1
|
Essential genes from genome-wide screenings as a resource for neuropsychiatric disorders gene discovery. Transl Psychiatry 2021; 11:317. [PMID: 34035214 PMCID: PMC8149887 DOI: 10.1038/s41398-021-01447-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Revised: 05/04/2021] [Accepted: 05/13/2021] [Indexed: 11/08/2022] Open
Abstract
Genome-wide screenings of "essential genes", i.e., genes required for an organism or cell survival, have been traditionally conducted in vitro in cancer cell lines, limiting the translation of results to other tissues and non-cancerous cells. Recently, an in vivo screening was conducted in adult mouse striatum tissue, providing the first genome-wide dataset of essential genes in neuronal cells. Here, we aim to investigate the role of essential genes in brain development and disease risk with a comprehensive set of bioinformatics tools, including integration with transcriptomic data from developing human brain, publicly available data from genome-wide association studies, de novo mutation datasets for different neuropsychiatric disorders, and case-control transcriptomic data from postmortem brain tissues. For the first time, we found that the expression of neuronal essential genes (NEGs) increases before birth during the early development of human brain and maintains a relatively high expression after birth. On the contrary, common essential genes from cancer cell line screenings (ACEGs) tend to be expressed at high levels during development but quickly drop after birth. Both gene sets were enriched in neurodevelopmental disorders, but only NEGs were robustly associated with neuropsychiatric disorders risk genes. Finally, NEGs were more likely to show differential expression in the brains of neuropsychiatric disorders patients than ACEGs. Overall, genome-wide central nervous system screening of essential genes can provide new insights into neuropsychiatric diseases.
Collapse
|
2
|
Alyousfi D, Baralle D, Collins A. Essentiality-specific pathogenicity prioritization gene score to improve filtering of disease sequence data. Brief Bioinform 2020; 22:1782-1789. [PMID: 32186701 DOI: 10.1093/bib/bbaa029] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2019] [Revised: 02/17/2020] [Accepted: 02/18/2020] [Indexed: 11/12/2022] Open
Abstract
The causal genetic variants underlying more than 50% of single gene (monogenic) disorders are yet to be discovered. Many patients with conditions likely to have a monogenic basis do not receive a confirmed molecular diagnosis which has potential impacts on clinical management. We have developed a gene-specific score, essentiality-specific pathogenicity prioritization (ESPP), to guide the recognition of genes likely to underlie monogenic disease variation to assist in filtering of genome sequence data. When a patient genome is sequenced, there are frequently several plausibly pathogenic variants identified in different genes. Recognition of the single gene most likely to include pathogenic variation can guide the identification of a causal variant. The ESPP score integrates gene-level scores which are broadly related to gene essentiality. Previous work towards the recognition of monogenic disease genes proposed a model with increasing gene essentiality from 'non-essential' to 'essential' genes (for which pathogenic variation may be incompatible with survival) with genes liable to contain disease variation positioned between these two extremes. We demonstrate that the ESPP score is useful for recognizing genes with high potential for pathogenic disease-related variation. Genes classed as essential have particularly high scores, as do genes recently recognized as strong candidates for developmental disorders. Through the integration of individual gene-specific scores, which have different properties and assumptions, we demonstrate the utility of an essentiality-based gene score to improve sequence genome filtering.
Collapse
|
3
|
Cacheiro P, Muñoz-Fuentes V, Murray SA, Dickinson ME, Bucan M, Nutter LMJ, Peterson KA, Haselimashhadi H, Flenniken AM, Morgan H, Westerberg H, Konopka T, Hsu CW, Christiansen A, Lanza DG, Beaudet AL, Heaney JD, Fuchs H, Gailus-Durner V, Sorg T, Prochazka J, Novosadova V, Lelliott CJ, Wardle-Jones H, Wells S, Teboul L, Cater H, Stewart M, Hough T, Wurst W, Sedlacek R, Adams DJ, Seavitt JR, Tocchini-Valentini G, Mammano F, Braun RE, McKerlie C, Herault Y, de Angelis MH, Mallon AM, Lloyd KCK, Brown SDM, Parkinson H, Meehan TF, Smedley D. Human and mouse essentiality screens as a resource for disease gene discovery. Nat Commun 2020; 11:655. [PMID: 32005800 PMCID: PMC6994715 DOI: 10.1038/s41467-020-14284-2] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2019] [Accepted: 12/12/2019] [Indexed: 12/31/2022] Open
Abstract
The identification of causal variants in sequencing studies remains a considerable challenge that can be partially addressed by new gene-specific knowledge. Here, we integrate measures of how essential a gene is to supporting life, as inferred from viability and phenotyping screens performed on knockout mice by the International Mouse Phenotyping Consortium and essentiality screens carried out on human cell lines. We propose a cross-species gene classification across the Full Spectrum of Intolerance to Loss-of-function (FUSIL) and demonstrate that genes in five mutually exclusive FUSIL categories have differing biological properties. Most notably, Mendelian disease genes, particularly those associated with developmental disorders, are highly overrepresented among genes non-essential for cell survival but required for organism development. After screening developmental disorder cases from three independent disease sequencing consortia, we identify potentially pathogenic variants in genes not previously associated with rare diseases. We therefore propose FUSIL as an efficient approach for disease gene discovery.
Collapse
Grants
- UM1 HG008900 NHGRI NIH HHS
- UM1 HG006504 NHGRI NIH HHS
- MC_UP_1502/1 Medical Research Council
- UM1 HG006542 NHGRI NIH HHS
- UM1 OD023221 NIH HHS
- MC_U142684171 Medical Research Council
- MR/S006753/1 Medical Research Council
- UM1 HG006370 NHGRI NIH HHS
- UM1 HG006493 NHGRI NIH HHS
- U54 HG006370 NHGRI NIH HHS
- U54 HG006364 NHGRI NIH HHS
- MC_U142684172 Medical Research Council
- UM1 HG006348 NHGRI NIH HHS
- U42 OD011174 NIH HHS
- U42 OD011175 NIH HHS
- Wellcome Trust
- This work was supported by NIH grant U54 HG006370. IMPC-related mouse production and phenotyping was funded by the Government of Canada through Genome Canada and Ontario Genomics (OGI-051) for NorCOMM2 (C.M.) and the National Institutes of Health and OD, NCRR, NIDDK and NHLBI for KOMP and KOMP2 Projects U42 OD011175 and UM1OD023221 (C.M., K.C.K.L), Infrafrontier grant 01KX1012, EU Horizon2020: IPAD-MD funding 653961 (M.H.d.A); EUCOMM: LSHM-CT-2005-018931, EUCOMMTOOLS: FP7-HEALTH-F4-2010-261492 (W.G.W). UM1 HG006348; U42 OD011174; U54 HG005348 (A.L.B), NIH U54706HG006364 (A.L.B). Wellcome Trust grants WT098051 and WT206194 (D.A). The French National Centre for Scientific Research (CNRS), the French National Institute of Health and Medical Research (INSERM), the University of Strasbourg and the “Centre Europeen de Recherche en Biomedecine”, and the French state funds through the “Agence Nationale de la Recherche” under the frame programme Investissements d’Avenir labelled (ANR-10-IDEX-0002-02, ANR-10-LABX-0030-INRT, ANR-10-INBS-07 PHENOMIN (J.H.). This research was made possible through access to the data and findings generated by the 100,000 Genomes Project. The 100,000 Genomes Project is managed by Genomics England Limited (a wholly owned company of the Department of Health). The 100,000 Genomes Project is funded by the National Institute for Health Research and NHS England. The Wellcome Trust, Cancer Research UK and the Medical Research Council have also funded research infrastructure. The 100,000 Genomes Project uses data provided by patients and collected by the National Health Service as part of their care and support. We are also grateful for the data access provided by the DDD and CMG projects. The DDD study presents independent research commissioned by the Health Innovation Challenge Fund [grant number HICF-1009-003], a parallel funding partnership between Wellcome and the Department of Health, and the Wellcome Sanger Institute [grant number WT098051]. The views expressed in this publication are those of the author(s) and not necessarily those of Wellcome or the Department of Health. The study has UK Research Ethics Committee approval (10/H0305/83, granted by the Cambridge South REC, and GEN/284/12 granted by the Republic of Ireland REC). The research team acknowledges the support of the National Institute for Health Research, through the Comprehensive Clinical Research Network. The Centers for Mendelian Genomics are funded by the National Human Genome Research Institute, the National Heart, Lung, and Blood Institute, and the National Eye Institute. Broad Institute (UM1 HG008900), Johns Hopkins University School of Medicine/Baylor College of Medicine (UM1 HG006542), University of Washington (UM1 HG006493), Yale University (UM1 HG006504).
Collapse
Affiliation(s)
- Pilar Cacheiro
- Clinical Pharmacology, William Harvey Research Institute, School of Medicine and Dentistry, Queen Mary University of London, London, EC1M 6BQ, UK
| | - Violeta Muñoz-Fuentes
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | | | - Mary E Dickinson
- Departments of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, TX, 77030, USA
- Departments of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Maja Bucan
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Lauryl M J Nutter
- The Centre for Phenogenomics, The Hospital for Sick Children, Toronto, ON, M5T 3H7, Canada
| | | | - Hamed Haselimashhadi
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Ann M Flenniken
- The Centre for Phenogenomics, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON, M5T 3H7, Canada
| | - Hugh Morgan
- Medical Research Council Harwell Institute (Mammalian Genetics Unit and Mary Lyon Centre), Harwell, Oxfordshire, OX11 0RD, UK
| | - Henrik Westerberg
- Medical Research Council Harwell Institute (Mammalian Genetics Unit and Mary Lyon Centre), Harwell, Oxfordshire, OX11 0RD, UK
| | - Tomasz Konopka
- Clinical Pharmacology, William Harvey Research Institute, School of Medicine and Dentistry, Queen Mary University of London, London, EC1M 6BQ, UK
| | - Chih-Wei Hsu
- Departments of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Audrey Christiansen
- Departments of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Denise G Lanza
- Departments of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Arthur L Beaudet
- Departments of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Jason D Heaney
- Departments of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Helmut Fuchs
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764, Neuherberg, Germany
| | - Valerie Gailus-Durner
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764, Neuherberg, Germany
| | - Tania Sorg
- Université de Strasbourg, CNRS, INSERM, Institut Clinique de la Souris, PHENOMIN-ICS, 67404, Illkirch, France
| | - Jan Prochazka
- Czech Centre for Phenogenomics, Institute of Molecular Genetics of the Czech Academy of Sciences, Vestec, 252 50, Prague, Czech Republic
| | - Vendula Novosadova
- Czech Centre for Phenogenomics, Institute of Molecular Genetics of the Czech Academy of Sciences, Vestec, 252 50, Prague, Czech Republic
| | | | | | - Sara Wells
- Medical Research Council Harwell Institute (Mammalian Genetics Unit and Mary Lyon Centre), Harwell, Oxfordshire, OX11 0RD, UK
| | - Lydia Teboul
- Medical Research Council Harwell Institute (Mammalian Genetics Unit and Mary Lyon Centre), Harwell, Oxfordshire, OX11 0RD, UK
| | - Heather Cater
- Medical Research Council Harwell Institute (Mammalian Genetics Unit and Mary Lyon Centre), Harwell, Oxfordshire, OX11 0RD, UK
| | - Michelle Stewart
- Medical Research Council Harwell Institute (Mammalian Genetics Unit and Mary Lyon Centre), Harwell, Oxfordshire, OX11 0RD, UK
| | - Tertius Hough
- Medical Research Council Harwell Institute (Mammalian Genetics Unit and Mary Lyon Centre), Harwell, Oxfordshire, OX11 0RD, UK
| | - Wolfgang Wurst
- Institute of Developmental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health GmbH, 85764, Neuherberg, Germany
- Department of Developmental Genetics, Center of Life and Food Sciences Weihenstephan, Technische Universität München, 85764, Neuherberg, Germany
- Deutsches Institut für Neurodegenerative Erkrankungen (DZNE) Site Munich, Munich Cluster for Systems Neurology (SyNergy), Adolf-Butenandt-Institut, Ludwig-Maximilians-Universität München, 80336, Munich, Germany
| | - Radislav Sedlacek
- Czech Centre for Phenogenomics, Institute of Molecular Genetics of the Czech Academy of Sciences, Vestec, 252 50, Prague, Czech Republic
| | - David J Adams
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1SA, UK
| | - John R Seavitt
- Departments of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Glauco Tocchini-Valentini
- Monterotondo Mouse Clinic, Italian National Research Council (CNR), Institute of Cell Biology and Neurobiology, 00015, Monterotondo Scalo, Italy
| | - Fabio Mammano
- Monterotondo Mouse Clinic, Italian National Research Council (CNR), Institute of Cell Biology and Neurobiology, 00015, Monterotondo Scalo, Italy
| | | | - Colin McKerlie
- The Centre for Phenogenomics, The Hospital for Sick Children, Toronto, ON, M5T 3H7, Canada
- Translational Medicine, The Hospital for Sick Children, Toronto, ON, M5T 3H7, Canada
| | - Yann Herault
- Université de Strasbourg, CNRS, INSERM, Institut de Génétique, Biologie Moléculaire et Cellulaire, Institut Clinique de la Souris, IGBMC, PHENOMIN-ICS, 67404, Illkirch, France
| | - Martin Hrabě de Angelis
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764, Neuherberg, Germany
- Department of Experimental Genetics, Center of Life and Food Sciences Weihenstephan, Technische Universität München, 85354, Freising-Weihenstephan, Germany
- German Center for Diabetes Research (DZD), 85764, Neuherberg, Germany
| | - Ann-Marie Mallon
- Medical Research Council Harwell Institute (Mammalian Genetics Unit and Mary Lyon Centre), Harwell, Oxfordshire, OX11 0RD, UK
| | - K C Kent Lloyd
- Mouse Biology Program, University of California, Davis, CA, 95618, USA
| | - Steve D M Brown
- Medical Research Council Harwell Institute (Mammalian Genetics Unit and Mary Lyon Centre), Harwell, Oxfordshire, OX11 0RD, UK
| | - Helen Parkinson
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Terrence F Meehan
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Damian Smedley
- Clinical Pharmacology, William Harvey Research Institute, School of Medicine and Dentistry, Queen Mary University of London, London, EC1M 6BQ, UK.
| |
Collapse
|
4
|
Alyousfi D, Baralle D, Collins A. Gene-specific metrics to facilitate identification of disease genes for molecular diagnosis in patient genomes: a systematic review. Brief Funct Genomics 2018; 18:23-29. [DOI: 10.1093/bfgp/ely033] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2018] [Revised: 08/30/2018] [Accepted: 09/20/2018] [Indexed: 11/13/2022] Open
Affiliation(s)
- Dareen Alyousfi
- Genetic Epidemiology and Bioinformatics Research Group, Human Development and Health, Faculty of Medicine, University of Southampton, UK
| | - Diana Baralle
- Human Development and Health, Faculty of Medicine, University of Southampton, UK
- Wessex Clinical Genetics Service, Princess Anne Hospital, Southampton, UK
| | - Andrew Collins
- Genetic Epidemiology and Bioinformatics Research Group, Human Development and Health, Faculty of Medicine, University of Southampton, UK
| |
Collapse
|
5
|
Sanna-Cherchi S, Khan K, Westland R, Krithivasan P, Fievet L, Rasouly HM, Ionita-Laza I, Capone VP, Fasel DA, Kiryluk K, Kamalakaran S, Bodria M, Otto EA, Sampson MG, Gillies CE, Vega-Warner V, Vukojevic K, Pediaditakis I, Makar GS, Mitrotti A, Verbitsky M, Martino J, Liu Q, Na YJ, Goj V, Ardissino G, Gigante M, Gesualdo L, Janezcko M, Zaniew M, Mendelsohn CL, Shril S, Hildebrandt F, van Wijk JAE, Arapovic A, Saraga M, Allegri L, Izzi C, Scolari F, Tasic V, Ghiggeri GM, Latos-Bielenska A, Materna-Kiryluk A, Mane S, Goldstein DB, Lifton RP, Katsanis N, Davis EE, Gharavi AG. Exome-wide Association Study Identifies GREB1L Mutations in Congenital Kidney Malformations. Am J Hum Genet 2017; 101:789-802. [PMID: 29100090 DOI: 10.1016/j.ajhg.2017.09.018] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2017] [Accepted: 09/22/2017] [Indexed: 01/02/2023] Open
Abstract
Renal agenesis and hypodysplasia (RHD) are major causes of pediatric chronic kidney disease and are highly genetically heterogeneous. We conducted whole-exome sequencing in 202 case subjects with RHD and identified diagnostic mutations in genes known to be associated with RHD in 7/202 case subjects. In an additional affected individual with RHD and a congenital heart defect, we found a homozygous loss-of-function (LOF) variant in SLIT3, recapitulating phenotypes reported with Slit3 inactivation in the mouse. To identify genes associated with RHD, we performed an exome-wide association study with 195 unresolved case subjects and 6,905 control subjects. The top signal resided in GREB1L, a gene implicated previously in Hoxb1 and Shha signaling in zebrafish. The significance of the association, which was p = 2.0 × 10-5 for novel LOF, increased to p = 4.1 × 10-6 for LOF and deleterious missense variants combined, and augmented further after accounting for segregation and de novo inheritance of rare variants (joint p = 2.3 × 10-7). Finally, CRISPR/Cas9 disruption or knockdown of greb1l in zebrafish caused specific pronephric defects, which were rescued by wild-type human GREB1L mRNA, but not mRNA containing alleles identified in case subjects. Together, our study provides insight into the genetic landscape of kidney malformations in humans, presents multiple candidates, and identifies SLIT3 and GREB1L as genes implicated in the pathogenesis of RHD.
Collapse
Affiliation(s)
| | - Kamal Khan
- Center for Human Disease Modeling, Duke University, Durham, NC 27701, USA
| | - Rik Westland
- Division of Nephrology, Columbia University, New York, NY 10032, USA; Department of Pediatric Nephrology, VU University Medical Center, Amsterdam 1007 MB, the Netherlands
| | - Priya Krithivasan
- Division of Nephrology, Columbia University, New York, NY 10032, USA
| | - Lorraine Fievet
- Center for Human Disease Modeling, Duke University, Durham, NC 27701, USA
| | - Hila Milo Rasouly
- Division of Nephrology, Columbia University, New York, NY 10032, USA
| | | | | | - David A Fasel
- Division of Nephrology, Columbia University, New York, NY 10032, USA
| | - Krzysztof Kiryluk
- Division of Nephrology, Columbia University, New York, NY 10032, USA
| | - Sitharthan Kamalakaran
- Institute for Genomic Medicine, Columbia University Medical Center, New York, NY 10032, USA
| | - Monica Bodria
- Division of Nephrology, Dialysis, Transplantation, and Laboratory on Pathophysiology of Uremia, Istituto G. Gaslini, Genoa 16147, Italy
| | - Edgar A Otto
- University of Michigan School of Medicine, Department of Internal Medicine-Nephrology, Ann Arbor, MI 48109, USA
| | - Matthew G Sampson
- University of Michigan School of Medicine, Department of Pediatrics-Nephrology, Ann Arbor, MI 48109, USA
| | - Christopher E Gillies
- University of Michigan School of Medicine, Department of Pediatrics-Nephrology, Ann Arbor, MI 48109, USA
| | - Virginia Vega-Warner
- University of Michigan School of Medicine, Department of Pediatrics-Nephrology, Ann Arbor, MI 48109, USA
| | - Katarina Vukojevic
- Department of Anatomy, Histology, and Embryology, School of Medicine, University of Split, Split 21000, Croatia
| | - Igor Pediaditakis
- Center for Human Disease Modeling, Duke University, Durham, NC 27701, USA
| | - Gabriel S Makar
- Division of Nephrology, Columbia University, New York, NY 10032, USA
| | - Adele Mitrotti
- Division of Nephrology, Columbia University, New York, NY 10032, USA
| | - Miguel Verbitsky
- Division of Nephrology, Columbia University, New York, NY 10032, USA
| | - Jeremiah Martino
- Division of Nephrology, Columbia University, New York, NY 10032, USA
| | - Qingxue Liu
- Division of Nephrology, Columbia University, New York, NY 10032, USA
| | - Young-Ji Na
- Division of Nephrology, Columbia University, New York, NY 10032, USA
| | - Vinicio Goj
- Pediatric Unit, Fatebenefratelli Hospital, Milan 20121, Italy
| | - Gianluigi Ardissino
- Pediatric Nephrology and Dialysis Unit, Fondazione Ca' Granda IRCCS Ospedale Maggiore Policlinico Milano, 20122 Milan, Italy
| | - Maddalena Gigante
- Department of Medical and Surgical Sciences, University of Foggia, Foggia 71121, Italy
| | - Loreto Gesualdo
- Section of Nephrology, Department of Emergency and Organ Transplantation, University of Bari, Bari 70121, Italy
| | - Magdalena Janezcko
- Department of Medical Genetics, Chair of Pediatrics, Jagiellonian University, Collegium Medicum, Krakow 31-008, Poland
| | | | - Cathy Lee Mendelsohn
- Department of Urology, Pathology and Cell Biology, Genetics and Development, Columbia University, New York, NY 10032, USA
| | - Shirlee Shril
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Friedhelm Hildebrandt
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Joanna A E van Wijk
- Department of Pediatric Nephrology, VU University Medical Center, Amsterdam 1007 MB, the Netherlands
| | - Adela Arapovic
- Department of Pediatrics, University Hospital of Split, Split 21000, Croatia
| | - Marijan Saraga
- Department of Pediatrics, University Hospital of Split, Split 21000, Croatia; School of Medicine, University of Split, Split 21000, Croatia
| | - Landino Allegri
- Department of Medicine and Surgery, University of Parma, Parma 43100, Italy
| | - Claudia Izzi
- Cattedra di Nefrologia, Università di Brescia, Seconda Divisione di Nefrologia Azienda Ospedaliera Spedali Civili di Brescia Presidio di Montichiari, Brescia 25018, Italy; Dipartimento Ostetrico Ginecologico, Azienda Ospedaliera Spedali Civili di Brescia, Brescia 25018, Italy
| | - Francesco Scolari
- Cattedra di Nefrologia, Università di Brescia, Seconda Divisione di Nefrologia Azienda Ospedaliera Spedali Civili di Brescia Presidio di Montichiari, Brescia 25018, Italy
| | - Velibor Tasic
- Department of Pediatric Nephrology, University Children's Hospital, Medical Faculty of Skopje, Skopje 1000, Macedonia
| | - Gian Marco Ghiggeri
- Division of Nephrology, Dialysis, Transplantation, and Laboratory on Pathophysiology of Uremia, Istituto G. Gaslini, Genoa 16147, Italy
| | - Anna Latos-Bielenska
- Department of Medical Genetics, Poznan University of Medical Sciences, and Center for Medical Genetics GENESIS, Poznan 61-701, Poland
| | - Anna Materna-Kiryluk
- Department of Medical Genetics, Poznan University of Medical Sciences, and Center for Medical Genetics GENESIS, Poznan 61-701, Poland
| | - Shrikant Mane
- Department of Human Genetics, Yale University School of Medicine, New Haven, CT 06510, USA
| | - David B Goldstein
- Institute for Genomic Medicine, Columbia University Medical Center, New York, NY 10032, USA
| | - Richard P Lifton
- Department of Human Genetics, Yale University School of Medicine, New Haven, CT 06510, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
| | - Nicholas Katsanis
- Center for Human Disease Modeling, Duke University, Durham, NC 27701, USA
| | - Erica E Davis
- Center for Human Disease Modeling, Duke University, Durham, NC 27701, USA.
| | - Ali G Gharavi
- Division of Nephrology, Columbia University, New York, NY 10032, USA
| |
Collapse
|
6
|
Crawford BD, Gillies CE, Robertson CC, Kretzler M, Otto EA, Vega-Warner V, Sampson MG. Evaluating Mendelian nephrotic syndrome genes for evidence for risk alleles or oligogenicity that explain heritability. Pediatr Nephrol 2017; 32:467-476. [PMID: 27766458 PMCID: PMC5483602 DOI: 10.1007/s00467-016-3513-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/06/2016] [Revised: 08/25/2016] [Accepted: 08/29/2016] [Indexed: 01/08/2023]
Abstract
BACKGROUND More than 30 genes can harbor rare exonic variants sufficient to cause nephrotic syndrome (NS), and the number of genes implicated in monogenic NS continues to grow. However, outside the first year of life, the majority of affected patients, particularly in ancestrally mixed populations, do not have a known monogenic form of NS. Even in those children classified with a monogenic form of NS, there is phenotypic heterogeneity. Thus, we have only discovered a fraction of the heritability of NS-the underlying genetic factors contributing to phenotypic variation. Part of the "missing heritability" for NS has been posited to be explained by patients harboring coding variants across one or more previously implicated NS genes, insufficient to cause NS in a classical Mendelian manner, but that nonetheless have a sufficient impact on protein function to cause disease. However, systematic evaluation in patients with NS for rare or low-frequency risk alleles within single genes, or in combination across genes ("oligogenicity"), has not been reported. To determine whether, compared with a reference population, patients with NS have either a significantly increased burden of protein-altering variants ("risk-alleles"), or a unique combination of them ("oligogenicity"), in a set of 21 genes implicated in Mendelian forms of NS. METHODS In 303 patients with NS enrolled in the Nephrotic Syndrome Study Network (NEPTUNE), we performed targeted amplification paired with next-generation sequencing of 21 genes implicated in monogenic NS. We created a high-quality variant call set and compared it with a variant call set of the same genes in a reference population composed of 2,535 individuals from phase 3 of the 1000 Genomes Project. We created both a "stringent" and a "relaxed" pathogenicity-filtering pipeline, applied them to both cohorts, and computed the burden of variants in the entire gene set per cohort, the burden of variants in the entire gene set per individual, the burden of variants within a single gene per cohort, and unique combinations of variants across two or more genes per cohort. RESULTS With few exceptions when using the relaxed filter, and which are likely the result of confounding by population stratification, NS patients did not have a significantly increased burden of variants in Mendelian NS genes in comparison to a reference cohort, nor was there any evidence for oligogenicity. This was true when using both the relaxed and the stringent variant pathogenicity filter. CONCLUSION In our study, there were no significant differences in the burden or particular combinations of low-frequency or rare protein-altering variants in a previously implicated Mendelian NS genes cohort between North American patients with NS and a reference population. Studies in larger independent cohorts or meta-analyses are needed to assess the generalizability of our discoveries and also address whether there is in fact small but significant enrichment of risk alleles or oligogenicity in NS cases that was undetectable with this current sample size. It is still possible that rare protein-altering variants in these genes, insufficient to cause Mendelian disease, still contribute to NS as risk alleles and/or via oligogenicity. However, we suggest that more accurate bioinformatic analyses and the incorporation of functional assays would be necessary to identify bona fide instances of this form of genetic architecture as a contributor to the heritability of NS.
Collapse
Affiliation(s)
- Brendan D Crawford
- Department of Pediatrics, University of Michigan Medical School, 3560B MSRB 2, Ann Arbor, MI, USA
| | - Christopher E Gillies
- Department of Pediatrics, University of Michigan Medical School, 3560B MSRB 2, Ann Arbor, MI, USA
| | - Catherine C Robertson
- Department of Pediatrics, University of Michigan Medical School, 3560B MSRB 2, Ann Arbor, MI, USA
| | - Matthias Kretzler
- Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Edgar A Otto
- Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Virginia Vega-Warner
- Department of Pediatrics, University of Michigan Medical School, 3560B MSRB 2, Ann Arbor, MI, USA
| | - Matthew G Sampson
- Department of Pediatrics, University of Michigan Medical School, 3560B MSRB 2, Ann Arbor, MI, USA.
| |
Collapse
|
7
|
Sampson MG, Gillies CE, Robertson CC, Crawford B, Vega-Warner V, Otto EA, Kretzler M, Kang HM. Using Population Genetics to Interrogate the Monogenic Nephrotic Syndrome Diagnosis in a Case Cohort. J Am Soc Nephrol 2016; 27:1970-83. [PMID: 26534921 PMCID: PMC4926977 DOI: 10.1681/asn.2015050504] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2015] [Accepted: 09/06/2015] [Indexed: 01/02/2023] Open
Abstract
To maximize clinical benefits of genetic screening of patients with nephrotic syndrome (NS) to diagnose monogenic causes, reliably distinguishing NS-causing variants from the background of rare, noncausal variants prevalent in all genomes is vital. To determine the prevalence of monogenic NS in a North American case cohort while accounting for background prevalence of genetic variation, we sequenced 21 implicated monogenic NS genes in 312 participants from the Nephrotic Syndrome Study Network and 61 putative controls from the 1000 Genomes Project (1000G). These analyses were extended to available sequence data from approximately 2500 subjects from the 1000G. A typical pathogenicity filter identified causal variants for NS in 4.2% of patients and 5.8% of subjects from the 1000G. We devised a more stringent pathogenicity filtering strategy, reducing background prevalence of causal variants to 1.5%. When applying this stringent filter to patients, prevalence of monogenic NS was 2.9%; of these patients, 67% were pediatric, and 44% had FSGS on biopsy. The rate of complete remission did not associate with monogenic classification. Thus, we identified factors contributing to inaccurate monogenic classification of NS and developed a more accurate variant filtering strategy. The prevalence and clinical correlates of monogenic NS in this sporadically affected cohort differ substantially from those reported for patients referred for genetic analysis. Particularly in unselected, population-based cases, considering putative causal variants in known NS genes from a probabilistic rather than a deterministic perspective may be more precise. We also introduce GeneVetter, a web tool for monogenic assessment of rare disease.
Collapse
Affiliation(s)
| | | | | | | | | | - Edgar A Otto
- Departments of Pediatrics and Communicable Diseases, and
| | - Matthias Kretzler
- Internal Medicine, Division of Nephrology and Department of Computational Medicine and Bioinformatics, University of Michigan School of Medicine, Ann Arbor, Michigan; and
| | - Hyun Min Kang
- Department of Biostatistics, University of Michigan School of Public Health, Ann Arbor, Michigan
| |
Collapse
|