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Faas BHW, Westra D, de Munnik SA, van Rij M, Marcelis C, Joosten S, Krapels I, Vernimmen V, Heijligers M, Willemsen MH, de Leeuw N, Rinne T, Pfundt R, Smeekens SP, Stegmann SPA, Macville M, Sikkel E, Coumans A, Wijnberger L, Derks I, van Lent-Albrechts J, Hofste T, Timmermans R, van den End J, Stevens SJC, Feenstra I. All-in-one whole exome sequencing strategy with simultaneous copy number variant, single nucleotide variant and absence-of-heterozygosity analysis in fetuses with structural ultrasound anomalies: A 1-year experience. Prenat Diagn 2023; 43:527-543. [PMID: 36647814 DOI: 10.1002/pd.6314] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Revised: 01/06/2023] [Accepted: 01/11/2023] [Indexed: 01/18/2023]
Abstract
OBJECTIVE We performed a 1-year evaluation of a novel strategy of simultaneously analyzing single nucleotide variants (SNVs), copy number variants (CNVs) and copy-number-neutral Absence-of-Heterozygosity from Whole Exome Sequencing (WES) data for prenatal diagnosis of fetuses with ultrasound (US) anomalies and a non-causative QF-PCR result. METHODS After invasive diagnostics, whole exome parent-offspring trio-sequencing with exome-wide CNV analysis was performed in pregnancies with fetal US anomalies and a non-causative QF-PCR result (WES-CNV). On request, additional SNV-analysis, restricted to (the) requested gene panel(s) only (with the option of whole exome SNV-analysis afterward) was performed simultaneously (WES-CNV/SNV) or as rapid SNV-re-analysis, following a normal CNV analysis. RESULTS In total, 415 prenatal samples were included. Following a non-causative QF-PCR result, WES-CNV analysis was initially requested for 74.3% of the chorionic villus (CV) samples and 45% of the amniotic fluid (AF) samples. In case WES-CNV analysis did not reveal a causative aberration, SNV-re-analysis was requested in 41.7% of the CV samples and 17.5% of the AF samples. All initial analyses could be finished within 2 weeks after sampling. For SNV-re-analysis during pregnancy, turn-around-times (TATs) varied between one and 8 days. CONCLUSION We show a highly efficient all-in-one WES-based strategy, with short TATs, and the option of rapid SNV-re-analysis after a normal CNV result.
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Affiliation(s)
- Brigitte H W Faas
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Dineke Westra
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Sonja A de Munnik
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands.,Department of Clinical Genetics, Maastricht University Medical Centre, Maastricht, The Netherlands
| | - Maartje van Rij
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Carlo Marcelis
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Sara Joosten
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Ingrid Krapels
- Department of Clinical Genetics, Maastricht University Medical Centre, Maastricht, The Netherlands
| | - Vivian Vernimmen
- Department of Clinical Genetics, Maastricht University Medical Centre, Maastricht, The Netherlands
| | - Malou Heijligers
- Department of Clinical Genetics, Maastricht University Medical Centre, Maastricht, The Netherlands
| | - Marjolein H Willemsen
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Nicole de Leeuw
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Tuula Rinne
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Rolph Pfundt
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Sanne P Smeekens
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Sander P A Stegmann
- Department of Clinical Genetics, Maastricht University Medical Centre, Maastricht, The Netherlands
| | - Merryn Macville
- Department of Clinical Genetics, Maastricht University Medical Centre, Maastricht, The Netherlands
| | - Esther Sikkel
- Department of Obstetrics and Gynaecology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Audrey Coumans
- Department of Obstetrics and Gynaecology, Maastricht University Medical Centre, Maastricht, The Netherlands
| | - Lia Wijnberger
- Department of Obstetrics and Gynaecology, Rijnstate Hospital, Arnhem, The Netherlands
| | - Irma Derks
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | | | - Tom Hofste
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Raoul Timmermans
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Janneke van den End
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Servi J C Stevens
- Department of Clinical Genetics, Maastricht University Medical Centre, Maastricht, The Netherlands
| | - Ilse Feenstra
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
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Kleefstra T, van Zelst-Stams WA, Nillesen WM, Cormier-Daire V, Houge G, Foulds N, van Dooren M, Willemsen MH, Pfundt R, Turner A, Wilson M, McGaughran J, Rauch A, Zenker M, Adam MP, Innes M, Davies C, López AGM, Casalone R, Weber A, Brueton LA, Navarro AD, Bralo MP, Venselaar H, Stegmann SPA, Yntema HG, van Bokhoven H, Brunner HG. Further clinical and molecular delineation of the 9q subtelomeric deletion syndrome supports a major contribution of EHMT1 haploinsufficiency to the core phenotype. J Med Genet 2009; 46:598-606. [PMID: 19264732 DOI: 10.1136/jmg.2008.062950] [Citation(s) in RCA: 144] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
BACKGROUND The 9q subtelomeric deletion syndrome (9qSTDS) is clinically characterised by moderate to severe mental retardation, childhood hypotonia and facial dysmorphisms. In addition, congenital heart defects, urogenital defects, epilepsy and behavioural problems are frequently observed. The syndrome can be either caused by a submicroscopic 9q34.3 deletion or by intragenic EHMT1 mutations leading to haploinsufficiency of the EHMT1 gene. So far it has not been established if and to what extent other genes in the 9q34.3 region contribute to the phenotype observed in deletion cases. This study reports the largest cohort of 9qSTDS cases so far. METHODS AND RESULTS By a multiplex ligation dependent probe amplification (MLPA) approach, the authors identified and characterised 16 novel submicroscopic 9q deletions. Direct sequence analysis of the EHMT1 gene in 24 patients exhibiting the 9qSTD phenotype without such deletion identified six patients with an intragenic EHMT1 mutation. Five of these mutations predict a premature termination codon whereas one mutation gives rise to an amino acid substitution in a conserved domain of the protein. CONCLUSIONS The data do not provide any evidence for phenotype-genotype correlations between size of the deletions or type of mutations and severity of clinical features. Therefore, the authors confirm the EHMT1 gene to be the major determinant of the 9qSTDS phenotype. Interestingly, five of six patients who had reached adulthood had developed severe psychiatric pathology, which may indicate that EHMT1 haploinsufficiency is associated with neurodegeneration in addition to neurodevelopmental defect.
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Affiliation(s)
- T Kleefstra
- Department of Human Genetics, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands.
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