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Verwilt J, Hellemans J, Sante T, Mestdagh P, Vandesompele J. Evaluation of efficiency and sensitivity of 1D and 2D sample pooling strategies for SARS-CoV-2 RT-qPCR screening purposes. Sci Rep 2022; 12:6603. [PMID: 35459775 PMCID: PMC9033859 DOI: 10.1038/s41598-022-10581-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Accepted: 04/06/2022] [Indexed: 11/22/2022] Open
Abstract
To increase the throughput, lower the cost, and save scarce test reagents, laboratories can pool patient samples before SARS-CoV-2 RT-qPCR testing. While different sample pooling methods have been proposed and effectively implemented in some laboratories, no systematic and large-scale evaluations exist using real-life quantitative data gathered throughout the different epidemiological stages. Here, we use anonymous data from 9673 positive cases to model, simulate and compare 1D and 2D pooling strategies. We show that the optimal choice of pooling method and pool size is an intricate decision with a testing population-dependent efficiency-sensitivity trade-off and present an online tool to provide the reader with custom real-time 1D pooling strategy recommendations.
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Affiliation(s)
- Jasper Verwilt
- OncoRNALab, Cancer Research Institute Ghent, Corneel Heymanslaan 10, 9000, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Corneel Heymanslaan 10, 9000, Ghent, Belgium
- Center for Medical Genetics, Ghent University, Corneel Heymanslaan 10, 9000, Ghent, Belgium
| | - Jan Hellemans
- Biogazelle, Technologiepark 82, 9052, Zwijnaarde, Belgium
| | - Tom Sante
- Department of Biomolecular Medicine, Ghent University, Corneel Heymanslaan 10, 9000, Ghent, Belgium
- Center for Medical Genetics, Ghent University, Corneel Heymanslaan 10, 9000, Ghent, Belgium
| | - Pieter Mestdagh
- OncoRNALab, Cancer Research Institute Ghent, Corneel Heymanslaan 10, 9000, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Corneel Heymanslaan 10, 9000, Ghent, Belgium
- Center for Medical Genetics, Ghent University, Corneel Heymanslaan 10, 9000, Ghent, Belgium
- Biogazelle, Technologiepark 82, 9052, Zwijnaarde, Belgium
| | - Jo Vandesompele
- OncoRNALab, Cancer Research Institute Ghent, Corneel Heymanslaan 10, 9000, Ghent, Belgium.
- Department of Biomolecular Medicine, Ghent University, Corneel Heymanslaan 10, 9000, Ghent, Belgium.
- Center for Medical Genetics, Ghent University, Corneel Heymanslaan 10, 9000, Ghent, Belgium.
- Biogazelle, Technologiepark 82, 9052, Zwijnaarde, Belgium.
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Van der Linden M, Raman L, Vander Trappen A, Dheedene A, De Smet M, Sante T, Creytens D, Lievens Y, Menten B, Van Dorpe J, Van Roy N. Detection of Copy Number Alterations by Shallow Whole-Genome Sequencing of Formalin-Fixed, Paraffin-Embedded Tumor Tissue. Arch Pathol Lab Med 2019; 144:974-981. [PMID: 31846367 DOI: 10.5858/arpa.2019-0010-oa] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
CONTEXT.— In routine clinical practice, tumor tissue is stored in formalin-fixed, paraffin-embedded blocks. However, the use of formalin-fixed, paraffin-embedded tissue for genome analysis is challenged by poorer DNA quality and quantity. Although several studies have reported genome-wide massive parallel sequencing applied on formalin-fixed, paraffin-embedded samples for mutation analysis, copy number analysis is not yet commonly performed. OBJECTIVE.— To evaluate the use of formalin-fixed, paraffin-embedded tissue for copy number alteration detection using shallow whole-genome sequencing, more generally referred to as copy number variation sequencing. DESIGN.— We selected samples from 21 patients, covering a range of different tumor entities. The performance of copy number detection was compared across 3 setups: array comparative genomic hybridization in combination with fresh material; copy number variation sequencing on fresh material; and copy number variation sequencing on formalin-fixed, paraffin-embedded material. RESULTS.— Very similar copy number profiles between paired samples were obtained. Although formalin-fixed, paraffin-embedded profiles often displayed more noise, detected copy numbers seemed equally reliable if the tumor fraction was at least 20%. CONCLUSIONS.— Copy number variation sequencing of formalin-fixed, paraffin-embedded material represents a trustworthy method. It is very likely that copy number variation sequencing of routinely obtained biopsy material will become important for individual patient care and research. Moreover, the basic technology needed for copy number variation sequencing is present in most molecular diagnostics laboratories.
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Affiliation(s)
- Malaïka Van der Linden
- From the Department of Pathology (Ms Van der Linden, Mr Raman, and Drs Creytens and Van Dorpe), the Center for Medical Genetics Ghent (Messrs Vander Trappen and De Smet and Drs Dheedene, Sante, Menten and Van Roy), and the Department of Radiation Oncology (Dr Lievens), Ghent University Hospital, Ghent, Belgium; and Cancer Research Institute Ghent, Ghent, Belgium (Ms Van der Linden and Drs Creytens, Lievens, Menten, Van Dorpe, and Van Roy)
| | - Lennart Raman
- From the Department of Pathology (Ms Van der Linden, Mr Raman, and Drs Creytens and Van Dorpe), the Center for Medical Genetics Ghent (Messrs Vander Trappen and De Smet and Drs Dheedene, Sante, Menten and Van Roy), and the Department of Radiation Oncology (Dr Lievens), Ghent University Hospital, Ghent, Belgium; and Cancer Research Institute Ghent, Ghent, Belgium (Ms Van der Linden and Drs Creytens, Lievens, Menten, Van Dorpe, and Van Roy)
| | - Ansel Vander Trappen
- From the Department of Pathology (Ms Van der Linden, Mr Raman, and Drs Creytens and Van Dorpe), the Center for Medical Genetics Ghent (Messrs Vander Trappen and De Smet and Drs Dheedene, Sante, Menten and Van Roy), and the Department of Radiation Oncology (Dr Lievens), Ghent University Hospital, Ghent, Belgium; and Cancer Research Institute Ghent, Ghent, Belgium (Ms Van der Linden and Drs Creytens, Lievens, Menten, Van Dorpe, and Van Roy)
| | - Annelies Dheedene
- From the Department of Pathology (Ms Van der Linden, Mr Raman, and Drs Creytens and Van Dorpe), the Center for Medical Genetics Ghent (Messrs Vander Trappen and De Smet and Drs Dheedene, Sante, Menten and Van Roy), and the Department of Radiation Oncology (Dr Lievens), Ghent University Hospital, Ghent, Belgium; and Cancer Research Institute Ghent, Ghent, Belgium (Ms Van der Linden and Drs Creytens, Lievens, Menten, Van Dorpe, and Van Roy)
| | - Matthias De Smet
- From the Department of Pathology (Ms Van der Linden, Mr Raman, and Drs Creytens and Van Dorpe), the Center for Medical Genetics Ghent (Messrs Vander Trappen and De Smet and Drs Dheedene, Sante, Menten and Van Roy), and the Department of Radiation Oncology (Dr Lievens), Ghent University Hospital, Ghent, Belgium; and Cancer Research Institute Ghent, Ghent, Belgium (Ms Van der Linden and Drs Creytens, Lievens, Menten, Van Dorpe, and Van Roy)
| | - Tom Sante
- From the Department of Pathology (Ms Van der Linden, Mr Raman, and Drs Creytens and Van Dorpe), the Center for Medical Genetics Ghent (Messrs Vander Trappen and De Smet and Drs Dheedene, Sante, Menten and Van Roy), and the Department of Radiation Oncology (Dr Lievens), Ghent University Hospital, Ghent, Belgium; and Cancer Research Institute Ghent, Ghent, Belgium (Ms Van der Linden and Drs Creytens, Lievens, Menten, Van Dorpe, and Van Roy)
| | - David Creytens
- From the Department of Pathology (Ms Van der Linden, Mr Raman, and Drs Creytens and Van Dorpe), the Center for Medical Genetics Ghent (Messrs Vander Trappen and De Smet and Drs Dheedene, Sante, Menten and Van Roy), and the Department of Radiation Oncology (Dr Lievens), Ghent University Hospital, Ghent, Belgium; and Cancer Research Institute Ghent, Ghent, Belgium (Ms Van der Linden and Drs Creytens, Lievens, Menten, Van Dorpe, and Van Roy)
| | - Yolande Lievens
- From the Department of Pathology (Ms Van der Linden, Mr Raman, and Drs Creytens and Van Dorpe), the Center for Medical Genetics Ghent (Messrs Vander Trappen and De Smet and Drs Dheedene, Sante, Menten and Van Roy), and the Department of Radiation Oncology (Dr Lievens), Ghent University Hospital, Ghent, Belgium; and Cancer Research Institute Ghent, Ghent, Belgium (Ms Van der Linden and Drs Creytens, Lievens, Menten, Van Dorpe, and Van Roy)
| | - Björn Menten
- From the Department of Pathology (Ms Van der Linden, Mr Raman, and Drs Creytens and Van Dorpe), the Center for Medical Genetics Ghent (Messrs Vander Trappen and De Smet and Drs Dheedene, Sante, Menten and Van Roy), and the Department of Radiation Oncology (Dr Lievens), Ghent University Hospital, Ghent, Belgium; and Cancer Research Institute Ghent, Ghent, Belgium (Ms Van der Linden and Drs Creytens, Lievens, Menten, Van Dorpe, and Van Roy)
| | - Jo Van Dorpe
- From the Department of Pathology (Ms Van der Linden, Mr Raman, and Drs Creytens and Van Dorpe), the Center for Medical Genetics Ghent (Messrs Vander Trappen and De Smet and Drs Dheedene, Sante, Menten and Van Roy), and the Department of Radiation Oncology (Dr Lievens), Ghent University Hospital, Ghent, Belgium; and Cancer Research Institute Ghent, Ghent, Belgium (Ms Van der Linden and Drs Creytens, Lievens, Menten, Van Dorpe, and Van Roy)
| | - Nadine Van Roy
- From the Department of Pathology (Ms Van der Linden, Mr Raman, and Drs Creytens and Van Dorpe), the Center for Medical Genetics Ghent (Messrs Vander Trappen and De Smet and Drs Dheedene, Sante, Menten and Van Roy), and the Department of Radiation Oncology (Dr Lievens), Ghent University Hospital, Ghent, Belgium; and Cancer Research Institute Ghent, Ghent, Belgium (Ms Van der Linden and Drs Creytens, Lievens, Menten, Van Dorpe, and Van Roy)
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Hemelsoet DM, Vanlander AV, Smet J, Vantroys E, Acou M, Goethals I, Sante T, Seneca S, Menten B, Van Coster R. Leigh syndrome followed by parkinsonism in an adult with homozygous c.626C>T mutation in MTFMT. Neurol Genet 2018; 4:e298. [PMID: 30569017 PMCID: PMC6278240 DOI: 10.1212/nxg.0000000000000298] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/06/2018] [Accepted: 10/15/2018] [Indexed: 01/30/2023]
Abstract
Objective To report the clinical, radiologic, biochemical, and molecular characteristics in a 46-year-old participant with adult-onset Leigh syndrome (LS), followed by parkinsonism. Methods Case description with diagnostic workup included blood and CSF analysis, skeletal muscle investigations, blue native polyacrylamide gel electrophoresis, whole exome sequencing targeting nuclear genes involved in mitochondrial transcription and translation, cerebral MRI, 123I-FP-CIT brain single-photon emission computed tomography (SPECT), and C-11 raclopride positron emission tomography (PET). Results The participant was found to have a defect in the oxidative phosphorylation caused by a c.626C>T mutation in the gene coding for mitochondrial methionyl-tRNA formyltransferase (MTFMT), which is a pathogenic mutation affecting intramitochondrial protein translation. The proband had a normal concentration of lactate in blood and no abnormal microscopic findings in skeletal muscle. Cerebral MRI showed bilateral lesions in the striatum, mesencephalon, pons, and medial thalamus. Lactate concentration in CSF was increased. FP-CIT SPECT and C-11 raclopride PET demonstrated a defect in the dopaminergic system. Conclusions We report on a case with adult-onset LS related to a MTFMT mutation. Two years after the onset of symptoms of LS, the proband developed a parkinson-like disease. The c.626C>T mutation is the most common pathogenic mutation found in 22 patients reported earlier in the literature with a defect in MTFMT. The age of the previously reported cases varied between 14 months and 24 years. Our report expands the phenotypical spectrum of MTFMT-related neurologic disease and provides clinical evidence for involvement of MTFMT in extrapyramidal syndromes.
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Affiliation(s)
- Dimitri M Hemelsoet
- Department of Neurology (D.M.H.), Ghent University Hospital; Department of Pediatrics (A.V.V., J.S., E.V., R.V.C.), Division of Pediatric Neurology and Metabolism, Ghent University Hospital; Department of Radiology (M.A.), Ghent University Hospital; Department of Nuclear Medicine (I.G.), Ghent University Hospital; Center for Medical Genetics Ghent (T.S., B.M.), Ghent University, Belgium; and Center for Medical Genetics (S.S.), UZ Brussel and Reproduction Genetics and Regenerative Medicine, Vrije Universiteit Brussel, Brussels, Belgium
| | - Arnaud V Vanlander
- Department of Neurology (D.M.H.), Ghent University Hospital; Department of Pediatrics (A.V.V., J.S., E.V., R.V.C.), Division of Pediatric Neurology and Metabolism, Ghent University Hospital; Department of Radiology (M.A.), Ghent University Hospital; Department of Nuclear Medicine (I.G.), Ghent University Hospital; Center for Medical Genetics Ghent (T.S., B.M.), Ghent University, Belgium; and Center for Medical Genetics (S.S.), UZ Brussel and Reproduction Genetics and Regenerative Medicine, Vrije Universiteit Brussel, Brussels, Belgium
| | - Joél Smet
- Department of Neurology (D.M.H.), Ghent University Hospital; Department of Pediatrics (A.V.V., J.S., E.V., R.V.C.), Division of Pediatric Neurology and Metabolism, Ghent University Hospital; Department of Radiology (M.A.), Ghent University Hospital; Department of Nuclear Medicine (I.G.), Ghent University Hospital; Center for Medical Genetics Ghent (T.S., B.M.), Ghent University, Belgium; and Center for Medical Genetics (S.S.), UZ Brussel and Reproduction Genetics and Regenerative Medicine, Vrije Universiteit Brussel, Brussels, Belgium
| | - Elise Vantroys
- Department of Neurology (D.M.H.), Ghent University Hospital; Department of Pediatrics (A.V.V., J.S., E.V., R.V.C.), Division of Pediatric Neurology and Metabolism, Ghent University Hospital; Department of Radiology (M.A.), Ghent University Hospital; Department of Nuclear Medicine (I.G.), Ghent University Hospital; Center for Medical Genetics Ghent (T.S., B.M.), Ghent University, Belgium; and Center for Medical Genetics (S.S.), UZ Brussel and Reproduction Genetics and Regenerative Medicine, Vrije Universiteit Brussel, Brussels, Belgium
| | - Marjan Acou
- Department of Neurology (D.M.H.), Ghent University Hospital; Department of Pediatrics (A.V.V., J.S., E.V., R.V.C.), Division of Pediatric Neurology and Metabolism, Ghent University Hospital; Department of Radiology (M.A.), Ghent University Hospital; Department of Nuclear Medicine (I.G.), Ghent University Hospital; Center for Medical Genetics Ghent (T.S., B.M.), Ghent University, Belgium; and Center for Medical Genetics (S.S.), UZ Brussel and Reproduction Genetics and Regenerative Medicine, Vrije Universiteit Brussel, Brussels, Belgium
| | - Ingeborg Goethals
- Department of Neurology (D.M.H.), Ghent University Hospital; Department of Pediatrics (A.V.V., J.S., E.V., R.V.C.), Division of Pediatric Neurology and Metabolism, Ghent University Hospital; Department of Radiology (M.A.), Ghent University Hospital; Department of Nuclear Medicine (I.G.), Ghent University Hospital; Center for Medical Genetics Ghent (T.S., B.M.), Ghent University, Belgium; and Center for Medical Genetics (S.S.), UZ Brussel and Reproduction Genetics and Regenerative Medicine, Vrije Universiteit Brussel, Brussels, Belgium
| | - Tom Sante
- Department of Neurology (D.M.H.), Ghent University Hospital; Department of Pediatrics (A.V.V., J.S., E.V., R.V.C.), Division of Pediatric Neurology and Metabolism, Ghent University Hospital; Department of Radiology (M.A.), Ghent University Hospital; Department of Nuclear Medicine (I.G.), Ghent University Hospital; Center for Medical Genetics Ghent (T.S., B.M.), Ghent University, Belgium; and Center for Medical Genetics (S.S.), UZ Brussel and Reproduction Genetics and Regenerative Medicine, Vrije Universiteit Brussel, Brussels, Belgium
| | - Sara Seneca
- Department of Neurology (D.M.H.), Ghent University Hospital; Department of Pediatrics (A.V.V., J.S., E.V., R.V.C.), Division of Pediatric Neurology and Metabolism, Ghent University Hospital; Department of Radiology (M.A.), Ghent University Hospital; Department of Nuclear Medicine (I.G.), Ghent University Hospital; Center for Medical Genetics Ghent (T.S., B.M.), Ghent University, Belgium; and Center for Medical Genetics (S.S.), UZ Brussel and Reproduction Genetics and Regenerative Medicine, Vrije Universiteit Brussel, Brussels, Belgium
| | - Bjorn Menten
- Department of Neurology (D.M.H.), Ghent University Hospital; Department of Pediatrics (A.V.V., J.S., E.V., R.V.C.), Division of Pediatric Neurology and Metabolism, Ghent University Hospital; Department of Radiology (M.A.), Ghent University Hospital; Department of Nuclear Medicine (I.G.), Ghent University Hospital; Center for Medical Genetics Ghent (T.S., B.M.), Ghent University, Belgium; and Center for Medical Genetics (S.S.), UZ Brussel and Reproduction Genetics and Regenerative Medicine, Vrije Universiteit Brussel, Brussels, Belgium
| | - Rudy Van Coster
- Department of Neurology (D.M.H.), Ghent University Hospital; Department of Pediatrics (A.V.V., J.S., E.V., R.V.C.), Division of Pediatric Neurology and Metabolism, Ghent University Hospital; Department of Radiology (M.A.), Ghent University Hospital; Department of Nuclear Medicine (I.G.), Ghent University Hospital; Center for Medical Genetics Ghent (T.S., B.M.), Ghent University, Belgium; and Center for Medical Genetics (S.S.), UZ Brussel and Reproduction Genetics and Regenerative Medicine, Vrije Universiteit Brussel, Brussels, Belgium
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De Wilde B, Beckers A, Lindner S, Kristina A, De Preter K, Depuydt P, Mestdagh P, Sante T, Lefever S, Hertwig F, Peng Z, Shi LM, Lee S, Vandermarliere E, Martens L, Menten B, Schramm A, Fischer M, Schulte J, Vandesompele J, Speleman F. The mutational landscape of MYCN, Lin28b and ALKF1174L driven murine neuroblastoma mimics human disease. Oncotarget 2017; 9:8334-8349. [PMID: 29492199 PMCID: PMC5823580 DOI: 10.18632/oncotarget.23614] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [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] [Received: 03/01/2017] [Accepted: 10/28/2017] [Indexed: 12/27/2022] Open
Abstract
Genetically engineered mouse models have proven to be essential tools for unraveling fundamental aspects of cancer biology and for testing novel therapeutic strategies. To optimally serve these goals, it is essential that the mouse model faithfully recapitulates the human disease. Recently, novel mouse models for neuroblastoma have been developed. Here, we report on the further genomic characterization through exome sequencing and DNA copy number analysis of four of the currently available murine neuroblastoma model systems (ALK, Th-MYCN, Dbh-MYCN and Lin28b). The murine tumors revealed a low number of genomic alterations – in keeping with human neuroblastoma - and a positive correlation of the number of genetic lesions with the time to onset of tumor formation was observed. Gene copy number alterations are the hallmark of both murine and human disease and frequently affect syntenic genomic regions. Despite low mutational load, the genes mutated in murine disease were found to be enriched for genes mutated in human disease. Taken together, our study further supports the validity of the tested mouse models for mechanistic and preclinical studies of human neuroblastoma.
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Affiliation(s)
- Bram De Wilde
- Center for Medical Genetics, Ghent University, Ghent, Belgium.,Cancer Research Institute Ghent, Ghent University, Ghent, Belgium
| | | | - Sven Lindner
- Department of Pediatric Oncology and Hematology, University Children's Hospital, Essen, Germany
| | - Althoff Kristina
- Department of Pediatric Oncology and Hematology, University Children's Hospital, Essen, Germany
| | - Katleen De Preter
- Center for Medical Genetics, Ghent University, Ghent, Belgium.,Cancer Research Institute Ghent, Ghent University, Ghent, Belgium
| | - Pauline Depuydt
- Center for Medical Genetics, Ghent University, Ghent, Belgium.,Cancer Research Institute Ghent, Ghent University, Ghent, Belgium
| | - Pieter Mestdagh
- Center for Medical Genetics, Ghent University, Ghent, Belgium.,Cancer Research Institute Ghent, Ghent University, Ghent, Belgium
| | - Tom Sante
- Center for Medical Genetics, Ghent University, Ghent, Belgium
| | - Steve Lefever
- Center for Medical Genetics, Ghent University, Ghent, Belgium.,Cancer Research Institute Ghent, Ghent University, Ghent, Belgium
| | - Falk Hertwig
- Department of Experimental Pediatric Oncology, University Children's Hospital of Cologne, Cologne, Germany.,Center for Molecular Medicine Cologne, University of Cologne, Cologne, Germany
| | - Zhiyu Peng
- BGI-Shenzhen, Bei Shan Industrial Zone, Yantian District, Shenzhen, Guangdong, China
| | - Le-Ming Shi
- Center for Pharmacogenomics and Fudan-Zhangjiang Center for Clinical Genomics, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University, Shanghai, China
| | - Sangkyun Lee
- Department of Computer Science, Artificial Intelligence Group, TU Dortmund, Dortmund, Germany
| | - Elien Vandermarliere
- Medical Biotechnology Center, VIB, Ghent, Belgium.,Department of Biochemistry, Ghent University, Ghent, Belgium
| | - Lennart Martens
- Medical Biotechnology Center, VIB, Ghent, Belgium.,Department of Biochemistry, Ghent University, Ghent, Belgium
| | - Björn Menten
- Center for Medical Genetics, Ghent University, Ghent, Belgium
| | - Alexander Schramm
- Department of Pediatric Oncology and Hematology, University Children's Hospital, Essen, Germany
| | - Matthias Fischer
- Department of Experimental Pediatric Oncology, University Children's Hospital of Cologne, Cologne, Germany.,Center for Molecular Medicine Cologne, University of Cologne, Cologne, Germany
| | - Johannes Schulte
- Pediatric Oncology and Hematology, Charité University Medicine, Berlin, Germany
| | - Jo Vandesompele
- Center for Medical Genetics, Ghent University, Ghent, Belgium.,Cancer Research Institute Ghent, Ghent University, Ghent, Belgium
| | - Frank Speleman
- Center for Medical Genetics, Ghent University, Ghent, Belgium.,Cancer Research Institute Ghent, Ghent University, Ghent, Belgium
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5
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Van Roy N, Van Der Linden M, Menten B, Dheedene A, Vandeputte C, Van Dorpe J, Laureys G, Renard M, Sante T, Lammens T, De Wilde B, Speleman F, De Preter K. Shallow Whole Genome Sequencing on Circulating Cell-Free DNA Allows Reliable Noninvasive Copy-Number Profiling in Neuroblastoma Patients. Clin Cancer Res 2017; 23:6305-6314. [PMID: 28710315 DOI: 10.1158/1078-0432.ccr-17-0675] [Citation(s) in RCA: 80] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2017] [Revised: 06/02/2017] [Accepted: 07/10/2017] [Indexed: 11/16/2022]
Abstract
Purpose: Neuroblastoma (NB) is a heterogeneous disease characterized by distinct clinical features and by the presence of typical copy-number alterations (CNAs). Given the strong association of these CNA profiles with prognosis, analysis of the CNA profile at diagnosis is mandatory. Therefore, we tested whether the analysis of circulating cell-free DNA (cfDNA) present in plasma samples of patients with NB could offer a valuable alternative to primary tumor DNA for CNA profiling.Experimental Design: In 37 patients with NB, cfDNA analysis using shallow whole genome sequencing (sWGS) was compared with arrayCGH analysis of primary tumor tissue.Results: Comparison of CNA profiles on cfDNA showed highly concordant patterns, particularly in high-stage patients. Numerical chromosome imbalances as well as large and focal structural aberrations including MYCN and LIN28B amplification and ATRX deletion could be readily detected with sWGS using a low input of cfDNA.Conclusions: In conclusion, sWGS analysis on cfDNA offers a cost-effective, noninvasive, rapid, robust and sensitive alternative for tumor DNA copy-number profiling in most patients with NB. Clin Cancer Res; 23(20); 6305-14. ©2017 AACR.
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Affiliation(s)
- Nadine Van Roy
- Center for Medical Genetics, Ghent University, Ghent, Belgium.,Cancer Research Institute Ghent, Ghent University, Ghent, Belgium
| | - Malaïka Van Der Linden
- Center for Medical Genetics, Ghent University, Ghent, Belgium.,Department of Pathology, Ghent University, Ghent, Belgium
| | - Björn Menten
- Center for Medical Genetics, Ghent University, Ghent, Belgium
| | | | - Charlotte Vandeputte
- Center for Medical Genetics, Ghent University, Ghent, Belgium.,Cancer Research Institute Ghent, Ghent University, Ghent, Belgium
| | - Jo Van Dorpe
- Department of Pathology, Ghent University, Ghent, Belgium
| | - Geneviève Laureys
- Cancer Research Institute Ghent, Ghent University, Ghent, Belgium.,Department of Pediatric Hematology-Oncology and Stem Cell Transplantation, Ghent University Hospital, Ghent, Belgium
| | - Marleen Renard
- Department of Pediatric Hematology-Oncology and Stem Cell Transplantation, Leuven University Hospital, Leuven, Belgium
| | - Tom Sante
- Center for Medical Genetics, Ghent University, Ghent, Belgium
| | - Tim Lammens
- Cancer Research Institute Ghent, Ghent University, Ghent, Belgium.,Department of Pediatric Hematology-Oncology and Stem Cell Transplantation, Ghent University Hospital, Ghent, Belgium
| | - Bram De Wilde
- Cancer Research Institute Ghent, Ghent University, Ghent, Belgium.,Department of Pediatric Hematology-Oncology and Stem Cell Transplantation, Ghent University Hospital, Ghent, Belgium
| | - Frank Speleman
- Center for Medical Genetics, Ghent University, Ghent, Belgium.,Cancer Research Institute Ghent, Ghent University, Ghent, Belgium
| | - Katleen De Preter
- Center for Medical Genetics, Ghent University, Ghent, Belgium. .,Cancer Research Institute Ghent, Ghent University, Ghent, Belgium
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6
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Vantroys E, Smet J, Vanlander A, De Paepe B, Vergult S, Sante T, Menten B, Van Coster R. Mild early epileptic encephalopathy evolving to spastic paraplegia, neurogenic bladder and generalized slow colon transit in an 18-year old patient with pathogenic mutations in FARS2. Neuromuscul Disord 2016. [DOI: 10.1016/j.nmd.2016.06.323] [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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7
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Van Cauwenbergh C, Van Schil K, Cannoodt R, Bauwens M, Van Laethem T, De Jaegere S, Steyaert W, Sante T, Menten B, Leroy BP, Coppieters F, De Baere E. arrEYE: a customized platform for high-resolution copy number analysis of coding and noncoding regions of known and candidate retinal dystrophy genes and retinal noncoding RNAs. Genet Med 2016; 19:457-466. [PMID: 27608171 PMCID: PMC5392597 DOI: 10.1038/gim.2016.119] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [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: 04/13/2016] [Accepted: 07/06/2016] [Indexed: 12/13/2022] Open
Abstract
Purpose: Our goal was to design a customized microarray, arrEYE, for high-resolution copy number variant (CNV) analysis of known and candidate genes for inherited retinal dystrophy (iRD) and retina-expressed noncoding RNAs (ncRNAs). Methods: arrEYE contains probes for the full genomic region of 106 known iRD genes, including those implicated in retinitis pigmentosa (RP) (the most frequent iRD), cone–rod dystrophies, macular dystrophies, and an additional 60 candidate iRD genes and 196 ncRNAs. Eight CNVs in iRD genes identified by other techniques were used as positive controls. The test cohort consisted of 57 patients with autosomal dominant, X-linked, or simplex RP. Results: In an RP patient, a novel heterozygous deletion of exons 7 and 8 of the HGSNAT gene was identified: c.634-408_820+338delinsAGAATATG, p.(Glu212Glyfs*2). A known variant was found on the second allele: c.1843G>A, p.(Ala615Thr). Furthermore, we expanded the allelic spectrum of USH2A and RCBTB1 with novel CNVs. Conclusion: The arrEYE platform revealed subtle single-exon to larger CNVs in iRD genes that could be characterized at the nucleotide level, facilitated by the high resolution of the platform. We report the first CNV in HGSNAT that, combined with another mutation, leads to RP, further supporting its recently identified role in nonsyndromic iRD. Genet Med19 4, 457–466.
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Affiliation(s)
- Caroline Van Cauwenbergh
- Center for Medical Genetics Ghent, Ghent University and Ghent University Hospital, Ghent, Belgium
| | - Kristof Van Schil
- Center for Medical Genetics Ghent, Ghent University and Ghent University Hospital, Ghent, Belgium
| | - Robrecht Cannoodt
- Center for Medical Genetics Ghent, Ghent University and Ghent University Hospital, Ghent, Belgium.,Data Mining and Modeling for Biomedicine group, VIB Inflammation Research Center, Ghent, Belgium.,Department of Internal Medicine, Ghent University, Ghent, Belgium
| | - Miriam Bauwens
- Center for Medical Genetics Ghent, Ghent University and Ghent University Hospital, Ghent, Belgium
| | - Thalia Van Laethem
- Center for Medical Genetics Ghent, Ghent University and Ghent University Hospital, Ghent, Belgium
| | - Sarah De Jaegere
- Center for Medical Genetics Ghent, Ghent University and Ghent University Hospital, Ghent, Belgium
| | - Wouter Steyaert
- Center for Medical Genetics Ghent, Ghent University and Ghent University Hospital, Ghent, Belgium
| | - Tom Sante
- Center for Medical Genetics Ghent, Ghent University and Ghent University Hospital, Ghent, Belgium
| | - Björn Menten
- Center for Medical Genetics Ghent, Ghent University and Ghent University Hospital, Ghent, Belgium
| | - Bart P Leroy
- Center for Medical Genetics Ghent, Ghent University and Ghent University Hospital, Ghent, Belgium.,Department of Ophthalmology, Ghent University and Ghent University Hospital, Ghent, Belgium.,Division of Ophthalmology and Center for Cellular & Molecular Therapeutics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Frauke Coppieters
- Center for Medical Genetics Ghent, Ghent University and Ghent University Hospital, Ghent, Belgium
| | - Elfride De Baere
- Center for Medical Genetics Ghent, Ghent University and Ghent University Hospital, Ghent, Belgium
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8
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Dheedene A, Sante T, De Smet M, Vanbellinghen JF, Grisart B, Vergult S, Janssens S, Menten B. Implementation of non-invasive prenatal testing by semiconductor sequencing in a genetic laboratory. Prenat Diagn 2016; 36:699-707. [PMID: 27176606 PMCID: PMC5108441 DOI: 10.1002/pd.4841] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [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: 12/31/2015] [Revised: 04/15/2016] [Accepted: 05/10/2016] [Indexed: 12/16/2022]
Abstract
OBJECTIVES To implement non-invasive prenatal testing (NIPT) for fetal aneuploidies with semiconductor sequencing in an academic cytogenomic laboratory and to evaluate the first 15-month experience on clinical samples. METHODS We validated a NIPT protocol for cell-free fetal DNA sequencing from maternal plasma for the detection of trisomy 13, 18 and 21 on a semiconductor sequencing instrument. Fetal DNA fraction calculation for all samples and several quality parameters were implemented in the workflow. One thousand eighty-one clinical NIPT samples were analysed, following the described protocol. RESULTS Non-invasive prenatal testing was successfully implemented and validated on 201 normal and 74 aneuploid samples. From 1081 clinical samples, 17 samples showed an abnormal result: 14 trisomy 21 samples, one trisomy 18 and one trisomy 16 were detected. Also a maternal copy number variation on chromosome 13 was observed, which could potentially lead to a false positive trisomy 13 result. One sex discordant result was reported, possibly attributable to a vanishing twin. Moreover, our combined fetal fraction calculation enabled a more reliable risk estimate for trisomy 13, 18 and 21. CONCLUSIONS Non-invasive prenatal testing for trisomy 21, 18 and 13 has a very high specificity and sensitivity. Because of several biological phenomena, diagnostic invasive confirmation of abnormal results remains required. © 2016 The Authors. Prenatal Diagnosis published by John Wiley & Sons, Ltd.
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Affiliation(s)
- Annelies Dheedene
- Center for Medical Genetics Ghent, Ghent University Hospital, Ghent University, Ghent, Belgium
| | - Tom Sante
- Center for Medical Genetics Ghent, Ghent University Hospital, Ghent University, Ghent, Belgium
| | - Matthias De Smet
- Center for Medical Genetics Ghent, Ghent University Hospital, Ghent University, Ghent, Belgium
| | - Jean-François Vanbellinghen
- Plateforme de Biologie Moléculaire, Département des Laboratoires, Cliniques Universitaires Saint-Luc, Bruxelles, Belgium
| | - Bernard Grisart
- Centre de Génétique Humaine, Institut de Pathologie et Génétique, Charleroi, Belgium
| | - Sarah Vergult
- Center for Medical Genetics Ghent, Ghent University Hospital, Ghent University, Ghent, Belgium
| | - Sandra Janssens
- Center for Medical Genetics Ghent, Ghent University Hospital, Ghent University, Ghent, Belgium
| | - Björn Menten
- Center for Medical Genetics Ghent, Ghent University Hospital, Ghent University, Ghent, Belgium
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Deleye L, Dheedene A, De Coninck D, Sante T, Christodoulou C, Heindryckx B, Van den Abbeel E, De Sutter P, Deforce D, Menten B, Van Nieuwerburgh F. Shallow whole genome sequencing is well suited for the detection of chromosomal aberrations in human blastocysts. Fertil Steril 2015; 104:1276-85.e1. [DOI: 10.1016/j.fertnstert.2015.07.1144] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2015] [Revised: 06/24/2015] [Accepted: 07/06/2015] [Indexed: 01/27/2023]
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10
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Vanlander AV, Menten B, Smet J, De Meirleir L, Sante T, De Paepe B, Seneca S, Pearce SF, Powell CA, Vergult S, Michotte A, De Latter E, Vantomme L, Minczuk M, Van Coster R. Two siblings with homozygous pathogenic splice-site variant in mitochondrial asparaginyl-tRNA synthetase (NARS2). Hum Mutat 2015; 36:222-31. [PMID: 25385316 DOI: 10.1002/humu.22728] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [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: 07/14/2014] [Accepted: 10/28/2014] [Indexed: 12/13/2022]
Abstract
A homozygous missense mutation (c.822G>C) was found in the gene encoding the mitochondrial asparaginyl-tRNA synthetase (NARS2) in two siblings born to consanguineous parents. These siblings presented with different phenotypes: one had mild intellectual disability and epilepsy in childhood, whereas the other had severe myopathy. Biochemical analysis of the oxidative phosphorylation (OXPHOS) complexes in both siblings revealed a combined complex I and IV deficiency in skeletal muscle. In-gel activity staining after blue native-polyacrylamide gel electrophoresis confirmed the decreased activity of complex I and IV, and, in addition, showed the presence of complex V subcomplexes. Considering the consanguineous descent, homozygosity mapping and whole-exome sequencing were combined revealing the presence of one single missense mutation in the shared homozygous region. The c.822G>C variant affects the 3' splice site of exon 7, leading to skipping of the whole exon 7 and a part of exon 8 in the NARS2 mRNA. In EBV-transformed lymphoblasts, a specific decrease in the amount of charged mt-tRNA(Asn) was demonstrated as compared with controls. This confirmed the pathogenic nature of the variant. To conclude, the reported variant in NARS2 results in a combined OXPHOS complex deficiency involving complex I and IV, making NARS2 a new member of disease-associated aaRS2.
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Affiliation(s)
- Arnaud V Vanlander
- Department of Pediatric Neurology and Metabolism, Ghent University Hospital, Belgium
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11
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Deleye L, De Coninck D, Christodoulou C, Sante T, Dheedene A, Heindryckx B, Van den Abbeel E, De Sutter P, Menten B, Deforce D, Van Nieuwerburgh F. Whole genome amplification with SurePlex results in better copy number alteration detection using sequencing data compared to the MALBAC method. Sci Rep 2015; 5:11711. [PMID: 26122179 PMCID: PMC4485032 DOI: 10.1038/srep11711] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [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: 01/22/2015] [Accepted: 06/03/2015] [Indexed: 11/09/2022] Open
Abstract
Current whole genome amplification (WGA) methods lead to amplification bias resulting in over- and under-represented regions in the genome. Nevertheless, certain WGA methods, such as SurePlex and subsequent arrayCGH analysis, make it possible to detect copy number alterations (CNAs) at a 10 Mb resolution. A more uniform WGA combined with massive parallel sequencing (MPS), however, could allow detection at higher resolution and lower cost. Recently, MALBAC, a new WGA method, claims unparalleled performance. Here, we compared the well-established SurePlex and MALBAC WGA for their ability to detect CNAs in MPS generated data and, in addition, compared PCR-free MPS library preparation with the standard enrichment PCR library preparation. Results showed that SurePlex amplification led to more uniformity across the genome, allowing for a better CNA detection with less false positives compared to MALBAC amplified samples. An even more uniform coverage was observed in samples following a PCR-free library preparation. In general, the combination of SurePlex and MPS led to the same chromosomal profile compared to a reference arrayCGH from unamplified genomic DNA, underlining the large potential of MPS techniques in CNA detection from a limited number of DNA material.
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Affiliation(s)
- Lieselot Deleye
- Laboratory of Pharmaceutical Biotechnology, Ghent University, Ottergemsesteenweg 460, 9000 Ghent, Belgium
| | - Dieter De Coninck
- Laboratory of Pharmaceutical Biotechnology, Ghent University, Ottergemsesteenweg 460, 9000 Ghent, Belgium
| | | | - Tom Sante
- Center for Medical Genetics, Ghent University, De Pintelaan 185, 9000 Ghent, Belgium
| | - Annelies Dheedene
- Center for Medical Genetics, Ghent University, De Pintelaan 185, 9000 Ghent, Belgium
| | - Björn Heindryckx
- Department for Reproductive Medicine, Ghent University Hospital, De Pintelaan 185, 9000 Ghent, Belgium
| | - Etienne Van den Abbeel
- Department for Reproductive Medicine, Ghent University Hospital, De Pintelaan 185, 9000 Ghent, Belgium
| | - Petra De Sutter
- Department for Reproductive Medicine, Ghent University Hospital, De Pintelaan 185, 9000 Ghent, Belgium
| | - Björn Menten
- Center for Medical Genetics, Ghent University, De Pintelaan 185, 9000 Ghent, Belgium
| | - Dieter Deforce
- Laboratory of Pharmaceutical Biotechnology, Ghent University, Ottergemsesteenweg 460, 9000 Ghent, Belgium
| | - Filip Van Nieuwerburgh
- Laboratory of Pharmaceutical Biotechnology, Ghent University, Ottergemsesteenweg 460, 9000 Ghent, Belgium
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12
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Sante T, Vergult S, Volders PJ, Kloosterman WP, Trooskens G, De Preter K, Dheedene A, Speleman F, De Meyer T, Menten B. ViVar: a comprehensive platform for the analysis and visualization of structural genomic variation. PLoS One 2014; 9:e113800. [PMID: 25503062 PMCID: PMC4264741 DOI: 10.1371/journal.pone.0113800] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2014] [Accepted: 10/20/2014] [Indexed: 01/06/2023] Open
Abstract
Structural genomic variations play an important role in human disease and phenotypic diversity. With the rise of high-throughput sequencing tools, mate-pair/paired-end/single-read sequencing has become an important technique for the detection and exploration of structural variation. Several analysis tools exist to handle different parts and aspects of such sequencing based structural variation analyses pipelines. A comprehensive analysis platform to handle all steps, from processing the sequencing data, to the discovery and visualization of structural variants, is missing. The ViVar platform is built to handle the discovery of structural variants, from Depth Of Coverage analysis, aberrant read pair clustering to split read analysis. ViVar provides you with powerful visualization options, enables easy reporting of results and better usability and data management. The platform facilitates the processing, analysis and visualization, of structural variation based on massive parallel sequencing data, enabling the rapid identification of disease loci or genes. ViVar allows you to scale your analysis with your work load over multiple (cloud) servers, has user access control to keep your data safe and is easy expandable as analysis techniques advance. URL: https://www.cmgg.be/vivar/
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Affiliation(s)
- Tom Sante
- Center for Medical Genetics, Faculty of Medicine and Health Sciences, Ghent University, Gent, Belgium
| | - Sarah Vergult
- Center for Medical Genetics, Faculty of Medicine and Health Sciences, Ghent University, Gent, Belgium
| | - Pieter-Jan Volders
- Center for Medical Genetics, Faculty of Medicine and Health Sciences, Ghent University, Gent, Belgium
| | - Wigard P. Kloosterman
- Department of Medical Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Geert Trooskens
- BioBix, Faculty of Bioscience Engineering, Ghent University, Gent, Belgium
| | - Katleen De Preter
- Center for Medical Genetics, Faculty of Medicine and Health Sciences, Ghent University, Gent, Belgium
| | - Annelies Dheedene
- Center for Medical Genetics, Faculty of Medicine and Health Sciences, Ghent University, Gent, Belgium
| | - Frank Speleman
- Center for Medical Genetics, Faculty of Medicine and Health Sciences, Ghent University, Gent, Belgium
| | - Tim De Meyer
- BioBix, Faculty of Bioscience Engineering, Ghent University, Gent, Belgium
| | - Björn Menten
- Center for Medical Genetics, Faculty of Medicine and Health Sciences, Ghent University, Gent, Belgium
- * E-mail:
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13
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Vergult S, Van Binsbergen E, Sante T, Nowak S, Vanakker O, Claes K, Poppe B, Van der Aa N, van Roosmalen MJ, Duran K, Tavakoli-Yaraki M, Swinkels M, van den Boogaard MJ, van Haelst M, Roelens F, Speleman F, Cuppen E, Mortier G, Kloosterman WP, Menten B. Mate pair sequencing for the detection of chromosomal aberrations in patients with intellectual disability and congenital malformations. Eur J Hum Genet 2013; 22:652-9. [PMID: 24105367 DOI: 10.1038/ejhg.2013.220] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2013] [Revised: 08/13/2013] [Accepted: 08/29/2013] [Indexed: 12/20/2022] Open
Abstract
Recently, microarrays have replaced karyotyping as a first tier test in patients with idiopathic intellectual disability and/or multiple congenital abnormalities (ID/MCA) in many laboratories. Although in about 14-18% of such patients, DNA copy-number variants (CNVs) with clinical significance can be detected, microarrays have the disadvantage of missing balanced rearrangements, as well as providing no information about the genomic architecture of structural variants (SVs) like duplications and complex rearrangements. Such information could possibly lead to a better interpretation of the clinical significance of the SV. In this study, the clinical use of mate pair next-generation sequencing was evaluated for the detection and further characterization of structural variants within the genomes of 50 ID/MCA patients. Thirty of these patients carried a chromosomal aberration that was previously detected by array CGH or karyotyping and suspected to be pathogenic. In the remaining 20 patients no causal SVs were found and only benign aberrations were detected by conventional techniques. Combined cluster and coverage analysis of the mate pair data allowed precise breakpoint detection and further refinement of previously identified balanced and (complex) unbalanced aberrations, pinpointing the causal gene for some patients. We conclude that mate pair sequencing is a powerful technology that can provide rapid and unequivocal characterization of unbalanced and balanced SVs in patient genomes and can be essential for the clinical interpretation of some SVs.
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Affiliation(s)
- Sarah Vergult
- Center for Medical Genetics, Ghent University, Ghent, Belgium
| | - Ellen Van Binsbergen
- Department of Medical Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Tom Sante
- Center for Medical Genetics, Ghent University, Ghent, Belgium
| | - Silke Nowak
- Center for Medical Genetics, Ghent University, Ghent, Belgium
| | | | - Kathleen Claes
- Center for Medical Genetics, Ghent University, Ghent, Belgium
| | - Bruce Poppe
- Center for Medical Genetics, Ghent University, Ghent, Belgium
| | - Nathalie Van der Aa
- Department for Medical Genetics, University Hospital of Antwerp, Antwerp, Belgium
| | - Markus J van Roosmalen
- Department of Medical Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Karen Duran
- Department of Medical Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
| | | | - Marielle Swinkels
- Department of Medical Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
| | | | - Mieke van Haelst
- Department of Medical Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
| | | | - Frank Speleman
- Center for Medical Genetics, Ghent University, Ghent, Belgium
| | - Edwin Cuppen
- Department of Medical Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Geert Mortier
- 1] Center for Medical Genetics, Ghent University, Ghent, Belgium [2] Department for Medical Genetics, University Hospital of Antwerp, Antwerp, Belgium
| | - Wigard P Kloosterman
- Department of Medical Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Björn Menten
- Center for Medical Genetics, Ghent University, Ghent, Belgium
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14
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Verdin H, D'haene B, Beysen D, Novikova Y, Menten B, Sante T, Lapunzina P, Nevado J, Carvalho CMB, Lupski JR, De Baere E. Microhomology-mediated mechanisms underlie non-recurrent disease-causing microdeletions of the FOXL2 gene or its regulatory domain. PLoS Genet 2013; 9:e1003358. [PMID: 23516377 PMCID: PMC3597517 DOI: 10.1371/journal.pgen.1003358] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2012] [Accepted: 01/18/2013] [Indexed: 11/17/2022] Open
Abstract
Genomic disorders are often caused by recurrent copy number variations (CNVs), with nonallelic homologous recombination (NAHR) as the underlying mechanism. Recently, several microhomology-mediated repair mechanisms—such as microhomology-mediated end-joining (MMEJ), fork stalling and template switching (FoSTeS), microhomology-mediated break-induced replication (MMBIR), serial replication slippage (SRS), and break-induced SRS (BISRS)—were described in the etiology of non-recurrent CNVs in human disease. In addition, their formation may be stimulated by genomic architectural features. It is, however, largely unexplored to what extent these mechanisms contribute to rare, locus-specific pathogenic CNVs. Here, fine-mapping of 42 microdeletions of the FOXL2 locus, encompassing FOXL2 (32) or its regulatory domain (10), serves as a model for rare, locus-specific CNVs implicated in genetic disease. These deletions lead to blepharophimosis syndrome (BPES), a developmental condition affecting the eyelids and the ovary. For breakpoint mapping we used targeted array-based comparative genomic hybridization (aCGH), quantitative PCR (qPCR), long-range PCR, and Sanger sequencing of the junction products. Microhomology, ranging from 1 bp to 66 bp, was found in 91.7% of 24 characterized breakpoint junctions, being significantly enriched in comparison with a random control sample. Our results show that microhomology-mediated repair mechanisms underlie at least 50% of these microdeletions. Moreover, genomic architectural features, like sequence motifs, non-B DNA conformations, and repetitive elements, were found in all breakpoint regions. In conclusion, the majority of these microdeletions result from microhomology-mediated mechanisms like MMEJ, FoSTeS, MMBIR, SRS, or BISRS. Moreover, we hypothesize that the genomic architecture might drive their formation by increasing the susceptibility for DNA breakage or promote replication fork stalling. Finally, our locus-centered study, elucidating the etiology of a large set of rare microdeletions involved in a monogenic disorder, can serve as a model for other clustered, non-recurrent microdeletions in genetic disease. Genomic disorder is a general term describing conditions caused by genomic aberrations leading to a copy number change of one or more genes. Copy number changes with the same length and clustered breakpoints for a group of patients with the same disorder are named recurrent rearrangements. These originate mostly from a well-studied mechanism, namely nonallelic homologous recombination (NAHR). In contrast, non-recurrent rearrangements vary in size, have scattered breakpoints, and can originate from several different mechanisms that are not fully understood. Here we tried to gain further insight into the extent to which these mechanisms contribute to non-recurrent rearrangements and into the possible role of the surrounding genomic architecture. To this end, we investigated a unique group of patients with non-recurrent deletions of the FOXL2 region causing blepharophimosis syndrome. We observed that the majority of these deletions can result from several mechanisms mediated by microhomology. Furthermore, our data suggest that rare pathogenic microdeletions do not occur at random genome sequences, but are possibly guided by the surrounding genomic architecture. Finally, our study, elucidating the etiology of a unique cohort of locus-specific microdeletions implicated in genetic disease, can serve as a model for the formation of genomic aberrations in other genetic disorders.
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Affiliation(s)
- Hannah Verdin
- Center for Medical Genetics, Ghent University, Ghent, Belgium
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15
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Kumps C, Fieuw A, Mestdagh P, Menten B, Lefever S, Pattyn F, De Brouwer S, Sante T, Schulte JH, Schramm A, Van Roy N, Van Maerken T, Noguera R, Combaret V, Devalck C, Westermann F, Laureys G, Eggert A, Vandesompele J, De Preter K, Speleman F. Focal DNA copy number changes in neuroblastoma target MYCN regulated genes. PLoS One 2013; 8:e52321. [PMID: 23308108 PMCID: PMC3537730 DOI: 10.1371/journal.pone.0052321] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2012] [Accepted: 11/16/2012] [Indexed: 02/07/2023] Open
Abstract
Neuroblastoma is an embryonic tumor arising from immature sympathetic nervous system cells. Recurrent genomic alterations include MYCN and ALK amplification as well as recurrent patterns of gains and losses of whole or large partial chromosome segments. A recent whole genome sequencing effort yielded no frequently recurring mutations in genes other than those affecting ALK. However, the study further stresses the importance of DNA copy number alterations in this disease, in particular for genes implicated in neuritogenesis. Here we provide additional evidence for the importance of focal DNA copy number gains and losses, which are predominantly observed in MYCN amplified tumors. A focal 5 kb gain encompassing the MYCN regulated miR-17∼92 cluster as sole gene was detected in a neuroblastoma cell line and further analyses of the array CGH data set demonstrated enrichment for other MYCN target genes in focal gains and amplifications. Next we applied an integrated genomics analysis to prioritize MYCN down regulated genes mediated by MYCN driven miRNAs within regions of focal heterozygous or homozygous deletion. We identified RGS5, a negative regulator of G-protein signaling implicated in vascular normalization, invasion and metastasis, targeted by a focal homozygous deletion, as a new MYCN target gene, down regulated through MYCN activated miRNAs. In addition, we expand the miR-17∼92 regulatory network controlling TGFß signaling in neuroblastoma with the ring finger protein 11 encoding gene RNF11, which was previously shown to be targeted by the miR-17∼92 member miR-19b. Taken together, our data indicate that focal DNA copy number imbalances in neuroblastoma (1) target genes that are implicated in MYCN signaling, possibly selected to reinforce MYCN oncogene addiction and (2) serve as a resource for identifying new molecular targets for treatment.
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Affiliation(s)
- Candy Kumps
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
| | - Annelies Fieuw
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
| | - Pieter Mestdagh
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
| | - Björn Menten
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
| | - Steve Lefever
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
| | - Filip Pattyn
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
| | - Sara De Brouwer
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
| | - Tom Sante
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
| | - Johannes Hubertus Schulte
- Department of Pediatric Oncology and Haematology, University Children's Hospital Essen, Essen, Germany
| | - Alexander Schramm
- Department of Pediatric Oncology and Haematology, University Children's Hospital Essen, Essen, Germany
| | - Nadine Van Roy
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
| | - Tom Van Maerken
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
| | - Rosa Noguera
- Department of Pathology, Medical School, University of Valencia, Valencia, Spain
| | - Valérie Combaret
- Centre Léon Bérard, FNCLCC, Laboratoire de Recherche Translationnelle, Lyon, France
| | - Christine Devalck
- Children's University Hospital, Hematology-Oncology, Brussels, Belgium
| | - Frank Westermann
- Department of Tumor Genetics, German Cancer Research Center, Heidelberg, Germany
| | - Geneviève Laureys
- Department of Pediatric Hematology-Oncology, Ghent University Hospital, Ghent, Belgium
| | - Angelika Eggert
- Department of Pediatric Oncology and Haematology, University Children's Hospital Essen, Essen, Germany
| | - Jo Vandesompele
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
| | - Katleen De Preter
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
| | - Frank Speleman
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
- * E-mail:
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Vergult S, Hoogeboom AJM, Bijlsma EK, Sante T, Klopocki E, De Wilde B, Jongmans M, Thiel C, Verheij JBGM, Perez-Aytes A, Van Esch H, Kuechler A, Barge-Schaapveld DQCM, Sznajer Y, Mortier G, Menten B. Complex genetics of radial ray deficiencies: screening of a cohort of 54 patients. Genet Med 2012; 15:195-202. [DOI: 10.1038/gim.2012.120] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
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Van Dycke A, Raedt R, Dauwe I, Sante T, Wyckhuys T, Meurs A, Vonck K, Wadman W, Boon P. Continuous local intrahippocampal delivery of adenosine reduces seizure frequency in rats with spontaneous seizures. Epilepsia 2010; 51:1721-8. [DOI: 10.1111/j.1528-1167.2010.02700.x] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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