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Krzyzewska IM, Maas SM, Henneman P, Lip KVD, Venema A, Baranano K, Chassevent A, Aref-Eshghi E, van Essen AJ, Fukuda T, Ikeda H, Jacquemont M, Kim HG, Labalme A, Lewis SME, Lesca G, Madrigal I, Mahida S, Matsumoto N, Rabionet R, Rajcan-Separovic E, Qiao Y, Sadikovic B, Saitsu H, Sweetser DA, Alders M, Mannens MMAM. A genome-wide DNA methylation signature for SETD1B-related syndrome. Clin Epigenetics 2019; 11:156. [PMID: 31685013 PMCID: PMC6830011 DOI: 10.1186/s13148-019-0749-3] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [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: 07/15/2019] [Accepted: 09/22/2019] [Indexed: 01/02/2023] Open
Abstract
SETD1B is a component of a histone methyltransferase complex that specifically methylates Lys-4 of histone H3 (H3K4) and is responsible for the epigenetic control of chromatin structure and gene expression. De novo microdeletions encompassing this gene as well as de novo missense mutations were previously linked to syndromic intellectual disability (ID). Here, we identify a specific hypermethylation signature associated with loss of function mutations in the SETD1B gene which may be used as an epigenetic marker supporting the diagnosis of syndromic SETD1B-related diseases. We demonstrate the clinical utility of this unique epi-signature by reclassifying previously identified SETD1B VUS (variant of uncertain significance) in two patients.
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Affiliation(s)
- I M Krzyzewska
- Amsterdam UMC, Department of Clinical Genetics, Genome Diagnostics laboratory Amsterdam, Reproduction & Development, University of Amsterdam, Meibergdreef 9, Amsterdam, The Netherlands
| | - S M Maas
- Amsterdam UMC, Department of Pediatrics, University of Amsterdam, Meibergdreef 9, Amsterdam, The Netherlands
| | - P Henneman
- Amsterdam UMC, Department of Clinical Genetics, Genome Diagnostics laboratory Amsterdam, Reproduction & Development, University of Amsterdam, Meibergdreef 9, Amsterdam, The Netherlands
| | - K V D Lip
- Amsterdam UMC, Department of Clinical Genetics, Genome Diagnostics laboratory Amsterdam, Reproduction & Development, University of Amsterdam, Meibergdreef 9, Amsterdam, The Netherlands
| | - A Venema
- Amsterdam UMC, Department of Clinical Genetics, Genome Diagnostics laboratory Amsterdam, Reproduction & Development, University of Amsterdam, Meibergdreef 9, Amsterdam, The Netherlands
| | - K Baranano
- Kennedy Krieger Institute, Department of Neurogenetics, 801 N. Broadway, Rm 564, Baltimore, MD, 21205, USA
| | - A Chassevent
- Kennedy Krieger Institute, Department of Neurogenetics, 801 N. Broadway, Rm 564, Baltimore, MD, 21205, USA
| | - E Aref-Eshghi
- Department of Pathology and Laboratory Medicine, Western University, 800 Commissioner's Road E, London, ON, N6A 5W9, Canada
| | - A J van Essen
- University Medical Centre Groningen, University of Groningen, Department of Medical Genetics, Hanzeplein 1, 9713 GZ, Groningen, The Netherlands
| | - T Fukuda
- Department of Pediatrics, Hamamatsu University School of Medicine, 1-20-1 Handayama, Higashi-ku, Hamamatsu, 431-3192, Japan
| | - H Ikeda
- National Epilepsy Centre, NHO, Shizuoka Institute of Epilepsy and Neurological Disorders, 886 Urushiyama, Aoi-ku, Shizuoka, 420-8688, Japan
| | - M Jacquemont
- Department of medical genetics, CHU La Reunion-Groupe Hospitalier Sud Reunion, La Reunion, France
| | - H-G Kim
- Neurological Disorder Center Qatar Biomedical Research Institute, Hamad Bin Khalifa University, Doha, Qatar
| | - A Labalme
- Department of medical genetics, Hospices Civils de Lyon, Bron, France
| | - S M E Lewis
- Department of Medical Genetics, Children's & Women's Health Centre of British Columbia University of British Columbia, C234-4500 Oak Street, Vancouver, British Columbia, V6H 3N1, Canada
| | - G Lesca
- Department of medical genetics, Hospices Civils de Lyon, Bron, France
| | - I Madrigal
- Biochemistry and Molecular Genetics Service, Hospital Clínic, Institut d'Investigacions Biomèdiques August Pi I Sunyer (IDIBAPS), Center for Biomedical Network Research on Rare Diseases (CIBERER), Barcelona, Spain
| | - S Mahida
- Kennedy Krieger Institute, Department of Neurogenetics, 801 N. Broadway, Rm 564, Baltimore, MD, 21205, USA
| | - N Matsumoto
- Department of Human Genetics, Graduate School of Medicine, Yokohama City University, Fukuura 3-9, Kanazawa-ku, Yokohama, 236-0004, Japan
| | - R Rabionet
- Department of Genetics, Microbiology and Statistics, Faculty of Biology, University of Barcelona, av diagonal 643, 08028, Barcelona, Spain
| | - E Rajcan-Separovic
- Department of Medical Genetics, Children's & Women's Health Centre of British Columbia University of British Columbia, C234-4500 Oak Street, Vancouver, British Columbia, V6H 3N1, Canada
| | - Y Qiao
- Department of Medical Genetics, Children's & Women's Health Centre of British Columbia University of British Columbia, C234-4500 Oak Street, Vancouver, British Columbia, V6H 3N1, Canada
| | - B Sadikovic
- Department of Pathology and Laboratory Medicine, Western University, 800 Commissioner's Road E, London, ON, N6A 5W9, Canada
| | - H Saitsu
- Department of Biochemistry, Hamamatsu University School of Medicine, 1-20-1 Handayama, Higashi-ku, Hamamatsu, 431-3192, Japan
| | - D A Sweetser
- MassGeneral Hospital, Division of Medical Genetics and Metabolism, 175 Cambridge St, Suite 500, Boston, Massachusetts, 02114, USA
| | - M Alders
- Amsterdam UMC, Department of Clinical Genetics, Genome Diagnostics laboratory Amsterdam, Reproduction & Development, University of Amsterdam, Meibergdreef 9, Amsterdam, The Netherlands.
| | - M M A M Mannens
- Amsterdam UMC, Department of Clinical Genetics, Genome Diagnostics laboratory Amsterdam, Reproduction & Development, University of Amsterdam, Meibergdreef 9, Amsterdam, The Netherlands
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Qiao Y, Tyson C, Hrynchak M, Lopez-Rangel E, Hildebrand J, Martell S, Fawcett C, Kasmara L, Calli K, Harvard C, Liu X, Holden JJA, Lewis SME, Rajcan-Separovic E. Clinical application of 2.7M Cytogenetics array for CNV detection in subjects with idiopathic autism and/or intellectual disability. Clin Genet 2012; 83:145-54. [PMID: 22369279 DOI: 10.1111/j.1399-0004.2012.01860.x] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Higher resolution whole-genome arrays facilitate the identification of smaller copy number variations (CNVs) and their integral genes contributing to autism and/or intellectual disability (ASD/ID). Our study describes the use of one of the highest resolution arrays, the Affymetrix(®) Cytogenetics 2.7M array, coupled with quantitative multiplex polymerase chain reaction (PCR) of short fluorescent fragments (QMPSF) for detection and validation of small CNVs. We studied 82 subjects with ASD and ID in total (30 in the validation and 52 in the application cohort) and detected putatively pathogenic CNVs in 6/52 cases from the application cohort. This included a 130-kb maternal duplication spanning exons 64-79 of the DMD gene which was found in a 3-year-old boy manifesting autism and mild neuromotor delays. Other pathogenic CNVs involved 4p14, 12q24.31, 14q32.31, 15q13.2-13.3, and 17p13.3. We established the optimal experimental conditions which, when applied to select small CNVs for QMPSF confirmation, reduced the false positive rate from 60% to 25%. Our work suggests that selection of small CNVs based on the function of integral genes, followed by review of array experimental parameters resulting in highest confirmation rate using multiplex PCR, may enhance the usefulness of higher resolution platforms for ASD and ID gene discovery.
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Affiliation(s)
- Y Qiao
- BC Child and Family Research Institute, Vancouver, BC, Canada
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