1
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Moore AR, Yu J, Pei Y, Cheng EWY, Taylor Tavares AL, Walker WT, Thomas NS, Kamath A, Ibitoye R, Josifova D, Wilsdon A, Ross A, Calder AD, Offiah AC, Wilkie AOM, Taylor JC, Pagnamenta AT. Use of genome sequencing to hunt for cryptic second-hit variants: analysis of 31 cases recruited to the 100 000 Genomes Project. J Med Genet 2023; 60:1235-1244. [PMID: 37558402 PMCID: PMC10715503 DOI: 10.1136/jmg-2023-109362] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Accepted: 07/28/2023] [Indexed: 08/11/2023]
Abstract
BACKGROUND Current clinical testing methods used to uncover the genetic basis of rare disease have inherent limitations, which can lead to causative pathogenic variants being missed. Within the rare disease arm of the 100 000 Genomes Project (100kGP), families were recruited under the clinical indication 'single autosomal recessive mutation in rare disease'. These participants presented with strong clinical suspicion for a specific autosomal recessive disorder, but only one suspected pathogenic variant had been identified through standard-of-care testing. Whole genome sequencing (WGS) aimed to identify cryptic 'second-hit' variants. METHODS To investigate the 31 families with available data that remained unsolved following formal review within the 100kGP, SVRare was used to aggregate structural variants present in <1% of 100kGP participants. Small variants were assessed using population allele frequency data and SpliceAI. Literature searches and publicly available online tools were used for further annotation of pathogenicity. RESULTS Using these strategies, 8/31 cases were solved, increasing the overall diagnostic yield of this cohort from 10/41 (24.4%) to 18/41 (43.9%). Exemplar cases include a patient with cystic fibrosis harbouring a novel exonic LINE1 insertion in CFTR and a patient with generalised arterial calcification of infancy with complex interlinked duplications involving exons 2-6 of ENPP1. Although ambiguous by short-read WGS, the ENPP1 variant structure was resolved using optical genome mapping and RNA analysis. CONCLUSION Systematic examination of cryptic variants across a multi-disease cohort successfully identifies additional pathogenic variants. WGS data analysis in autosomal recessive rare disease should consider complex structural and small intronic variants as potentially pathogenic second hits.
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Affiliation(s)
- A Rachel Moore
- Wellcome Centre for Human Genetics, NIHR Oxford Biomedical Research Centre, University of Oxford, Oxford, UK
- Cambridge Genomics Laboratory, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Jing Yu
- Wellcome Centre for Human Genetics, NIHR Oxford Biomedical Research Centre, University of Oxford, Oxford, UK
- Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK
| | - Yang Pei
- Clinical Genetics Group, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | | | | | - Woolf T Walker
- School of Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, UK
- PCD Centre, University Hospital Southampton NHS Foundation Trust, Southampton, UK
| | - N Simon Thomas
- Wessex Regional Genetics Laboratory, Salisbury NHS Foundation Trust, Salisbury, UK
| | - Arveen Kamath
- All Wales Medical Genomics Service, University Hospital of Wales, Cardiff, UK
| | - Rita Ibitoye
- North West Thames Regional Genetics Service, Northwick Park Hospital, Harrow, London, UK
| | - Dragana Josifova
- Department of Clinical Genetics, Guy's and St Thomas' Hospitals NHS Trust, London, UK
| | - Anna Wilsdon
- Clinical Genetics, Nottingham City Hospital, Nottingham, UK
| | - Alison Ross
- Clinical Genetics, NHS Grampian, Aberdeen, UK
| | - Alistair D Calder
- Radiology Department, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - Amaka C Offiah
- Department of Oncology and Metabolism, The University of Sheffield, Sheffield, UK
| | - Andrew O M Wilkie
- Clinical Genetics Group, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Jenny C Taylor
- Wellcome Centre for Human Genetics, NIHR Oxford Biomedical Research Centre, University of Oxford, Oxford, UK
| | - Alistair T Pagnamenta
- Wellcome Centre for Human Genetics, NIHR Oxford Biomedical Research Centre, University of Oxford, Oxford, UK
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2
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Konrad EDH, Nardini N, Caliebe A, Nagel I, Young D, Horvath G, Santoro SL, Shuss C, Ziegler A, Bonneau D, Kempers M, Pfundt R, Legius E, Bouman A, Stuurman KE, Õunap K, Pajusalu S, Wojcik MH, Vasileiou G, Le Guyader G, Schnelle HM, Berland S, Zonneveld-Huijssoon E, Kersten S, Gupta A, Blackburn PR, Ellingson MS, Ferber MJ, Dhamija R, Klee EW, McEntagart M, Lichtenbelt KD, Kenney A, Vergano SA, Abou Jamra R, Platzer K, Ella Pierpont M, Khattar D, Hopkin RJ, Martin RJ, Jongmans MCJ, Chang VY, Martinez-Agosto JA, Kuismin O, Kurki MI, Pietiläinen O, Palotie A, Maarup TJ, Johnson DS, Venborg Pedersen K, Laulund LW, Lynch SA, Blyth M, Prescott K, Canham N, Ibitoye R, Brilstra EH, Shinawi M, Fassi E, Sticht H, Gregor A, Van Esch H, Zweier C. CTCF variants in 39 individuals with a variable neurodevelopmental disorder broaden the mutational and clinical spectrum. Genet Med 2019; 21:2723-2733. [PMID: 31239556 PMCID: PMC6892744 DOI: 10.1038/s41436-019-0585-z] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [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: 04/03/2019] [Accepted: 06/06/2019] [Indexed: 12/28/2022] Open
Abstract
Purpose Pathogenic variants in the chromatin organizer CTCF were previously reported in seven individuals
with a neurodevelopmental disorder (NDD). Methods Through international collaboration we collected data from 39
subjects with variants in CTCF. We performed
transcriptome analysis on RNA from blood samples and utilized Drosophila melanogaster to investigate the impact
of Ctcf dosage alteration on nervous system
development and function. Results The individuals in our cohort carried 2 deletions, 8 likely
gene-disruptive, 2 splice-site, and 20 different missense variants, most of them
de novo. Two cases were familial. The associated phenotype was of variable
severity extending from mild developmental delay or normal IQ to severe
intellectual disability. Feeding difficulties and behavioral abnormalities were
common, and variable other findings including growth restriction and cardiac
defects were observed. RNA-sequencing in five individuals identified 3828
deregulated genes enriched for known NDD genes and biological processes such as
transcriptional regulation. Ctcf dosage
alteration in Drosophila resulted in impaired
gross neurological functioning and learning and memory deficits. Conclusion We significantly broaden the mutational and clinical spectrum ofCTCF-associated NDDs. Our data shed light
onto the functional role of CTCF by identifying deregulated genes and show that
Ctcf alterations result in nervous system defects in Drosophila.
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Affiliation(s)
- Enrico D H Konrad
- Institute of Human Genetics, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Erlangen, Germany
| | - Niels Nardini
- Institute of Human Genetics, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Erlangen, Germany
| | - Almuth Caliebe
- Institute of Human Genetics, Universitätsklinikum Schleswig Holstein Campus Kiel and Christian-Albrechts-Universität, Kiel, Germany
| | - Inga Nagel
- Institute of Human Genetics, Universitätsklinikum Schleswig Holstein Campus Kiel and Christian-Albrechts-Universität, Kiel, Germany.,Institute of Experimental and Clinical Pharmacology, University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - Dana Young
- Adult Metabolic Diseases Clinic, Vancouver General Hospital, Vancouver, BC, Canada
| | - Gabriella Horvath
- Adult Metabolic Diseases Clinic, Vancouver General Hospital, Vancouver, BC, Canada
| | - Stephanie L Santoro
- Division of Molecular and Human Genetics, Nationwide Children's Hospital, Columbus, OH, USA
| | - Christine Shuss
- Division of Molecular and Human Genetics, Nationwide Children's Hospital, Columbus, OH, USA
| | - Alban Ziegler
- Département de Biochimie et Génétique, CHU Angers et Mitolab INSERM 1083-CNRS 6015, Angers, France
| | - Dominique Bonneau
- Département de Biochimie et Génétique, CHU Angers et Mitolab INSERM 1083-CNRS 6015, Angers, France
| | - Marlies Kempers
- Department of Human Genetics, Radboud University Medical Center and Radboud Institute for Molecular Life Sciences, Nijmegen, The Netherlands
| | - Rolph Pfundt
- Department of Human Genetics, Radboud University Medical Center and Radboud Institute for Molecular Life Sciences, Nijmegen, The Netherlands
| | - Eric Legius
- Department of Human Genetics, KU Leuven and Center for Human Genetics, University Hospital Leuven, KU Leuven, Leuven, Belgium
| | - Arjan Bouman
- Department of Clinical Genetics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Kyra E Stuurman
- Department of Clinical Genetics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Katrin Õunap
- Department of Clinical Genetics, United Laboratories, Tartu University Hospital, Tartu, Estonia.,Department of Clinical Genetics, Institute of Clinical Medicine, University of Tartu, Tartu, Estonia.,The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Sander Pajusalu
- Department of Clinical Genetics, United Laboratories, Tartu University Hospital, Tartu, Estonia.,Department of Clinical Genetics, Institute of Clinical Medicine, University of Tartu, Tartu, Estonia.,Department of Genetics, Yale University School of Medicine, New Haven, CT, USA
| | - Monica H Wojcik
- The Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Divisions of Genetics and Genomics and Newborn Medicine, Department of Pediatrics, Boston Children's Hospital, Boston, MA, USA
| | - Georgia Vasileiou
- Institute of Human Genetics, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Erlangen, Germany
| | | | - Hege M Schnelle
- Department of Medical Genetics, Haukeland University Hospital, Bergen, Norway
| | - Siren Berland
- Department of Medical Genetics, Haukeland University Hospital, Bergen, Norway
| | - Evelien Zonneveld-Huijssoon
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Simone Kersten
- Department of Human Genetics, Radboud University Medical Center and Radboud Institute for Molecular Life Sciences, Nijmegen, The Netherlands
| | - Aditi Gupta
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA
| | - Patrick R Blackburn
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Marissa S Ellingson
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Matthew J Ferber
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Radhika Dhamija
- Department of Clinical Genomics, Mayo Clinic, Scottsdale, AZ, USA
| | - Eric W Klee
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA
| | - Meriel McEntagart
- South West Thames Regional Genetics Centre, St. George's Healthcare NHS Trust, St. George's, University of London, London, UK
| | - Klaske D Lichtenbelt
- Department of Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Amy Kenney
- Division of Medical Genetics and Metabolism, Children's Hospital of The King's Daughters, Norfolk, VA, USA
| | - Samantha A Vergano
- Division of Medical Genetics and Metabolism, Children's Hospital of The King's Daughters, Norfolk, VA, USA
| | - Rami Abou Jamra
- Institute of Human Genetics, University of Leipzig Medical Center, Leipzig, Germany
| | - Konrad Platzer
- Institute of Human Genetics, University of Leipzig Medical Center, Leipzig, Germany
| | - Mary Ella Pierpont
- Department of Pediatrics, Division of Genetics and Metabolism, University of Minnesota, Minneapolis, MN, USA
| | - Divya Khattar
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Robert J Hopkin
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Richard J Martin
- The Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
| | - Marjolijn C J Jongmans
- Department of Human Genetics, Radboud University Medical Center and Radboud Institute for Molecular Life Sciences, Nijmegen, The Netherlands
| | - Vivian Y Chang
- Division of Pediatric Hematology-Oncology, Department of Pediatrics, David Geffen School of Medicine, Los Angeles, CA, USA.,Jonsson Comprehensive Cancer Center, University of California, Los Angeles, CA, USA
| | - Julian A Martinez-Agosto
- Division of Medical Genetics, Department of Pediatrics, David Geffen School of Medicine, University of California, Los Angeles, CA, USA.,Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
| | - Outi Kuismin
- Institute for Molecular Medicine Finland, University of Helsinki, Helsinki, Finland.,PEDEGO Research Unit, University of Oulu, Oulu, Finland.,Medical Research Center, Oulu University Hospital, University of Oulu, Oulu, Finland.,Department of Clinical Genetics, Oulu University Hospital, Oulu, Finland
| | - Mitja I Kurki
- Institute for Molecular Medicine Finland, University of Helsinki, Helsinki, Finland.,Psychiatric & Neurodevelopmental Genetics Unit, Massachusetts General Hospital, Boston, MA, USA.,The Stanley Center for Psychiatric Research, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Olli Pietiläinen
- The Stanley Center for Psychiatric Research, The Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Department of Stem Cell and Regenerative Biology, University of Harvard, Cambridge, MA, USA
| | - Aarno Palotie
- Institute for Molecular Medicine Finland, University of Helsinki, Helsinki, Finland.,Psychiatric & Neurodevelopmental Genetics Unit, Massachusetts General Hospital, Boston, MA, USA.,The Stanley Center for Psychiatric Research, The Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA.,Department of Neurology, Massachusetts General Hospital, Boston, MA, USA
| | | | | | | | - Lone W Laulund
- Department of Pediatrics, Odense University Hospital, Odense, Denmark
| | - Sally A Lynch
- University College Dublin and Temple Street Children's Hospital, Dublin, Ireland
| | - Moira Blyth
- Yorkshire Regional Genetics Service, Chapel Allerton Hospital, Leeds Teaching Hospitals NHS Trust, Leeds, UK
| | - Katrina Prescott
- Yorkshire Regional Genetics Service, Chapel Allerton Hospital, Leeds Teaching Hospitals NHS Trust, Leeds, UK
| | - Natalie Canham
- North West Thames Regional Genetics Service, Northwick Park Hospital, Harrow, UK
| | - Rita Ibitoye
- North West Thames Regional Genetics Service, Northwick Park Hospital, Harrow, UK
| | - Eva H Brilstra
- Department of Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Marwan Shinawi
- Division of Genetics and Genomic Medicine, Department of Pediatrics, Washington University School of Medicine, St. Louis, MO, USA
| | - Emily Fassi
- Division of Genetics and Genomic Medicine, Department of Pediatrics, Washington University School of Medicine, St. Louis, MO, USA
| | | | - Heinrich Sticht
- Institute of Biochemistry, Emil-Fischer Center, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Anne Gregor
- Institute of Human Genetics, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Erlangen, Germany
| | - Hilde Van Esch
- Center for Human Genetics, University Hospital Leuven, KU Leuven, Leuven, Belgium
| | - Christiane Zweier
- Institute of Human Genetics, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Erlangen, Germany.
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3
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Bengani H, Handley M, Alvi M, Ibitoye R, Lees M, Lynch SA, Lam W, Fannemel M, Nordgren A, Malmgren H, Kvarnung M, Mehta S, McKee S, Whiteford M, Stewart F, Connell F, Clayton-Smith J, Mansour S, Mohammed S, Fryer A, Morton J, Grozeva D, Asam T, Moore D, Sifrim A, McRae J, Hurles ME, Firth HV, Raymond FL, Kini U, Nellåker C, Ddd Study, FitzPatrick DR. Clinical and molecular consequences of disease-associated de novo mutations in SATB2. Genet Med 2017; 19:900-908. [PMID: 28151491 PMCID: PMC5548934 DOI: 10.1038/gim.2016.211] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2016] [Accepted: 11/01/2016] [Indexed: 02/03/2023] Open
Abstract
PURPOSE To characterize features associated with de novo mutations affecting SATB2 function in individuals ascertained on the basis of intellectual disability. METHODS Twenty previously unreported individuals with 19 different SATB2 mutations (11 loss-of-function and 8 missense variants) were studied. Fibroblasts were used to measure mutant protein production. Subcellular localization and mobility of wild-type and mutant SATB2 were assessed using fluorescently tagged protein. RESULTS Recurrent clinical features included neurodevelopmental impairment (19/19), absent/near absent speech (16/19), normal somatic growth (17/19), cleft palate (9/19), drooling (12/19), and dental anomalies (8/19). Six of eight missense variants clustered in the first CUT domain. Sibling recurrence due to gonadal mosaicism was seen in one family. A nonsense mutation in the last exon resulted in production of a truncated protein retaining all three DNA-binding domains. SATB2 nuclear mobility was mutation-dependent; p.Arg389Cys in CUT1 increased mobility and both p.Gly515Ser in CUT2 and p.Gln566Lys between CUT2 and HOX reduced mobility. The clinical features in individuals with missense variants were indistinguishable from those with loss of function. CONCLUSION SATB2 haploinsufficiency is a common cause of syndromic intellectual disability. When mutant SATB2 protein is produced, the protein appears functionally inactive with a disrupted pattern of chromatin or matrix association.Genet Med advance online publication 02 February 2017.
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Affiliation(s)
- Hemant Bengani
- MRC Human Genetics Unit, IGMM, University of Edinburgh, Western General Hospital, Edinburgh, UK
| | - Mark Handley
- MRC Human Genetics Unit, IGMM, University of Edinburgh, Western General Hospital, Edinburgh, UK
| | - Mohsan Alvi
- Avdeling for Medisinsk Genetikk, Oslo Universitetssykehus, Oslo, Norway
| | - Rita Ibitoye
- Department of Clinical Genetics, Oxford University Hospitals NHS Trust, Oxford, UK
| | - Melissa Lees
- North East Regional Genetics Service, Great Ormond Street Hospital, London, UK
| | - Sally Ann Lynch
- National Centre for Medical Genetics, Our Lady's Children's Hospital, Dublin, Ireland
| | - Wayne Lam
- South East Scotland Genetic Service, Western General Hospital, Edinburgh, UK
| | | | - Ann Nordgren
- Clinical Genetics Unit, Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
| | - H Malmgren
- Clinical Genetics Unit, Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
| | - M Kvarnung
- Clinical Genetics Unit, Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
| | - Sarju Mehta
- Department of Clinical Genetics, Cambridge University Hospitals NHS Foundation, Cambridge, UK
| | - Shane McKee
- Northern Ireland Regional Genetics Centre, Belfast City Hospital, Belfast, UK
| | - Margo Whiteford
- West of Scotland Genetic Services, Queen Elizabeth University Hospital, Glasgow, UK
| | - Fiona Stewart
- Northern Ireland Regional Genetics Centre, Belfast City Hospital, Belfast, UK
| | - Fiona Connell
- South East Thames Regional Genetics Service, Guy's and St Thomas' NHS Foundation Trust, London, UK
| | | | - Sahar Mansour
- Department of Clinical Genetics, St Georges Hospital, Tooting, UK
| | - Shehla Mohammed
- South East Thames Regional Genetics Service, Guy's and St Thomas' NHS Foundation Trust, London, UK
| | - Alan Fryer
- Cheshire &Merseyside Regional Genetics Service, Liverpool Women's NHS foundation Trust, Liverpool, UK
| | - Jenny Morton
- West Midlands Regional Genetics Service, Birmingham Women's NHS Foundation Trust, Birmingham, UK
| | | | - Detelina Grozeva
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, UK
| | - Tara Asam
- South-East Scotland Regional Genetics Laboratories, Western General Hospital, Edinburgh, UK
| | - David Moore
- South-East Scotland Regional Genetics Laboratories, Western General Hospital, Edinburgh, UK
| | - Alejandro Sifrim
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Cambridge, UK
| | - Jeremy McRae
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Cambridge, UK
| | - Matthew E Hurles
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Cambridge, UK
| | - Helen V Firth
- Department of Clinical Genetics, Cambridge University Hospitals NHS Foundation, Cambridge, UK
| | - F Lucy Raymond
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, UK
| | - Usha Kini
- Department of Clinical Genetics, Oxford University Hospitals NHS Trust, Oxford, UK.,Spires Cleft Centre, John Radcliffe Hospital, Oxford, UK
| | - Christoffer Nellåker
- Nuffield Department of Obstetrics &Gynaecology, University of Oxford, Women's Centre, John Radcliffe Hospital, Oxford, UK.,Department of Engineering Science, University of Oxford, Institute of Biomedical Engineering, Oxford, UK.,Big Data Institute, University of Oxford, Oxford, UK
| | - Ddd Study
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Cambridge, UK
| | - David R FitzPatrick
- MRC Human Genetics Unit, IGMM, University of Edinburgh, Western General Hospital, Edinburgh, UK
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