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Antić Ž, Yu J, Bornhauser BC, Lelieveld SH, van der Ham CG, van Reijmersdal SV, Morgado L, Elitzur S, Bourquin JP, Cazzaniga G, Eckert C, Camós M, Sutton R, Cavé H, Moorman AV, Sonneveld E, Geurts van Kessel A, van Leeuwen FN, Hoogerbrugge PM, Waanders E, Kuiper RP. Clonal dynamics in pediatric B-cell precursor acute lymphoblastic leukemia with very early relapse. Pediatr Blood Cancer 2022; 69:e29361. [PMID: 34597466 DOI: 10.1002/pbc.29361] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/08/2021] [Revised: 08/18/2021] [Accepted: 08/31/2021] [Indexed: 01/08/2023]
Abstract
INTRODUCTION One-quarter of the relapses in children with B-cell precursor acute lymphoblastic leukemia (BCP-ALL) occur very early (within 18 months, before completion of treatment), and prognosis in these patients is worse compared to cases that relapse after treatment has ended. METHODS In this study, we performed a genomic analysis of diagnosis-relapse pairs of 12 children who relapsed very early, followed by a deep-sequencing validation of all identified mutations. In addition, we included one case with a good initial treatment response and on-treatment relapse at the end of upfront therapy. RESULTS We observed a dynamic clonal evolution in all cases, with relapse almost exclusively originating from a subclone at diagnosis. We identified several driver mutations that may have influenced the outgrowth of a minor clone at diagnosis to become the major clone at relapse. For example, a minimal residual disease (MRD)-based standard-risk patient with ETV6-RUNX1-positive leukemia developed a relapse from a TP53-mutated subclone after loss of the wildtype allele. Furthermore, two patients with TCF3-PBX1-positive leukemia that developed a very early relapse carried E1099K WHSC1 mutations at diagnosis, a hotspot mutation that was recurrently encountered in other very early TCF3-PBX1-positive leukemia relapses as well. In addition to alterations in known relapse drivers, we found two cases with truncating mutations in the cohesin gene RAD21. CONCLUSION Comprehensive genomic characterization of diagnosis-relapse pairs shows that very early relapses in BCP-ALL frequently arise from minor subclones at diagnosis. A detailed understanding of the therapeutic pressure driving these events may aid the development of improved therapies.
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Affiliation(s)
- Željko Antić
- Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands.,Department of Human Genetics, Hannover Medical School, Hannover, Germany
| | - Jiangyan Yu
- Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands.,Department of Human Genetics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Beat C Bornhauser
- Department of Oncology and Children's Research Centre, University Children's Hospital Zurich, Zurich, Switzerland
| | | | | | - Simon V van Reijmersdal
- Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands.,Department of Human Genetics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Lionel Morgado
- Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
| | - Sarah Elitzur
- Pediatric Hematology-Oncology, Schneider Children's Medical Center and Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Jean-Pierre Bourquin
- Department of Oncology and Children's Research Centre, University Children's Hospital Zurich, Zurich, Switzerland
| | - Giovanni Cazzaniga
- Centro Ricerca Tettamanti, Fondazione Tettamanti, University of Milan Bicocca, Monza, Italy
| | - Cornelia Eckert
- Pediatric Oncology/Hematology, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Mireia Camós
- Leukemia and Other Pediatric Hemopathies, Developmental Tumor Biology Group, Institut de Recerca Sant Joan de Déu, Barcelona, Spain.,Hematology Laboratory, Hospital Sant Joan de Deu Barcelona, Barcelona, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
| | - Rosemary Sutton
- Molecular Diagnostics, Children's Cancer Institute, University of New South Wales, Sydney, New South Wales, Australia
| | - Hélène Cavé
- Department of Genetics, Robert Debré Hospital, Assistance Publique-Hôpitaux de Paris (AP-HP), Paris, France.,INSERM U1131, Saint-Louis Research Institute, University of Paris, Paris, France
| | - Anthony V Moorman
- Wolfson Childhood Cancer Centre, Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, UK
| | - Edwin Sonneveld
- Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands.,Dutch Childhood Oncology Group, Utrecht, The Netherlands
| | - Ad Geurts van Kessel
- Department of Human Genetics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | | | - Peter M Hoogerbrugge
- Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands.,Dutch Childhood Oncology Group, Utrecht, The Netherlands
| | - Esmé Waanders
- Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands.,Department of Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Roland P Kuiper
- Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands.,Department of Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
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2
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Antić Ž, Lelieveld SH, van der Ham CG, Sonneveld E, Hoogerbrugge PM, Kuiper RP. Unravelling the Sequential Interplay of Mutational Mechanisms during Clonal Evolution in Relapsed Pediatric Acute Lymphoblastic Leukemia. Genes (Basel) 2021; 12:genes12020214. [PMID: 33540666 PMCID: PMC7913080 DOI: 10.3390/genes12020214] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Revised: 01/22/2021] [Accepted: 01/28/2021] [Indexed: 11/16/2022] Open
Abstract
Pediatric acute lymphoblastic leukemia (ALL) is the most common pediatric malignancy and is characterized by clonal heterogeneity. Genomic mutations can increase proliferative potential of leukemic cells and cause treatment resistance. However, mechanisms driving mutagenesis and clonal diversification in ALL are not fully understood. In this proof of principle study, we performed whole genome sequencing of two cases with multiple relapses in order to investigate whether groups of mutations separated in time show distinct mutational signatures. Based on mutation allele frequencies at diagnosis and subsequent relapses, we clustered mutations into groups and performed cluster-specific mutational profile analysis and de novo signature extraction. In patient 1, who experienced two relapses, the analysis unraveled a continuous interplay of aberrant activation induced cytidine deaminase (AID)/apolipoprotein B editing complex (APOBEC) activity. The associated signatures SBS2 and SBS13 were present already at diagnosis, and although emerging mutations were lost in later relapses, the process remained active throughout disease evolution. Patient 2 had three relapses. We identified episodic mutational processes at diagnosis and first relapse leading to mutations resembling ultraviolet light-driven DNA damage, and thiopurine-associated damage at first relapse. In conclusion, our data shows that investigation of mutational processes in clusters separated in time may aid in understanding the mutational mechanisms and discovery of underlying causes.
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Affiliation(s)
- Željko Antić
- Princess Máxima Center for Pediatric Oncology, 3584 CS Utrecht, The Netherlands; (Ž.A.); (S.H.L.); (C.G.v.d.H.); (E.S.); (P.M.H.)
| | - Stefan H. Lelieveld
- Princess Máxima Center for Pediatric Oncology, 3584 CS Utrecht, The Netherlands; (Ž.A.); (S.H.L.); (C.G.v.d.H.); (E.S.); (P.M.H.)
| | - Cédric G. van der Ham
- Princess Máxima Center for Pediatric Oncology, 3584 CS Utrecht, The Netherlands; (Ž.A.); (S.H.L.); (C.G.v.d.H.); (E.S.); (P.M.H.)
| | - Edwin Sonneveld
- Princess Máxima Center for Pediatric Oncology, 3584 CS Utrecht, The Netherlands; (Ž.A.); (S.H.L.); (C.G.v.d.H.); (E.S.); (P.M.H.)
- Dutch Childhood Oncology Group, 3584 CS Utrecht, The Netherlands
| | - Peter M. Hoogerbrugge
- Princess Máxima Center for Pediatric Oncology, 3584 CS Utrecht, The Netherlands; (Ž.A.); (S.H.L.); (C.G.v.d.H.); (E.S.); (P.M.H.)
- Dutch Childhood Oncology Group, 3584 CS Utrecht, The Netherlands
| | - Roland P. Kuiper
- Princess Máxima Center for Pediatric Oncology, 3584 CS Utrecht, The Netherlands; (Ž.A.); (S.H.L.); (C.G.v.d.H.); (E.S.); (P.M.H.)
- Department of Genetics, University Medical Center Utrecht, 3508 AB Utrecht, The Netherlands
- Correspondence: ; Tel.: +31-88-97-252-12
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3
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Kaplanis J, Samocha KE, Wiel L, Zhang Z, Arvai KJ, Eberhardt RY, Gallone G, Lelieveld SH, Martin HC, McRae JF, Short PJ, Torene RI, de Boer E, Danecek P, Gardner EJ, Huang N, Lord J, Martincorena I, Pfundt R, Reijnders MRF, Yeung A, Yntema HG, Vissers LELM, Juusola J, Wright CF, Brunner HG, Firth HV, FitzPatrick DR, Barrett JC, Hurles ME, Gilissen C, Retterer K. Evidence for 28 genetic disorders discovered by combining healthcare and research data. Nature 2020; 586:757-762. [PMID: 33057194 PMCID: PMC7116826 DOI: 10.1038/s41586-020-2832-5] [Citation(s) in RCA: 253] [Impact Index Per Article: 63.3] [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: 10/08/2019] [Accepted: 07/17/2020] [Indexed: 01/28/2023]
Abstract
De novo mutations in protein-coding genes are a well-established cause of developmental disorders1. However, genes known to be associated with developmental disorders account for only a minority of the observed excess of such de novo mutations1,2. Here, to identify previously undescribed genes associated with developmental disorders, we integrate healthcare and research exome-sequence data from 31,058 parent-offspring trios of individuals with developmental disorders, and develop a simulation-based statistical test to identify gene-specific enrichment of de novo mutations. We identified 285 genes that were significantly associated with developmental disorders, including 28 that had not previously been robustly associated with developmental disorders. Although we detected more genes associated with developmental disorders, much of the excess of de novo mutations in protein-coding genes remains unaccounted for. Modelling suggests that more than 1,000 genes associated with developmental disorders have not yet been described, many of which are likely to be less penetrant than the currently known genes. Research access to clinical diagnostic datasets will be critical for completing the map of genes associated with developmental disorders.
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Affiliation(s)
- Joanna Kaplanis
- Human Genetics Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Kaitlin E Samocha
- Human Genetics Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Laurens Wiel
- Department of Human Genetics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
- Centre for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | | | | | - Ruth Y Eberhardt
- Human Genetics Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Giuseppe Gallone
- Human Genetics Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Stefan H Lelieveld
- Department of Human Genetics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Hilary C Martin
- Human Genetics Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Jeremy F McRae
- Human Genetics Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Patrick J Short
- Human Genetics Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | | | - Elke de Boer
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Petr Danecek
- Human Genetics Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Eugene J Gardner
- Human Genetics Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Ni Huang
- Human Genetics Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Jenny Lord
- Human Genetics Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
- Human Development and Health, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Iñigo Martincorena
- Human Genetics Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Rolph Pfundt
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Margot R F Reijnders
- Department of Human Genetics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
- Department of Clinical Genetics, Maastricht University Medical Centre, Maastricht, The Netherlands
| | - Alison Yeung
- Victorian Clinical Genetics Services, Melbourne, Victoria, Australia
- Murdoch Children's Research Institute, Melbourne, Victoria, Australia
| | - Helger G Yntema
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Lisenka E L M Vissers
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
| | | | - Caroline F Wright
- Institute of Biomedical and Clinical Science, University of Exeter Medical School, Royal Devon & Exeter Hospital, Exeter, UK
| | - Han G Brunner
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
- Department of Clinical Genetics, Maastricht University Medical Centre, Maastricht, The Netherlands
- GROW School for Oncology and Developmental Biology, Maastricht University Medical Centre, Maastricht, The Netherlands
- MHENS School for Mental Health and Neuroscience, Maastricht University Medical Centre, Maastricht, The Netherlands
| | - Helen V Firth
- Human Genetics Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
- East Anglian Medical Genetics Service, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - David R FitzPatrick
- MRC Human Genetics Unit, MRC IGMM, University of Edinburgh, Western General Hospital, Edinburgh, UK
| | - Jeffrey C Barrett
- Human Genetics Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Matthew E Hurles
- Human Genetics Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK.
| | - Christian Gilissen
- Department of Human Genetics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
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4
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Wesdorp M, de Koning Gans PAM, Schraders M, Oostrik J, Huynen MA, Venselaar H, Beynon AJ, van Gaalen J, Piai V, Voermans N, van Rossum MM, Hartel BP, Lelieveld SH, Wiel L, Verbist B, Rotteveel LJ, van Dooren MF, Lichtner P, Kunst HPM, Feenstra I, Admiraal RJC, Yntema HG, Hoefsloot LH, Pennings RJE, Kremer H. Heterozygous missense variants of LMX1A lead to nonsyndromic hearing impairment and vestibular dysfunction. Hum Genet 2018; 137:389-400. [PMID: 29754270 PMCID: PMC5973959 DOI: 10.1007/s00439-018-1880-5] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [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: 10/29/2017] [Accepted: 03/31/2018] [Indexed: 12/20/2022]
Abstract
Unraveling the causes and pathomechanisms of progressive disorders is essential for the development of therapeutic strategies. Here, we identified heterozygous pathogenic missense variants of LMX1A in two families of Dutch origin with progressive nonsyndromic hearing impairment (HI), using whole exome sequencing. One variant, c.721G > C (p.Val241Leu), occurred de novo and is predicted to affect the homeodomain of LMX1A, which is essential for DNA binding. The second variant, c.290G > C (p.Cys97Ser), predicted to affect a zinc-binding residue of the second LIM domain that is involved in protein–protein interactions. Bi-allelic deleterious variants of Lmx1a are associated with a complex phenotype in mice, including deafness and vestibular defects, due to arrest of inner ear development. Although Lmx1a mouse mutants demonstrate neurological, skeletal, pigmentation and reproductive system abnormalities, no syndromic features were present in the participating subjects of either family. LMX1A has previously been suggested as a candidate gene for intellectual disability, but our data do not support this, as affected subjects displayed normal cognition. Large variability was observed in the age of onset (a)symmetry, severity and progression rate of HI. About half of the affected individuals displayed vestibular dysfunction and experienced symptoms thereof. The late-onset progressive phenotype and the absence of cochleovestibular malformations on computed tomography scans indicate that heterozygous defects of LMX1A do not result in severe developmental abnormalities in humans. We propose that a single LMX1A wild-type copy is sufficient for normal development but insufficient for maintenance of cochleovestibular function. Alternatively, minor cochleovestibular developmental abnormalities could eventually lead to the progressive phenotype seen in the families.
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Affiliation(s)
- Mieke Wesdorp
- Department of Otorhinolaryngology, Hearing and Genes, Radboud University Medical Center, Internal Postal Code 377, P.O. Box 9101, 6500 HB, Nijmegen, The Netherlands
- The Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
- Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Pia A M de Koning Gans
- Department of Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Margit Schraders
- Department of Otorhinolaryngology, Hearing and Genes, Radboud University Medical Center, Internal Postal Code 377, P.O. Box 9101, 6500 HB, Nijmegen, The Netherlands
- Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Jaap Oostrik
- Department of Otorhinolaryngology, Hearing and Genes, Radboud University Medical Center, Internal Postal Code 377, P.O. Box 9101, 6500 HB, Nijmegen, The Netherlands
- Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Martijn A Huynen
- Centre for Molecular and Biomolecular Informatics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Hanka Venselaar
- Centre for Molecular and Biomolecular Informatics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Andy J Beynon
- Department of Otorhinolaryngology, Hearing and Genes, Radboud University Medical Center, Internal Postal Code 377, P.O. Box 9101, 6500 HB, Nijmegen, The Netherlands
| | - Judith van Gaalen
- Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
- Department of Neurology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Vitória Piai
- Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
- Department of Medical Psychology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Nicol Voermans
- Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
- Department of Neurology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Michelle M van Rossum
- Department of Dermatology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Bas P Hartel
- Department of Otorhinolaryngology, Hearing and Genes, Radboud University Medical Center, Internal Postal Code 377, P.O. Box 9101, 6500 HB, Nijmegen, The Netherlands
- Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Stefan H Lelieveld
- The Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Laurens Wiel
- The Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
- Department of Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Berit Verbist
- Department of Radiology, Radboud University Medical Center, Nijmegen, The Netherlands
- Department of Radiology, Leiden University Medical Center, Leiden, The Netherlands
| | | | - Marieke F van Dooren
- Department of Clinical Genetics, Erasmus Medical Centre, Rotterdam, The Netherlands
| | - Peter Lichtner
- Institute of Human Genetics, Helmholtz Zentrum München, Neuherberg, Germany
| | - Henricus P M Kunst
- Department of Otorhinolaryngology, Hearing and Genes, Radboud University Medical Center, Internal Postal Code 377, P.O. Box 9101, 6500 HB, Nijmegen, The Netherlands
| | - Ilse Feenstra
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Ronald J C Admiraal
- Department of Otorhinolaryngology, Hearing and Genes, Radboud University Medical Center, Internal Postal Code 377, P.O. Box 9101, 6500 HB, Nijmegen, The Netherlands
| | - Helger G Yntema
- Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Lies H Hoefsloot
- Department of Clinical Genetics, Erasmus Medical Centre, Rotterdam, The Netherlands
| | - Ronald J E Pennings
- Department of Otorhinolaryngology, Hearing and Genes, Radboud University Medical Center, Internal Postal Code 377, P.O. Box 9101, 6500 HB, Nijmegen, The Netherlands
- Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Hannie Kremer
- Department of Otorhinolaryngology, Hearing and Genes, Radboud University Medical Center, Internal Postal Code 377, P.O. Box 9101, 6500 HB, Nijmegen, The Netherlands.
- Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands.
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands.
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5
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Reijnders MRF, Kousi M, van Woerden GM, Klein M, Bralten J, Mancini GMS, van Essen T, Proietti-Onori M, Smeets EEJ, van Gastel M, Stegmann APA, Stevens SJC, Lelieveld SH, Gilissen C, Pfundt R, Tan PL, Kleefstra T, Franke B, Elgersma Y, Katsanis N, Brunner HG. Variation in a range of mTOR-related genes associates with intracranial volume and intellectual disability. Nat Commun 2017; 8:1052. [PMID: 29051493 PMCID: PMC5648772 DOI: 10.1038/s41467-017-00933-6] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Accepted: 08/08/2017] [Indexed: 11/09/2022] Open
Abstract
De novo mutations in specific mTOR pathway genes cause brain overgrowth in the context of intellectual disability (ID). By analyzing 101 mMTOR-related genes in a large ID patient cohort and two independent population cohorts, we show that these genes modulate brain growth in health and disease. We report the mTOR activator gene RHEB as an ID gene that is associated with megalencephaly when mutated. Functional testing of mutant RHEB in vertebrate animal models indicates pathway hyperactivation with a concomitant increase in cell and head size, aberrant neuronal migration, and induction of seizures, concordant with the human phenotype. This study reveals that tight control of brain volume is exerted through a large community of mTOR-related genes. Human brain volume can be altered, by either rare disruptive events causing hyperactivation of the pathway, or through the collective effects of common alleles.
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Affiliation(s)
- M R F Reijnders
- Department of Human Genetics, Radboud University Medical Center, Donders Institute for Brain, Cognition and Behaviour, Nijmegen, 6500 GA, The Netherlands
| | - M Kousi
- Center for Human Disease Modeling, Duke University, Durham, NC, 27701, USA
| | - G M van Woerden
- Department of Neuroscience and ENCORE Expertise Center for Neurodevelopmental Disorders, Erasmus University Medical Center, 3015 CN, Rotterdam, The Netherlands
| | - M Klein
- Department of Human Genetics, Radboud University Medical Center, Donders Institute for Brain, Cognition and Behaviour, Nijmegen, 6500 GA, The Netherlands
| | - J Bralten
- Department of Human Genetics, Radboud University Medical Center, Donders Institute for Brain, Cognition and Behaviour, Nijmegen, 6500 GA, The Netherlands
| | - G M S Mancini
- Department of Clinical Genetics, Erasmus MC, Sophia Children's Hospital, 3000 CA, Rotterdam, The Netherlands
| | - T van Essen
- Department of Genetics, University of Groningen, University Medical Center of Groningen, 9700 RB, Groningen, The Netherlands
| | - M Proietti-Onori
- Department of Neuroscience and ENCORE Expertise Center for Neurodevelopmental Disorders, Erasmus University Medical Center, 3015 CN, Rotterdam, The Netherlands
| | - E E J Smeets
- Department of Clinical Genetics and School for Oncology & Developmental Biology (GROW), Maastricht University Medical Center, 6202 AZ, Maastricht, The Netherlands
| | - M van Gastel
- Department of Medical Care, SWZ zorg, 5691 AG, Son, The Netherlands
| | - A P A Stegmann
- Department of Clinical Genetics and School for Oncology & Developmental Biology (GROW), Maastricht University Medical Center, 6202 AZ, Maastricht, The Netherlands
| | - S J C Stevens
- Department of Clinical Genetics and School for Oncology & Developmental Biology (GROW), Maastricht University Medical Center, 6202 AZ, Maastricht, The Netherlands
| | - S H Lelieveld
- Department of Human Genetics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, 6500 GA, Nijmegen, The Netherlands
| | - C Gilissen
- Department of Human Genetics, Radboud University Medical Center, Donders Institute for Brain, Cognition and Behaviour, Nijmegen, 6500 GA, The Netherlands
| | - R Pfundt
- Department of Human Genetics, Radboud University Medical Center, Donders Institute for Brain, Cognition and Behaviour, Nijmegen, 6500 GA, The Netherlands
| | - P L Tan
- Center for Human Disease Modeling, Duke University, Durham, NC, 27701, USA
| | - T Kleefstra
- Department of Human Genetics, Radboud University Medical Center, Donders Institute for Brain, Cognition and Behaviour, Nijmegen, 6500 GA, The Netherlands
| | - B Franke
- Department of Human Genetics, Radboud University Medical Center, Donders Institute for Brain, Cognition and Behaviour, Nijmegen, 6500 GA, The Netherlands.,Department of Psychiatry, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, 6500 GA, Nijmegen, The Netherlands
| | - Y Elgersma
- Department of Neuroscience and ENCORE Expertise Center for Neurodevelopmental Disorders, Erasmus University Medical Center, 3015 CN, Rotterdam, The Netherlands
| | - N Katsanis
- Center for Human Disease Modeling, Duke University, Durham, NC, 27701, USA
| | - H G Brunner
- Department of Human Genetics, Radboud University Medical Center, Donders Institute for Brain, Cognition and Behaviour, Nijmegen, 6500 GA, The Netherlands. .,Department of Clinical Genetics and School for Oncology & Developmental Biology (GROW), Maastricht University Medical Center, 6202 AZ, Maastricht, The Netherlands.
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6
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Lelieveld SH, Wiel L, Venselaar H, Pfundt R, Vriend G, Veltman JA, Brunner HG, Vissers LE, Gilissen C. Spatial Clustering of de Novo Missense Mutations Identifies Candidate Neurodevelopmental Disorder-Associated Genes. Am J Hum Genet 2017; 101:478-484. [PMID: 28867141 DOI: 10.1016/j.ajhg.2017.08.004] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2017] [Accepted: 08/04/2017] [Indexed: 10/19/2022] Open
Abstract
Haploinsufficiency (HI) is the best characterized mechanism through which dominant mutations exert their effect and cause disease. Non-haploinsufficiency (NHI) mechanisms, such as gain-of-function and dominant-negative mechanisms, are often characterized by the spatial clustering of mutations, thereby affecting only particular regions or base pairs of a gene. Variants leading to haploinsufficency might occasionally cluster as well, for example in critical domains, but such clustering is on the whole less pronounced with mutations often spread throughout the gene. Here we exploit this property and develop a method to specifically identify genes with significant spatial clustering patterns of de novo mutations in large cohorts. We apply our method to a dataset of 4,061 de novo missense mutations from published exome studies of trios with intellectual disability and developmental disorders (ID/DD) and successfully identify 15 genes with clustering mutations, including 12 genes for which mutations are known to cause neurodevelopmental disorders. For 11 out of these 12, NHI mutation mechanisms have been reported. Additionally, we identify three candidate ID/DD-associated genes of which two have an established role in neuronal processes. We further observe a higher intolerance to normal genetic variation of the identified genes compared to known genes for which mutations lead to HI. Finally, 3D modeling of these mutations on their protein structures shows that 81% of the observed mutations are unlikely to affect the overall structural integrity and that they therefore most likely act through a mechanism other than HI.
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7
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Haer-Wigman L, van Zelst-Stams WA, Pfundt R, van den Born LI, Klaver CC, Verheij JB, Hoyng CB, Breuning MH, Boon CJ, Kievit AJ, Verhoeven VJ, Pott JW, Sallevelt SC, van Hagen JM, Plomp AS, Kroes HY, Lelieveld SH, Hehir-Kwa JY, Castelein S, Nelen M, Scheffer H, Lugtenberg D, Cremers FP, Hoefsloot L, Yntema HG. Diagnostic exome sequencing in 266 Dutch patients with visual impairment. Eur J Hum Genet 2017; 25:591-599. [PMID: 28224992 PMCID: PMC5437915 DOI: 10.1038/ejhg.2017.9] [Citation(s) in RCA: 75] [Impact Index Per Article: 10.7] [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: 06/11/2016] [Revised: 12/16/2016] [Accepted: 01/11/2017] [Indexed: 11/13/2022] Open
Abstract
Inherited eye disorders have a large clinical and genetic heterogeneity, which makes genetic diagnosis cumbersome. An exome-sequencing approach was developed in which data analysis was divided into two steps: the vision gene panel and exome analysis. In the vision gene panel analysis, variants in genes known to cause inherited eye disorders were assessed for pathogenicity. If no causative variants were detected and when the patient consented, the entire exome data was analyzed. A total of 266 Dutch patients with different types of inherited eye disorders, including inherited retinal dystrophies, cataract, developmental eye disorders and optic atrophy, were investigated. In the vision gene panel analysis (likely), causative variants were detected in 49% and in the exome analysis in an additional 2% of the patients. The highest detection rate of (likely) causative variants was in patients with inherited retinal dystrophies, for instance a yield of 63% in patients with retinitis pigmentosa. In patients with developmental eye defects, cataract and optic atrophy, the detection rate was 50, 33 and 17%, respectively. An exome-sequencing approach enables a genetic diagnosis in patients with different types of inherited eye disorders using one test. The exome approach has the same detection rate as targeted panel sequencing tests, but offers a number of advantages. For instance, the vision gene panel can be frequently and easily updated with additional (novel) eye disorder genes. Determination of the genetic diagnosis improved the clinical diagnosis, regarding the assessment of the inheritance pattern as well as future disease perspective.
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Affiliation(s)
- Lonneke Haer-Wigman
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands.,Radboud Institute of Molecular Life Sciences, Nijmegen, The Netherlands
| | | | - Rolph Pfundt
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands.,Radboud Institute of Molecular Life Sciences, Nijmegen, The Netherlands
| | | | - Caroline Cw Klaver
- Department of Ophthalmology, Erasmus Medical Center, Rotterdam, The Netherlands.,Department of Epidemiology, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Joke Bgm Verheij
- Department of Medical Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Carel B Hoyng
- Department of Ophthalmology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Martijn H Breuning
- Department of Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Camiel Jf Boon
- Department of Ophthalmology, Leiden University Medical Center, Leiden, The Netherlands
| | - Anneke J Kievit
- Department of Clinical Genetics, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Virginie Jm Verhoeven
- Department of Ophthalmology, Erasmus Medical Center, Rotterdam, The Netherlands.,Department of Clinical Genetics, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Jan Wr Pott
- Department of Ophthalmology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Suzanne Ceh Sallevelt
- Department of Clinical Genetics, Maastricht University Medical Center, Maastricht, The Netherlands
| | - Johanna M van Hagen
- Department of Clinical Genetics, VU University Medical Center, Amsterdam, The Netherlands
| | - Astrid S Plomp
- Department of Clinical Genetics, Academic Medical Center, Amsterdam, The Netherlands
| | - Hester Y Kroes
- Department of Medical Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Stefan H Lelieveld
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands.,Radboud Institute of Molecular Life Sciences, Nijmegen, The Netherlands
| | - Jayne Y Hehir-Kwa
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands.,Radboud Institute of Molecular Life Sciences, Nijmegen, The Netherlands
| | - Steven Castelein
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands.,Radboud Institute of Molecular Life Sciences, Nijmegen, The Netherlands
| | - Marcel Nelen
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands.,Radboud Institute of Molecular Life Sciences, Nijmegen, The Netherlands
| | - Hans Scheffer
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands.,Radboud Institute of Molecular Life Sciences, Nijmegen, The Netherlands
| | - Dorien Lugtenberg
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands.,Radboud Institute of Molecular Life Sciences, Nijmegen, The Netherlands
| | - Frans Pm Cremers
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands.,Radboud Institute of Molecular Life Sciences, Nijmegen, The Netherlands
| | - Lies Hoefsloot
- Department of Clinical Genetics, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Helger G Yntema
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands.,Radboud Institute of Molecular Life Sciences, Nijmegen, The Netherlands
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8
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Neveling K, Mensenkamp AR, Derks R, Kwint M, Ouchene H, Steehouwer M, van Lier B, Bosgoed E, Rikken A, Tychon M, Zafeiropoulou D, Castelein S, Hehir-Kwa J, Tjwan Thung D, Hofste T, Lelieveld SH, Bertens SMM, Adan IBJF, Eijkelenboom A, Tops BB, Yntema H, Stokowy T, Knappskog PM, Høberg-Vetti H, Steen VM, Boyle E, Martin B, Ligtenberg MJL, Shendure J, Nelen MR, Hoischen A. BRCA Testing by Single-Molecule Molecular Inversion Probes. Clin Chem 2016; 63:503-512. [PMID: 27974384 DOI: 10.1373/clinchem.2016.263897] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2016] [Accepted: 09/29/2016] [Indexed: 12/16/2022]
Abstract
BACKGROUND Despite advances in next generation DNA sequencing (NGS), NGS-based single gene tests for diagnostic purposes require improvements in terms of completeness, quality, speed, and cost. Single-molecule molecular inversion probes (smMIPs) are a technology with unrealized potential in the area of clinical genetic testing. In this proof-of-concept study, we selected 2 frequently requested gene tests, those for the breast cancer genes BRCA1 and BRCA2, and developed an automated work flow based on smMIPs. METHODS The BRCA1 and BRCA2 smMIPs were validated using 166 human genomic DNA samples with known variant status. A generic automated work flow was built to perform smMIP-based enrichment and sequencing for BRCA1, BRCA2, and the checkpoint kinase 2 (CHEK2) c.1100del variant. RESULTS Pathogenic and benign variants were analyzed in a subset of 152 previously BRCA-genotyped samples, yielding an analytical sensitivity and specificity of 100%. Following automation, blind analysis of 65 in-house samples and 267 Norwegian samples correctly identified all true-positive variants (>3000), with no false positives. Consequent to process optimization, turnaround times were reduced by 60% to currently 10-15 days. Copy number variants were detected with an analytical sensitivity of 100% and an analytical specificity of 88%. CONCLUSIONS smMIP-based genetic testing enables automated and reliable analysis of the coding sequences of BRCA1 and BRCA2. The use of single-molecule tags, double-tiled targeted enrichment, and capturing and sequencing in duplo, in combination with automated library preparation and data analysis, results in a robust process and reduces routine turnaround times. Furthermore, smMIP-based copy number variation analysis could make independent copy number variation tools like multiplex ligation-dependent probes amplification dispensable.
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Affiliation(s)
- Kornelia Neveling
- Department of Human Genetics, Radboud university medical center, Nijmegen, the Netherlands
| | - Arjen R Mensenkamp
- Department of Human Genetics, Radboud university medical center, Nijmegen, the Netherlands
| | - Ronny Derks
- Department of Human Genetics, Radboud university medical center, Nijmegen, the Netherlands
| | - Michael Kwint
- Department of Human Genetics, Radboud university medical center, Nijmegen, the Netherlands
| | - Hicham Ouchene
- Department of Human Genetics, Radboud university medical center, Nijmegen, the Netherlands
| | - Marloes Steehouwer
- Department of Human Genetics, Radboud university medical center, Nijmegen, the Netherlands
| | - Bart van Lier
- Department of Human Genetics, Radboud university medical center, Nijmegen, the Netherlands
| | - Ermanno Bosgoed
- Department of Human Genetics, Radboud university medical center, Nijmegen, the Netherlands
| | - Alwin Rikken
- Department of Human Genetics, Radboud university medical center, Nijmegen, the Netherlands
| | - Marloes Tychon
- Department of Human Genetics, Radboud university medical center, Nijmegen, the Netherlands
| | - Dimitra Zafeiropoulou
- Department of Human Genetics, Radboud university medical center, Nijmegen, the Netherlands
| | - Steven Castelein
- Department of Human Genetics, Radboud university medical center, Nijmegen, the Netherlands
| | - Jayne Hehir-Kwa
- Department of Human Genetics, Radboud university medical center, Nijmegen, the Netherlands
| | - Djie Tjwan Thung
- Department of Human Genetics, Radboud university medical center, Nijmegen, the Netherlands
| | - Tom Hofste
- Department of Human Genetics, Radboud university medical center, Nijmegen, the Netherlands
| | - Stefan H Lelieveld
- Department of Human Genetics, Radboud university medical center, Nijmegen, the Netherlands
| | - Stijn M M Bertens
- Department of Mechanical Engineering, Eindhoven University of Technology, Eindhoven, the Netherlands
| | - Ivo B J F Adan
- Department of Mechanical Engineering, Eindhoven University of Technology, Eindhoven, the Netherlands
| | - Astrid Eijkelenboom
- Department of Pathology, Radboud university medical center, Nijmegen, the Netherlands
| | - Bastiaan B Tops
- Department of Pathology, Radboud university medical center, Nijmegen, the Netherlands
| | - Helger Yntema
- Department of Human Genetics, Radboud university medical center, Nijmegen, the Netherlands
| | - Tomasz Stokowy
- Center for Medical Genetics and Molecular Medicine, Haukeland University Hospital, Bergen, Norway.,Western Norway Familial Cancer Center, Haukeland University Hospital, Bergen, Norway
| | - Per M Knappskog
- Center for Medical Genetics and Molecular Medicine, Haukeland University Hospital, Bergen, Norway
| | - Hildegunn Høberg-Vetti
- Center for Medical Genetics and Molecular Medicine, Haukeland University Hospital, Bergen, Norway.,Western Norway Familial Cancer Center, Haukeland University Hospital, Bergen, Norway
| | - Vidar M Steen
- Center for Medical Genetics and Molecular Medicine, Haukeland University Hospital, Bergen, Norway.,Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Evan Boyle
- Department of Genome Sciences, University of Washington, Seattle, WA
| | - Beth Martin
- Department of Genome Sciences, University of Washington, Seattle, WA
| | - Marjolijn J L Ligtenberg
- Department of Human Genetics, Radboud university medical center, Nijmegen, the Netherlands.,Department of Pathology, Radboud university medical center, Nijmegen, the Netherlands
| | - Jay Shendure
- Department of Genome Sciences, University of Washington, Seattle, WA
| | - Marcel R Nelen
- Department of Human Genetics, Radboud university medical center, Nijmegen, the Netherlands;
| | - Alexander Hoischen
- Department of Human Genetics, Radboud university medical center, Nijmegen, the Netherlands.,Donders Centre for Neuroscience, Radboud University Nijmegen, Nijmegen, the Netherlands
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9
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Stevens SJC, van Essen AJ, van Ravenswaaij CMA, Elias AF, Haven JA, Lelieveld SH, Pfundt R, Nillesen WM, Yntema HG, van Roozendaal K, Stegmann AP, Gilissen C, Brunner HG. Truncating de novo mutations in the Krüppel-type zinc-finger gene ZNF148 in patients with corpus callosum defects, developmental delay, short stature, and dysmorphisms. Genome Med 2016; 8:131. [PMID: 27964749 PMCID: PMC5155377 DOI: 10.1186/s13073-016-0386-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [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: 07/19/2016] [Accepted: 12/01/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Krüppel-type zinc finger genes (ZNF) constitute a large yet relatively poorly characterized gene family. ZNF genes encode proteins that recognize specific DNA motifs in gene promotors. They act as transcriptional co-activators or -repressors via interaction with chromatin remodeling proteins and other transcription factors. Only few ZNF genes are currently linked to human disorders and identification of ZNF gene-associated human diseases may help understand their function. Here we provide genetic, statistical, and clinical evidence to support association of ZNF148 with a new intellectual disability (ID) syndrome disorder. METHODS Routine diagnostic exome sequencing data were obtained from 2172 patients with ID and/or multiple congenital anomalies. RESULTS In a cohort of 2172 patient-parent trios referred for routine diagnostic whole exome sequencing for ID and/or multiple congenital anomalies (MCA) in the period 2012-2016, four patients were identified who carried de novo heterozygous nonsense or frameshift mutations in the ZNF148 gene. This was the only ZNF gene with recurrent truncating de novo mutations in this cohort. All mutations resulted in premature termination codons in the last exon of ZNF148. The number of the de novo truncating mutations in the ZNF148 gene was significantly enriched (p = 5.42 × 10-3). The newly described ZNF148-associated syndrome is characterized by underdevelopment of the corpus callosum, mild to moderate developmental delay and ID, variable microcephaly or mild macrocephaly, short stature, feeding problems, facial dysmorphisms, and cardiac and renal malformations. CONCLUSIONS We propose ZNF148 as a gene involved in a newly described ID syndrome with a recurrent phenotype and postulate that the ZNF148 is a hitherto unrecognized but crucial transcription factor in the development of the corpus callosum. Our study illustrates the advantage of whole exome sequencing in a large cohort using a parent-offspring trio approach for identifying novel genes involved in rare human diseases.
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Affiliation(s)
- Servi J C Stevens
- Department of Clinical Genetics, Maastricht University Medical Center (MUMC+), PO Box 5800, 6202, AZ, Maastricht, The Netherlands.
| | - Anthonie J van Essen
- Department of Genetics, University of Groningen, University Medical Center Groningen (UMCG), Groningen, The Netherlands
| | - Conny M A van Ravenswaaij
- Department of Genetics, University of Groningen, University Medical Center Groningen (UMCG), Groningen, The Netherlands
| | - Abdallah F Elias
- Department of Medical Genetics, Shodair Children's Hospital, Helena, MT, USA
| | - Jaclyn A Haven
- Department of Medical Genetics, Shodair Children's Hospital, Helena, MT, USA
| | - Stefan H Lelieveld
- Department of Genetics, Radboud University Medical Center (RUMC), Nijmegen, The Netherlands
| | - Rolph Pfundt
- Department of Genetics, Radboud University Medical Center (RUMC), Nijmegen, The Netherlands
| | - Willy M Nillesen
- Department of Genetics, Radboud University Medical Center (RUMC), Nijmegen, The Netherlands
| | - Helger G Yntema
- Department of Genetics, Radboud University Medical Center (RUMC), Nijmegen, The Netherlands
| | - Kees van Roozendaal
- Department of Clinical Genetics, Maastricht University Medical Center (MUMC+), PO Box 5800, 6202, AZ, Maastricht, The Netherlands.,Department of Genetics, Radboud University Medical Center (RUMC), Nijmegen, The Netherlands
| | - Alexander P Stegmann
- Department of Clinical Genetics, Maastricht University Medical Center (MUMC+), PO Box 5800, 6202, AZ, Maastricht, The Netherlands
| | - Christian Gilissen
- Department of Genetics, Radboud University Medical Center (RUMC), Nijmegen, The Netherlands
| | - Han G Brunner
- Department of Clinical Genetics, Maastricht University Medical Center (MUMC+), PO Box 5800, 6202, AZ, Maastricht, The Netherlands.,Department of Genetics, Radboud University Medical Center (RUMC), Nijmegen, The Netherlands
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10
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Abstract
With the widespread adoption of next generation sequencing technologies by the genetics community and the rapid decrease in costs per base, exome sequencing has become a standard within the repertoire of genetic experiments for both research and diagnostics. Although bioinformatics now offers standard solutions for the analysis of exome sequencing data, many challenges still remain; especially the increasing scale at which exome data are now being generated has given rise to novel challenges in how to efficiently store, analyze and interpret exome data of this magnitude. In this review we discuss some of the recent developments in bioinformatics for exome sequencing and the directions that this is taking us to. With these developments, exome sequencing is paving the way for the next big challenge, the application of whole genome sequencing.
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Affiliation(s)
- Stefan H Lelieveld
- Department of Human Genetics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Geert Grooteplein 10, 6525 GA, Nijmegen, The Netherlands
| | - Joris A Veltman
- Department of Human Genetics, Donders Centre for Neuroscience, Radboudumc, Geert Grooteplein 10, 6525 GA, Nijmegen, The Netherlands
- Department of Clinical Genetics, GROW-School for Oncology and Developmental Biology, Maastricht University Medical Centre, Universiteitssingel 50, 6229 ER, Maastricht, The Netherlands
| | - Christian Gilissen
- Department of Human Genetics, Donders Centre for Neuroscience, Radboudumc, Geert Grooteplein 10, 6525 GA, Nijmegen, The Netherlands.
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11
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Lelieveld SH, Schütte J, Dijkstra MJJ, Bawono P, Kinston SJ, Göttgens B, Heringa J, Bonzanni N. ConBind: motif-aware cross-species alignment for the identification of functional transcription factor binding sites. Nucleic Acids Res 2016; 44:e72. [PMID: 26721389 PMCID: PMC4856970 DOI: 10.1093/nar/gkv1518] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [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: 08/26/2014] [Revised: 12/15/2015] [Accepted: 12/16/2015] [Indexed: 12/23/2022] Open
Abstract
Eukaryotic gene expression is regulated by transcription factors (TFs) binding to promoter as well as distal enhancers. TFs recognize short, but specific binding sites (TFBSs) that are located within the promoter and enhancer regions. Functionally relevant TFBSs are often highly conserved during evolution leaving a strong phylogenetic signal. While multiple sequence alignment (MSA) is a potent tool to detect the phylogenetic signal, the current MSA implementations are optimized to align the maximum number of identical nucleotides. This approach might result in the omission of conserved motifs that contain interchangeable nucleotides such as the ETS motif (IUPAC code: GGAW). Here, we introduce ConBind, a novel method to enhance alignment of short motifs, even if their mutual sequence similarity is only partial. ConBind improves the identification of conserved TFBSs by improving the alignment accuracy of TFBS families within orthologous DNA sequences. Functional validation of the Gfi1b + 13 enhancer reveals that ConBind identifies additional functionally important ETS binding sites that were missed by all other tested alignment tools. In addition to the analysis of known regulatory regions, our web tool is useful for the analysis of TFBSs on so far unknown DNA regions identified through ChIP-sequencing.
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Affiliation(s)
- Stefan H Lelieveld
- Centre for Integrative Bioinformatics VU, VU University Amsterdam, Amsterdam 1081 HV, The Netherlands Department of Human Genetics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen 6525 GA, The Netherlands
| | - Judith Schütte
- Department of Haematology, Wellcome Trust-MRC Cambridge Stem Cell Institute & Cambridge Institute for Medical Research, Cambridge University, Cambridge CB2 0XY, UK Klinik für Hämatologie, Universitätsklinik Essen 45147, Germany
| | - Maurits J J Dijkstra
- Centre for Integrative Bioinformatics VU, VU University Amsterdam, Amsterdam 1081 HV, The Netherlands
| | - Punto Bawono
- Centre for Integrative Bioinformatics VU, VU University Amsterdam, Amsterdam 1081 HV, The Netherlands
| | - Sarah J Kinston
- Department of Haematology, Wellcome Trust-MRC Cambridge Stem Cell Institute & Cambridge Institute for Medical Research, Cambridge University, Cambridge CB2 0XY, UK
| | - Berthold Göttgens
- Department of Haematology, Wellcome Trust-MRC Cambridge Stem Cell Institute & Cambridge Institute for Medical Research, Cambridge University, Cambridge CB2 0XY, UK
| | - Jaap Heringa
- Centre for Integrative Bioinformatics VU, VU University Amsterdam, Amsterdam 1081 HV, The Netherlands
| | - Nicola Bonzanni
- Centre for Integrative Bioinformatics VU, VU University Amsterdam, Amsterdam 1081 HV, The Netherlands Computational Cancer Biology Group, Division of Molecular Carcinogenesis, The Netherlands Cancer Institute, Amsterdam 1066 CX, The Netherlands ENPICOM, Eindhoven 5632 CW, The Netherlands
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12
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Abstract
With the widespread adoption of next generation sequencing technologies by the genetics community and the rapid decrease in costs per base, exome sequencing has become a standard within the repertoire of genetic experiments for both research and diagnostics. Although bioinformatics now offers standard solutions for the analysis of exome sequencing data, many challenges still remain; especially the increasing scale at which exome data are now being generated has given rise to novel challenges in how to efficiently store, analyze and interpret exome data of this magnitude. In this review we discuss some of the recent developments in bioinformatics for exome sequencing and the directions that this is taking us to. With these developments, exome sequencing is paving the way for the next big challenge, the application of whole genome sequencing.
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Affiliation(s)
- Stefan H Lelieveld
- Department of Human Genetics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Geert Grooteplein 10, 6525 GA, Nijmegen, The Netherlands
| | - Joris A Veltman
- Department of Human Genetics, Donders Centre for Neuroscience, Radboudumc, Geert Grooteplein 10, 6525 GA, Nijmegen, The Netherlands.,Department of Clinical Genetics, GROW-School for Oncology and Developmental Biology, Maastricht University Medical Centre, Universiteitssingel 50, 6229 ER, Maastricht, The Netherlands
| | - Christian Gilissen
- Department of Human Genetics, Donders Centre for Neuroscience, Radboudumc, Geert Grooteplein 10, 6525 GA, Nijmegen, The Netherlands.
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13
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Lelieveld SH, Spielmann M, Mundlos S, Veltman JA, Gilissen C. Comparison of Exome and Genome Sequencing Technologies for the Complete Capture of Protein-Coding Regions. Hum Mutat 2015; 36:815-22. [PMID: 25973577 PMCID: PMC4755152 DOI: 10.1002/humu.22813] [Citation(s) in RCA: 123] [Impact Index Per Article: 13.7] [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: 02/19/2015] [Accepted: 04/30/2015] [Indexed: 01/20/2023]
Abstract
For next‐generation sequencing technologies, sufficient base‐pair coverage is the foremost requirement for the reliable detection of genomic variants. We investigated whether whole‐genome sequencing (WGS) platforms offer improved coverage of coding regions compared with whole‐exome sequencing (WES) platforms, and compared single‐base coverage for a large set of exome and genome samples. We find that WES platforms have improved considerably in the last years, but at comparable sequencing depth, WGS outperforms WES in terms of covered coding regions. At higher sequencing depth (95x–160x), WES successfully captures 95% of the coding regions with a minimal coverage of 20x, compared with 98% for WGS at 87‐fold coverage. Three different assessments of sequence coverage bias showed consistent biases for WES but not for WGS. We found no clear differences for the technologies concerning their ability to achieve complete coverage of 2,759 clinically relevant genes. We show that WES performs comparable to WGS in terms of covered bases if sequenced at two to three times higher coverage. This does, however, go at the cost of substantially more sequencing biases in WES approaches. Our findings will guide laboratories to make an informed decision on which sequencing platform and coverage to choose.
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Affiliation(s)
- Stefan H Lelieveld
- Department of Human Genetics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, 6525 GA, The Netherlands
| | - Malte Spielmann
- Institute for Medical Genetics and Human Genetics, Charité Universitätsmedizin Berlin, Berlin, Germany.,Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Stefan Mundlos
- Institute for Medical Genetics and Human Genetics, Charité Universitätsmedizin Berlin, Berlin, Germany.,Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Joris A Veltman
- Department of Human Genetics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, 6525 GA, The Netherlands.,Department of Clinical Genetics, Maastricht University Medical Centre, Maastricht, The Netherlands
| | - Christian Gilissen
- Department of Human Genetics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, 6525 GA, The Netherlands
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