| | - Chunhua Zhao
- Genetics and Genome Biology, Hospital for Sick Children, Toronto, ON, Canada
| | - Rob Nicolson
- Department of Psychiatry, University of Western Ontario, London, ON, Canada
| | - Stelios Georgiades
- Department of Psychiatry and Behavioural Neurosciences, McMaster University, Hamilton, ON, Canada
| | - Peter Szatmari
- The Margaret and Wallace McCain Centre for Child, Youth & Family Mental Health and Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, ON, Canada.,Department of Psychiatry, University of Toronto, Toronto, ON, Canada
| | - Stephen W Scherer
- Genetics and Genome Biology, Hospital for Sick Children, Toronto, ON, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada.,The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON, Canada.,McLaughlin Centre, University of Toronto, Toronto, ON, Canada
| | - Wendy Roberts
- Genetics and Genome Biology, Hospital for Sick Children, Toronto, ON, Canada
| | - Evdokia Anagnostou
- Holland Bloorview Kids Rehabilitation Hospital, Toronto, ON, Canada.,Department of Pediatrics, University of Toronto, Toronto, ON, Canada
| | - Rosanna Weksberg
- Genetics and Genome Biology, Hospital for Sick Children, Toronto, ON, Canada. .,Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada. .,Division of Clinical and Metabolic Genetics, The Hospital for Sick Children, 555 University Ave, Toronto, ON, M5G 1X8, Canada. .,Institute of Medical Science, School of Graduate Studies, University of Toronto, Toronto, ON, Canada.
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9
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McCready E, Butcher D, Woodside C, Kord D, Sur ML, Lytwyn A, Bell K, Nfonsam L, Choi C, Grafodatskaya D. 33. Tumor testing of DNA repair genes in high grade serous ovarian cancer (HGSOC); a potential tool for personalized therapy. Cancer Genet 2020. [DOI: 10.1016/j.cancergen.2020.04.037] [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: 11/25/2022]
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10
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Arts HH, Lynch L, Grafodatskaya D, Eng B, Malloy L, Duck J, White R, Woodside C, Bell K, Zbuk KM, McCready E. ATM whole gene deletion in an Italian family with hereditary pancreatic cancer: Challenges to cancer risk prediction associated with an 11q22.3 microdeletion. Cancer Genet 2019; 240:1-4. [PMID: 31671381 DOI: 10.1016/j.cancergen.2019.10.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [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: 12/17/2018] [Revised: 09/06/2019] [Accepted: 10/11/2019] [Indexed: 01/02/2023]
Abstract
Hereditary pancreatic cancer has been attributed to variants of several cancer predisposition genes including ATM. While heterozygous pathogenic variants in the ATM gene are implicated as a cause of familial breast and pancreatic cancers to our knowledge ATM whole gene deletions have not been previously reported. We describe a contiguous gene deletion of the ATM locus in a multi-generation family of Italian descent with a strong family history of pancreatic cancer. A deletion of one copy of the entire ATM gene was identified by routine panel testing and further characterized by chromosomal microarray analysis. An 11q22.3 microdeletion of approximately 960 kb was identified that is predicted to result in loss of 10 genes including ATM. The deletion was identified in two additional family members including a presymptomatic daughter and an affected sibling. A normal disomic complement of the 11q22.3 region was detected in a third family member with a history of prostate and pancreatic cancer. Additional family members were not available for testing. Given available evidence that ATM haploinsufficiency can increase cancer risk, we predict that the observed copy number loss has likely contributed to hereditary cancer in this family. However, absence of the familial microdeletion in at least one affected family member suggests that ATM deletions are unlikely the sole contributing factor influencing tumor development in affected individuals. This case highlights 11q22.3 microdeletions of the ATM gene region as a possible risk factor for hereditary cancer, including pancreatic cancer. The same case provides a further cautionary tale for over interpretation of cancer risk associated tumor suppressor microdeletions and suggests that the variant may not be sufficient for tumor development or may modify the cancer risks associated with other, yet unidentified hereditary cancer genes.
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Affiliation(s)
- Heleen H Arts
- McMaster University, Department of Pathology and Molecular Medicine, 1280 Main Street West, L8S 4L8, Hamilton, ON, Canada
| | - Lorrie Lynch
- Juravinski Cancer Centre, Hamilton Health Sciences, 699 Concession Street, L8V 5C2, Hamilton, ON, Canada
| | - Daria Grafodatskaya
- McMaster University, Department of Pathology and Molecular Medicine, 1280 Main Street West, L8S 4L8, Hamilton, ON, Canada; Hamilton Regional Laboratory Medicine Program, Hamilton Health Sciences, 1200 Main Street West, L8S 4J9, Hamilton, ON, Canada
| | - Barry Eng
- Hamilton Regional Laboratory Medicine Program, Hamilton Health Sciences, 1200 Main Street West, L8S 4J9, Hamilton, ON, Canada
| | - Lesley Malloy
- Hamilton Regional Laboratory Medicine Program, Hamilton Health Sciences, 1200 Main Street West, L8S 4J9, Hamilton, ON, Canada
| | - John Duck
- Hamilton Regional Laboratory Medicine Program, Hamilton Health Sciences, 1200 Main Street West, L8S 4J9, Hamilton, ON, Canada
| | - Robyn White
- Hamilton Regional Laboratory Medicine Program, Hamilton Health Sciences, 1200 Main Street West, L8S 4J9, Hamilton, ON, Canada
| | - Crystal Woodside
- Hamilton Regional Laboratory Medicine Program, Hamilton Health Sciences, 1200 Main Street West, L8S 4J9, Hamilton, ON, Canada
| | - Kathleen Bell
- Juravinski Cancer Centre, Hamilton Health Sciences, 699 Concession Street, L8V 5C2, Hamilton, ON, Canada; Department of Oncology, McMaster University, 699 Concession Street, L8V 5C2, Hamilton, ON, Canada
| | - Kevin M Zbuk
- Juravinski Cancer Centre, Hamilton Health Sciences, 699 Concession Street, L8V 5C2, Hamilton, ON, Canada; Department of Oncology, McMaster University, 699 Concession Street, L8V 5C2, Hamilton, ON, Canada
| | - Elizabeth McCready
- McMaster University, Department of Pathology and Molecular Medicine, 1280 Main Street West, L8S 4L8, Hamilton, ON, Canada; Hamilton Regional Laboratory Medicine Program, Hamilton Health Sciences, 1200 Main Street West, L8S 4J9, Hamilton, ON, Canada.
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11
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Yeung KS, Chung BHY, Choufani S, Mok MY, Wong WL, Mak CCY, Yang W, Lee PPW, Wong WHS, Chen YA, Grafodatskaya D, Wong RWS, Lau CS, Chan DTM, Weksberg R, Lau YL. Genome-Wide DNA Methylation Analysis of Chinese Patients with Systemic Lupus Erythematosus Identified Hypomethylation in Genes Related to the Type I Interferon Pathway. PLoS One 2017; 12:e0169553. [PMID: 28085900 PMCID: PMC5234836 DOI: 10.1371/journal.pone.0169553] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2016] [Accepted: 12/06/2016] [Indexed: 11/18/2022] Open
Abstract
Background Epigenetic variants have been shown in recent studies to be important contributors to the pathogenesis of systemic lupus erythematosus (SLE). Here, we report a 2-step study of discovery followed by replication to identify DNA methylation alterations associated with SLE in a Chinese population. Using a genome-wide DNA methylation microarray, the Illumina Infinium HumanMethylation450 BeadChip, we compared the methylation levels of CpG sites in DNA extracted from white blood cells from 12 female Chinese SLE patients and 10 healthy female controls. Results We identified 36 CpG sites with differential loss of DNA methylation and 8 CpG sites with differential gain of DNA methylation, representing 25 genes and 7 genes, respectively. Surprisingly, 42% of the hypomethylated CpG sites were located in CpG shores, which indicated the functional importance of the loss of DNA methylation. Microarray results were replicated in another cohort of 100 SLE patients and 100 healthy controls by performing bisulfite pyrosequencing of four hypomethylated genes, MX1, IFI44L, NLRC5 and PLSCR1. In addition, loss of DNA methylation in these genes was associated with an increase in mRNA expression. Gene ontology analysis revealed that the hypomethylated genes identified in the microarray study were overrepresented in the type I interferon pathway, which has long been implicated in the pathogenesis of SLE. Conclusion Our epigenetic findings further support the importance of the type I interferon pathway in SLE pathogenesis. Moreover, we showed that the DNA methylation signatures of SLE can be defined in unfractionated white blood cells.
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Affiliation(s)
- Kit San Yeung
- Department of Paediatrics and Adolescent Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Brian Hon-Yin Chung
- Department of Paediatrics and Adolescent Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
- * E-mail:
| | - Sanaa Choufani
- Genetics and Genome Biology Program, The Hospital for Sick Children Research Institute, Toronto, Canada
| | - Mo Yin Mok
- Department of Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
- Department of Biomedical Sciences, The City University of Hong Kong, Hong Kong, China
| | - Wai Lap Wong
- Department of Paediatrics and Adolescent Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Christopher Chun Yu Mak
- Department of Paediatrics and Adolescent Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Wanling Yang
- Department of Paediatrics and Adolescent Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Pamela Pui Wah Lee
- Department of Paediatrics and Adolescent Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Wilfred Hing Sang Wong
- Department of Paediatrics and Adolescent Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Yi-an Chen
- Genetics and Genome Biology Program, The Hospital for Sick Children Research Institute, Toronto, Canada
| | - Daria Grafodatskaya
- Genetics and Genome Biology Program, The Hospital for Sick Children Research Institute, Toronto, Canada
| | - Raymond Woon Sing Wong
- Department of Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Chak Sing Lau
- Department of Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Daniel Tak Mao Chan
- Department of Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Rosanna Weksberg
- Genetics and Genome Biology Program, The Hospital for Sick Children Research Institute, Toronto, Canada
- Division of Clinical and Metabolic Genetics, The Hospital for Sick Children, Toronto, Ontario, Canada
- Institute of Medical Science and Department of Pediatrics, University of Toronto, Toronto, Ontario, Canada
| | - Yu-Lung Lau
- Department of Paediatrics and Adolescent Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
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12
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Grafodatskaya D, Choufani S, Basran R, Weksberg R. An Update on Molecular Diagnostic Testing of Human Imprinting Disorders. J Pediatr Genet 2016; 6:3-17. [PMID: 28180023 DOI: 10.1055/s-0036-1593840] [Citation(s) in RCA: 10] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2015] [Accepted: 05/16/2016] [Indexed: 01/07/2023]
Abstract
Imprinted genes are expressed in a parent of origin manner. Dysregulation of imprinted genes expression causes various disorders associated with abnormalities of growth, neurodevelopment, and metabolism. Molecular mechanisms leading to imprinting disorders and strategies for their diagnosis are discussed in this review article.
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Affiliation(s)
- Daria Grafodatskaya
- Pathology and Molecular Medicine, McMaster University, Hamilton, Ontario, Canada
| | - Sanaa Choufani
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Raveen Basran
- Pediatric Laboratory Medicine, The Hospital for Sick Children, Toronto, Ontario, Canada; Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Rosanna Weksberg
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada; Division of Clinical and Metabolic Genetics, The Hospital for Sick Children, Toronto, Ontario, Canada; Institute of Medical Science, University of Toronto, Toronto, Ontario, Canada; Department of Pediatrics, University of Toronto, Toronto, Ontario, Canada; Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
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13
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Grafodatskaya D, Eng B, Waye JS, Juergens RA, McCready ME. Comparison of Three Commercially Available Platforms for Somatic Mutation Profiling in Solid Tumors. Cancer Genet 2016. [DOI: 10.1016/j.cancergen.2016.04.013] [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: 10/21/2022]
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14
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McCready E, Grafodatskaya D, Schenkel L, Dell E, Li C, Nowaczyk M, Pare G, Sadikovic B. Utility of Genomic Methylation Microarrays to Measure Spreading of X-Inactivation in Association with X;Autosome Translocations. Cancer Genet 2016. [DOI: 10.1016/j.cancergen.2016.04.049] [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: 10/21/2022]
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15
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Choufani S, Cytrynbaum C, Chung BHY, Turinsky AL, Grafodatskaya D, Chen YA, Cohen ASA, Dupuis L, Butcher DT, Siu MT, Luk HM, Lo IFM, Lam STS, Caluseriu O, Stavropoulos DJ, Reardon W, Mendoza-Londono R, Brudno M, Gibson WT, Chitayat D, Weksberg R. NSD1 mutations generate a genome-wide DNA methylation signature. Nat Commun 2015; 6:10207. [PMID: 26690673 PMCID: PMC4703864 DOI: 10.1038/ncomms10207] [Citation(s) in RCA: 133] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2015] [Accepted: 11/13/2015] [Indexed: 01/07/2023] Open
Abstract
Sotos syndrome (SS) represents an important human model system for the study of epigenetic regulation; it is an overgrowth/intellectual disability syndrome caused by mutations in a histone methyltransferase, NSD1. As layered epigenetic modifications are often interdependent, we propose that pathogenic NSD1 mutations have a genome-wide impact on the most stable epigenetic mark, DNA methylation (DNAm). By interrogating DNAm in SS patients, we identify a genome-wide, highly significant NSD1+/−-specific signature that differentiates pathogenic NSD1 mutations from controls, benign NSD1 variants and the clinically overlapping Weaver syndrome. Validation studies of independent cohorts of SS and controls assigned 100% of these samples correctly. This highly specific and sensitive NSD1+/− signature encompasses genes that function in cellular morphogenesis and neuronal differentiation, reflecting cardinal features of the SS phenotype. The identification of SS-specific genome-wide DNAm alterations will facilitate both the elucidation of the molecular pathophysiology of SS and the development of improved diagnostic testing. Sotos syndrome is an growth syndrome characterized by advanced growth in childhood, characteristic facial appearance and intellectual disability. Here the authors identify a genome-wide DNA methylation signature that accurately diagnoses Sotos Syndrome and distinguishes it from similar conditions.
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Affiliation(s)
- S Choufani
- Program in Genetics and Genome Biology, The Hospital for Sick Children, 555 University Avenue, Toronto, Ontario, Canada M5G 1X8
| | - C Cytrynbaum
- Program in Genetics and Genome Biology, The Hospital for Sick Children, 555 University Avenue, Toronto, Ontario, Canada M5G 1X8.,Division of Clinical and Metabolic Genetics, The Hospital for Sick Children, 555 University Avenue, Toronto, Ontario, Canada M5G 1X8.,Department of Molecular Genetics, University of Toronto, 27 King's College Circle, Toronto, Ontario, Canada M5S 1A1
| | - B H Y Chung
- Department of Pediatrics and Adolescent Medicine, Li Ka Shing Faculty of Medicine, University of Hong Kong, 6/F, William MW Mong Block, 21 Sassoon Road, Pokfulam, Hong Kong
| | - A L Turinsky
- Program in Genetics and Genome Biology, The Hospital for Sick Children, 555 University Avenue, Toronto, Ontario, Canada M5G 1X8.,Centre for Computational Medicine, The Hospital for Sick Children, 555 University Avenue, Toronto, Ontario, Canada M5G 1X8
| | - D Grafodatskaya
- Program in Genetics and Genome Biology, The Hospital for Sick Children, 555 University Avenue, Toronto, Ontario, Canada M5G 1X8
| | - Y A Chen
- Program in Genetics and Genome Biology, The Hospital for Sick Children, 555 University Avenue, Toronto, Ontario, Canada M5G 1X8.,Institute of Medical Science, School of Graduate Studies, University of Toronto, 2374-1 King's College Circle, Toronto, Ontario, Canada M5S 1A8
| | - A S A Cohen
- Department of Medical Genetics, UBC, Child and Family Research Institute, 950W 28th Avenue, Vancouver, British Columbia V5Z 4H4, USA
| | - L Dupuis
- Division of Clinical and Metabolic Genetics, The Hospital for Sick Children, 555 University Avenue, Toronto, Ontario, Canada M5G 1X8.,Department of Molecular Genetics, University of Toronto, 27 King's College Circle, Toronto, Ontario, Canada M5S 1A1
| | - D T Butcher
- Program in Genetics and Genome Biology, The Hospital for Sick Children, 555 University Avenue, Toronto, Ontario, Canada M5G 1X8
| | - M T Siu
- Program in Genetics and Genome Biology, The Hospital for Sick Children, 555 University Avenue, Toronto, Ontario, Canada M5G 1X8
| | - H M Luk
- Clinical Genetics Service, Department of Health, Cheung Sha Wan Jockey Club Clinic, 1/F-3/F, 2 Kwong Lee Road, Sham Shui Po, Kowloon, Hong Kong
| | - I F M Lo
- Clinical Genetics Service, Department of Health, Cheung Sha Wan Jockey Club Clinic, 1/F-3/F, 2 Kwong Lee Road, Sham Shui Po, Kowloon, Hong Kong
| | - S T S Lam
- Clinical Genetics Service, Department of Health, Cheung Sha Wan Jockey Club Clinic, 1/F-3/F, 2 Kwong Lee Road, Sham Shui Po, Kowloon, Hong Kong
| | - O Caluseriu
- Department of Medical Genetics, University of Alberta, 116 Street and 85 Avenue, Edmonton, Alberta, Canada T6G 2R3
| | - D J Stavropoulos
- Pediatric Laboratory Medicine, The Hospital for Sick Children, 555 University Avenue, Toronto, Ontario, Canada M5G 1X8.,Laboratory Medicine and Pathobiology, University of Toronto, 27 King's College Circle, Toronto, Ontario, Canada M5S 1A1
| | - W Reardon
- Our Lady's Hospital for Sick Children, Crumlin D12 N512 Ireland
| | - R Mendoza-Londono
- Program in Genetics and Genome Biology, The Hospital for Sick Children, 555 University Avenue, Toronto, Ontario, Canada M5G 1X8.,Division of Clinical and Metabolic Genetics, The Hospital for Sick Children, 555 University Avenue, Toronto, Ontario, Canada M5G 1X8.,Department of Pediatrics, University of Toronto, 27 King's College Circle, Toronto, Ontario, Canada M5S 1A1
| | - M Brudno
- Program in Genetics and Genome Biology, The Hospital for Sick Children, 555 University Avenue, Toronto, Ontario, Canada M5G 1X8.,Centre for Computational Medicine, The Hospital for Sick Children, 555 University Avenue, Toronto, Ontario, Canada M5G 1X8.,Department of Computer Science, University of Toronto, 27 King's College Circle, Toronto, Ontario, Canada M5S 1A1
| | - W T Gibson
- Department of Medical Genetics, UBC, Child and Family Research Institute, 950W 28th Avenue, Vancouver, British Columbia V5Z 4H4, USA
| | - D Chitayat
- Division of Clinical and Metabolic Genetics, The Hospital for Sick Children, 555 University Avenue, Toronto, Ontario, Canada M5G 1X8.,Department of Molecular Genetics, University of Toronto, 27 King's College Circle, Toronto, Ontario, Canada M5S 1A1.,Department of Pediatrics, University of Toronto, 27 King's College Circle, Toronto, Ontario, Canada M5S 1A1.,Prenatal Diagnosis and Medical Genetics Program, Mount Sinai Hospital, 600 University Avenue, Toronto, Ontario, Canada M5G 1X5
| | - R Weksberg
- Program in Genetics and Genome Biology, The Hospital for Sick Children, 555 University Avenue, Toronto, Ontario, Canada M5G 1X8.,Division of Clinical and Metabolic Genetics, The Hospital for Sick Children, 555 University Avenue, Toronto, Ontario, Canada M5G 1X8.,Department of Molecular Genetics, University of Toronto, 27 King's College Circle, Toronto, Ontario, Canada M5S 1A1.,Institute of Medical Science, School of Graduate Studies, University of Toronto, 2374-1 King's College Circle, Toronto, Ontario, Canada M5S 1A8.,Department of Pediatrics, University of Toronto, 27 King's College Circle, Toronto, Ontario, Canada M5S 1A1
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16
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Grafodatskaya D, Dell E, Li C, McCready E. MG-121 Complexity of phenotypes of females with unbalanced x-autosomal translocations exemplified by a case with 46, x,der (x)t (x;16)(p11.2;p13.2) karyotype. J Med Genet 2015. [DOI: 10.1136/jmedgenet-2015-103578.21] [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: 11/04/2022]
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17
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Metsu S, Rainger JK, Debacker K, Bernhard B, Rooms L, Grafodatskaya D, Weksberg R, Fombonne E, Taylor MS, Scherer SW, Kooy RF, FitzPatrick DR. A CGG-repeat expansion mutation in ZNF713 causes FRA7A: association with autistic spectrum disorder in two families. Hum Mutat 2015; 35:1295-300. [PMID: 25196122 DOI: 10.1002/humu.22683] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [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: 04/01/2014] [Accepted: 08/15/2014] [Indexed: 11/09/2022]
Abstract
We report de novo occurrence of the 7p11.2 folate-sensitive fragile site FRA7A in a male with an autistic spectrum disorder (ASD) due to a CGG-repeat expansion mutation (∼450 repeats) in a 5' intron of ZNF713. This expanded allele showed hypermethylation of the adjacent CpG island with reduced ZNF713 expression observed in a proband-derived lymphoblastoid cell line (LCL). His unaffected mother carried an unmethylated premutation (85 repeats). This CGG-repeat showed length polymorphism in control samples (five to 22 repeats). In a second unrelated family, three siblings with ASD and their unaffected father were found to carry FRA7A premutations, which were partially or mosaically methylated. In one of the affected siblings, mitotic instability of the premutation was observed. ZNF713 expression in LCLs in this family was increased in three of these four premutation carriers. A firm link cannot yet be established between ASD and the repeat expansion mutation but plausible pathogenic mechanisms are discussed.
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Affiliation(s)
- Sofie Metsu
- Department of Medical Genetics, University of Antwerp, Antwerp, Belgium
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18
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Ferreira JC, Choufani S, Grafodatskaya D, Butcher DT, Zhao C, Chitayat D, Shuman C, Kingdom J, Keating S, Weksberg R. WNT2promoter methylation in human placenta is associated with low birthweight percentile in the neonate. Epigenetics 2014; 6:440-9. [DOI: 10.4161/epi.6.4.14554] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
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19
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Grafodatskaya D, Chung BHY, Butcher DT, Turinsky AL, Goodman SJ, Choufani S, Chen YA, Lou Y, Zhao C, Rajendram R, Abidi FE, Skinner C, Stavropoulos J, Bondy CA, Hamilton J, Wodak S, Scherer SW, Schwartz CE, Weksberg R. Multilocus loss of DNA methylation in individuals with mutations in the histone H3 lysine 4 demethylase KDM5C. BMC Med Genomics 2013; 6:1. [PMID: 23356856 PMCID: PMC3573947 DOI: 10.1186/1755-8794-6-1] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.7] [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: 10/02/2012] [Accepted: 01/14/2013] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND A number of neurodevelopmental syndromes are caused by mutations in genes encoding proteins that normally function in epigenetic regulation. Identification of epigenetic alterations occurring in these disorders could shed light on molecular pathways relevant to neurodevelopment. RESULTS Using a genome-wide approach, we identified genes with significant loss of DNA methylation in blood of males with intellectual disability and mutations in the X-linked KDM5C gene, encoding a histone H3 lysine 4 demethylase, in comparison to age/sex matched controls. Loss of DNA methylation in such individuals is consistent with known interactions between DNA methylation and H3 lysine 4 methylation. Further, loss of DNA methylation at the promoters of the three top candidate genes FBXL5, SCMH1, CACYBP was not observed in more than 900 population controls. We also found that DNA methylation at these three genes in blood correlated with dosage of KDM5C and its Y-linked homologue KDM5D. In addition, parallel sex-specific DNA methylation profiles in brain samples from control males and females were observed at FBXL5 and CACYBP. CONCLUSIONS We have, for the first time, identified epigenetic alterations in patient samples carrying a mutation in a gene involved in the regulation of histone modifications. These data support the concept that DNA methylation and H3 lysine 4 methylation are functionally interdependent. The data provide new insights into the molecular pathogenesis of intellectual disability. Further, our data suggest that some DNA methylation marks identified in blood can serve as biomarkers of epigenetic status in the brain.
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Affiliation(s)
- Daria Grafodatskaya
- Genetics and Genome Biology Program, Hospital for Sick Children, Toronto, ON, Canada
| | - Barian HY Chung
- Division of Clinical and Metabolic Genetics, Hospital for Sick Children, Toronto, ON, Canada
- Centre of Reproduction, Growth & Development, Department of Pediatrics & Adolescent Medicine, The University of Hong Kong, Hong Kong, Hong Kong
| | - Darci T Butcher
- Genetics and Genome Biology Program, Hospital for Sick Children, Toronto, ON, Canada
| | - Andrei L Turinsky
- Program in Molecular Structure and Function, Hospital for Sick Children, Toronto, ON, Canada
| | - Sarah J Goodman
- Centre of Reproduction, Growth & Development, Department of Pediatrics & Adolescent Medicine, The University of Hong Kong, Hong Kong, Hong Kong
| | - Sana Choufani
- Centre of Reproduction, Growth & Development, Department of Pediatrics & Adolescent Medicine, The University of Hong Kong, Hong Kong, Hong Kong
| | - Yi-An Chen
- Genetics and Genome Biology Program, Hospital for Sick Children, Toronto, ON, Canada
| | - Youliang Lou
- Genetics and Genome Biology Program, Hospital for Sick Children, Toronto, ON, Canada
| | - Chunhua Zhao
- Genetics and Genome Biology Program, Hospital for Sick Children, Toronto, ON, Canada
| | - Rageen Rajendram
- Genetics and Genome Biology Program, Hospital for Sick Children, Toronto, ON, Canada
| | - Fatima E Abidi
- J.C. Self Research Institute, Greenwood Genetic Center, Greenwood, SC, USA
| | - Cindy Skinner
- J.C. Self Research Institute, Greenwood Genetic Center, Greenwood, SC, USA
| | - James Stavropoulos
- Department of Pediatric Laboratory Medicine, Hospital for Sick Children, Toronto, ON, Canada
| | - Carolyn A Bondy
- Developmental Endocrinology Branch, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Jill Hamilton
- Division of Endocrinology, Department of Pediatrics, Hospital for Sick Children, Toronto, ON, Canada
- Department of Pediatrics, University of Toronto, Toronto, ON, Canada
| | - Shoshana Wodak
- Program in Molecular Structure and Function, Hospital for Sick Children, Toronto, ON, Canada
- Department of Molecular and Medical Genetics, University of Toronto, Toronto, ON, Canada
| | - Stephen W Scherer
- Department of Molecular and Medical Genetics, University of Toronto, Toronto, ON, Canada
- The Centre for Applied Genomics, Hospital for Sick Children, Toronto, ON, Canada
| | - Charles E Schwartz
- J.C. Self Research Institute, Greenwood Genetic Center, Greenwood, SC, USA
| | - Rosanna Weksberg
- Division of Clinical and Metabolic Genetics, Hospital for Sick Children, Toronto, ON, Canada
- Department of Pediatrics, University of Toronto, Toronto, ON, Canada
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20
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Chen YA, Lemire M, Choufani S, Butcher DT, Grafodatskaya D, Zanke BW, Gallinger S, Hudson TJ, Weksberg R. Discovery of cross-reactive probes and polymorphic CpGs in the Illumina Infinium HumanMethylation450 microarray. Epigenetics 2013; 8:203-9. [PMID: 23314698 PMCID: PMC3592906 DOI: 10.4161/epi.23470] [Citation(s) in RCA: 1041] [Impact Index Per Article: 94.6] [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] [Indexed: 12/15/2022] Open
Abstract
DNA methylation, an important type of epigenetic modification in humans, participates in crucial cellular processes, such as embryonic development, X-inactivation, genomic imprinting and chromosome stability. Several platforms have been developed to study genome-wide DNA methylation. Many investigators in the field have chosen the Illumina Infinium HumanMethylation microarray for its ability to reliably assess DNA methylation following sodium bisulfite conversion. Here, we analyzed methylation profiles of 489 adult males and 357 adult females generated by the Infinium HumanMethylation450 microarray. Among the autosomal CpG sites that displayed significant methylation differences between the two sexes, we observed a significant enrichment of cross-reactive probes co-hybridizing to the sex chromosomes with more than 94% sequence identity. This could lead investigators to mistakenly infer the existence of significant autosomal sex-associated methylation. Using sequence identity cutoffs derived from the sex methylation analysis, we concluded that 6% of the array probes can potentially generate spurious signals because of co-hybridization to alternate genomic sequences highly homologous to the intended targets. Additionally, we discovered probes targeting polymorphic CpGs that overlapped SNPs. The methylation levels detected by these probes are simply the reflection of underlying genetic polymorphisms but could be misinterpreted as true signals. The existence of probes that are cross-reactive or of target polymorphic CpGs in the Illumina HumanMethylation microarrays can confound data obtained from such microarrays. Therefore, investigators should exercise caution when significant biological associations are found using these array platforms. A list of all cross-reactive probes and polymorphic CpGs identified by us are annotated in this paper.
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Affiliation(s)
- Yi-an Chen
- Genetics and Genome Biology Program, Hospital for Sick Children, Toronto, ON, Canada
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Chen YA, Choufani S, Grafodatskaya D, Butcher DT, Ferreira JC, Weksberg R. Cross-reactive DNA microarray probes lead to false discovery of autosomal sex-associated DNA methylation. Am J Hum Genet 2012; 91:762-4. [PMID: 23040499 DOI: 10.1016/j.ajhg.2012.06.020] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2012] [Revised: 06/12/2012] [Accepted: 06/12/2012] [Indexed: 01/19/2023] Open
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Chung BHY, Drmic I, Marshall CR, Grafodatskaya D, Carter M, Fernandez BA, Weksberg R, Roberts W, Scherer SW. Phenotypic spectrum associated with duplication of Xp11.22-p11.23 includes Autism Spectrum Disorder. Eur J Med Genet 2011; 54:e516-20. [PMID: 21689796 DOI: 10.1016/j.ejmg.2011.05.008] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2011] [Accepted: 05/26/2011] [Indexed: 12/13/2022]
Abstract
Dup(X)(p11.22-p11.23) has been shown to be associated with intellectual disability (ID, also referred to as mental retardation). Here, we characterize a 4.64 Mb de novo duplication of the same Xp11.22-p11.23 ID region in a female, but for this reference case the diagnosis was Autism Spectrum Disorder (ASD). Besides ASD, she also had very persistent trichotillomania, anxiety symptoms and some non-specific dysmorphic features. We report the detailed clinical features, as well as refine the rearrangement breakpoints of this disease-associated copy number variation region, which encompasses more than 50 genes. We propose that in addition to ID, the phenotypic spectrum associated with dup(X)(p11.22-p11.23) can include ASD, language impairment, and/or other primary psychiatric disorders.
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Affiliation(s)
- Brian H Y Chung
- Genetics and Genome Biology, Research Institute, The Hospital for Sick Children, Toronto, ON, Canada
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23
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Rajendram R, Ferreira JC, Grafodatskaya D, Choufani S, Chiang T, Pu S, Butcher DT, Wodak SJ, Weksberg R. Assessment of methylation level prediction accuracy in methyl-DNA immunoprecipitation and sodium bisulfite based microarray platforms. Epigenetics 2011; 6:410-5. [PMID: 21343703 DOI: 10.4161/epi.6.4.14763] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
In this study, we verified the accuracy of two array methods--methylated DNA immunoprecipitation coupled with CpG island microarrays (MeDIP-CGI-arrays) and sodium bisulfite conversion based microarrays (BC-arrays)--in predicting regional methylation levels as measured by pyrosequencing of bisulfite converted DNA (BC-pyrosequencing). To test the accuracy of these methods we used the Agilent Human CpG island and the Illumina HumanMethylation27 microarrays respectively, and compared microarray outputs to the data from targeted BC-pyrosequencing assays from several genomic regions of corresponding samples. We observed relatively high correlation with BC-pyrosequencing data for both array platforms, R = 0.87 for BC-Array and R = 0.79 for MeDIP-CGI array. However, MeDIP-CGI array were less reliable in predicting intermediate levels of DNA methylation. Several bioinformatics strategies, to ameliorate the performance of the MeDIP-CGI-Arrays did not improve the correlation with BC-pyrosequencing data. The high scalability, low cost and simpler analysis of BC-arrays, together with the recent extended coverage may make them a more versatile methylation analysis tool.
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Affiliation(s)
- Rageen Rajendram
- Program in Biological Sciences, University of Toronto, Ontario, Canada
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Cheung AYL, Horvath LM, Grafodatskaya D, Pasceri P, Weksberg R, Hotta A, Carrel L, Ellis J. Isolation of MECP2-null Rett Syndrome patient hiPS cells and isogenic controls through X-chromosome inactivation. Hum Mol Genet 2011; 20:2103-15. [PMID: 21372149 PMCID: PMC3090191 DOI: 10.1093/hmg/ddr093] [Citation(s) in RCA: 199] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Rett syndrome (RTT) is a neurodevelopmental autism spectrum disorder that affects girls due primarily to mutations in the gene encoding methyl-CpG binding protein 2 (MECP2). The majority of RTT patients carry missense and nonsense mutations leading to a hypomorphic MECP2, while null mutations leading to the complete absence of a functional protein are rare. MECP2 is an X-linked gene subject to random X-chromosome inactivation resulting in mosaic expression of mutant MECP2. The lack of human brain tissue motivates the need for alternative human cellular models to study RTT. Here we report the characterization of a MECP2 mutation in a classic female RTT patient involving rearrangements that remove exons 3 and 4 creating a functionally null mutation. To generate human neuron models of RTT, we isolated human induced pluripotent stem (hiPS) cells from RTT patient fibroblasts. RTT-hiPS cells retained the MECP2 mutation, are pluripotent and fully reprogrammed, and retained an inactive X-chromosome in a nonrandom pattern. Taking advantage of the latter characteristic, we obtained a pair of isogenic wild-type and mutant MECP2 expressing RTT-hiPS cell lines that retained this MECP2 expression pattern upon differentiation into neurons. Phenotypic analysis of mutant RTT-hiPS cell-derived neurons demonstrated a reduction in soma size compared with the isogenic control RTT-hiPS cell-derived neurons from the same RTT patient. Analysis of isogenic control and mutant hiPS cell-derived neurons represents a promising source for understanding the pathogenesis of RTT and the role of MECP2 in human neurons.
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Affiliation(s)
- Aaron Y L Cheung
- Program in Developmental and Stem Cell Biology, The Hospital for Sick Children, Toronto, Ontario, Canada
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Choufani S, Shapiro JS, Susiarjo M, Butcher DT, Grafodatskaya D, Lou Y, Ferreira JC, Pinto D, Scherer SW, Shaffer LG, Coullin P, Caniggia I, Beyene J, Slim R, Bartolomei MS, Weksberg R. A novel approach identifies new differentially methylated regions (DMRs) associated with imprinted genes. Genome Res 2011; 21:465-76. [PMID: 21324877 DOI: 10.1101/gr.111922.110] [Citation(s) in RCA: 90] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Imprinted genes are critical for normal human growth and neurodevelopment. They are characterized by differentially methylated regions (DMRs) of DNA that confer parent of origin-specific transcription. We developed a new strategy to identify imprinted gene-associated DMRs. Using genome-wide methylation profiling of sodium bisulfite modified DNA from normal human tissues of biparental origin, candidate DMRs were identified by selecting CpGs with methylation levels consistent with putative allelic differential methylation. In parallel, the methylation profiles of tissues of uniparental origin, i.e., paternally-derived androgenetic complete hydatidiform moles (AnCHMs), and maternally-derived mature cystic ovarian teratoma (MCT), were examined and then used to identify CpGs with parent of origin-specific DNA methylation. With this approach, we found known DMRs associated with imprinted genomic regions as well as new DMRs for known imprinted genes, NAP1L5 and ZNF597, and novel candidate imprinted genes. The paternally methylated DMR for one candidate, AXL, a receptor tyrosine kinase, was also validated in experiments with mouse embryos that demonstrated Axl was expressed preferentially from the maternal allele in a DNA methylation-dependent manner.
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Affiliation(s)
- Sanaa Choufani
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario M5G 1X8, Canada
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Grafodatskaya D, Chung B, Szatmari P, Weksberg R. Autism spectrum disorders and epigenetics. J Am Acad Child Adolesc Psychiatry 2010; 49:794-809. [PMID: 20643313 DOI: 10.1016/j.jaac.2010.05.005] [Citation(s) in RCA: 135] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/22/2009] [Revised: 05/05/2010] [Accepted: 05/10/2010] [Indexed: 10/18/2022]
Abstract
OBJECTIVE Current research suggests that the causes of autism spectrum disorders (ASD) are multifactorial and include both genetic and environmental factors. Several lines of evidence suggest that epigenetics also plays an important role in ASD etiology and that it might, in fact, integrate genetic and environmental influences to dysregulate neurodevelopmental processes. The objective of this review is to illustrate how epigenetic modifications that are known to alter gene expression without changing primary DNA sequence may play a role in the etiology of ASD. METHOD In this review, we summarize current knowledge about epigenetic modifications to genes and genomic regions possibly involved in the etiology of ASD. RESULTS Several genetic syndromes comorbid with ASD, which include Rett, Fragile X, Prader-Willi, Angelman, and CHARGE (Coloboma of the eye, Heart defects, Atresia of the nasal choanae, Retardation of growth and/or development, Genital and/or urinary abnormalities, and Ear abnormalities and deafness), all demonstrate dysregulation of epigenetic marks or epigenetic mechanisms. We report also on genes or genomic regions exhibiting abnormal epigenetic regulation in association with either syndromic (15q11-13 maternal duplication) or nonsyndromic forms of ASD. Finally, we discuss the state of current knowledge regarding the etiologic role of environmental factors linked to both the development of ASD and epigenetic dysregulation. CONCLUSION Data reviewed in this article highlight a variety of situations in which epigenetic dysregulation is associated with the development of ASD, thereby supporting a role for epigenetics in the multifactorial etiologies of ASD.
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Grafodatskaya D, Choufani S, Ferreira J, Butcher D, Lou Y, Zhao C, Scherer S, Weksberg R. EBV transformation and cell culturing destabilizes DNA methylation in human lymphoblastoid cell lines. Genomics 2010; 95:73-83. [DOI: 10.1016/j.ygeno.2009.12.001] [Citation(s) in RCA: 92] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2009] [Revised: 11/25/2009] [Accepted: 12/01/2009] [Indexed: 11/29/2022]
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Grafodatskaya D, Rens W, Wallis MC, Trifonov V, O'Brien PCM, Clarke O, Graves JAM, Ferguson-Smith MA. Search for the sex-determining switch in monotremes: mapping WT1, SF1, LHX1, LHX2, FGF9, WNT4, RSPO1 and GATA4 in platypus. Chromosome Res 2007; 15:777-85. [PMID: 17717721 DOI: 10.1007/s10577-007-1161-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2007] [Revised: 05/29/2007] [Accepted: 05/29/2007] [Indexed: 10/22/2022]
Abstract
The duck-billed platypus has five pairs of sex chromosomes, but there is no information about the primary sex-determining switch in this species. As there is no apparent SRY orthologue in platypus, another gene must acquire the function of a key regulator of the gonadal male or female fate. SOX9 was ruled out from being this key regulator as it maps to an autosome in platypus. To check whether other genes in mammalian gonadogenesis could be the primary switch in monotremes, we have mapped a number of candidates in platypus. We report here the autosomal location of WT1, SF1, LHX1, LHX9, FGF9, WNT4 and RSPO1 in platypus, thus excluding these from being key regulators of sex determination in this species. We found that GATA4 maps to sex chromosomes Y1 and X2; however, it lies in the pairing region shown by chromosome painting to be homologous, so is unlikely to be either male-specific or differentially dosed in male and female.
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Affiliation(s)
- Daria Grafodatskaya
- Cambridge Resource Centre for Comparative Genomics, Department of Veterinary Medicine, University of Cambridge, Cambridge, CB3 OES, UK
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