2
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Shadrina M, Kalay Ö, Demirkaya-Budak S, LeDuc CA, Chung WK, Turgut D, Budak G, Arslan E, Semenyuk V, Davis-Dusenbery B, Seidman CE, Yost HJ, Jain A, Gelb BD. Automated Identification of Germline de novo Mutations in Family Trios: A Consensus-Based Informatic Approach. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.08.584100. [PMID: 38559260 PMCID: PMC10979888 DOI: 10.1101/2024.03.08.584100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Accurate identification of germline de novo variants (DNVs) remains a challenging problem despite rapid advances in sequencing technologies as well as methods for the analysis of the data they generate, with putative solutions often involving ad hoc filters and visual inspection of identified variants. Here, we present a purely informatic method for the identification of DNVs by analyzing short-read genome sequencing data from proband-parent trios. Our method evaluates variant calls generated by three genome sequence analysis pipelines utilizing different algorithms-GATK HaplotypeCaller, DeepTrio and Velsera GRAF-exploring the assumption that a requirement of consensus can serve as an effective filter for high-quality DNVs. We assessed the efficacy of our method by testing DNVs identified using a previously established, highly accurate classification procedure that partially relied on manual inspection and used Sanger sequencing to validate a DNV subset comprising less confident calls. The results show that our method is highly precise and that applying a force-calling procedure to putative variants further removes false-positive calls, increasing precision of the workflow to 99.6%. Our method also identified novel DNVs, 87% of which were validated, indicating it offers a higher recall rate without compromising accuracy. We have implemented this method as an automated bioinformatics workflow suitable for large-scale analyses without need for manual intervention.
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Affiliation(s)
- Mariya Shadrina
- Mindich Child Health and Development Institute and the Department of Genetics and Genomic Sciences, Icahn School of Medicine, New York, NY, USA
| | - Özem Kalay
- Velsera Inc, 529 Main St, Suite 6610, Charlestown, MA, USA
| | | | - Charles A. LeDuc
- Department of Pediatrics, Columbia University, New York, NY, USA
| | - Wendy K. Chung
- Department of Pediatrics, Boston Children’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Deniz Turgut
- Velsera Inc, 529 Main St, Suite 6610, Charlestown, MA, USA
| | - Gungor Budak
- Velsera Inc, 529 Main St, Suite 6610, Charlestown, MA, USA
| | - Elif Arslan
- Velsera Inc, 529 Main St, Suite 6610, Charlestown, MA, USA
| | | | | | - Christine E. Seidman
- Division of Cardiovascular Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - H. Joseph Yost
- Molecular Medicine Program, University of Utah, Salt Lake City, UT, USA
| | - Amit Jain
- Velsera Inc, 529 Main St, Suite 6610, Charlestown, MA, USA
| | - Bruce D. Gelb
- Mindich Child Health and Development Institute and the Department of Genetics and Genomic Sciences, Icahn School of Medicine, New York, NY, USA
- Department of Pediatrics, Icahn School of Medicine, New York, NY, USA
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3
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Mattison KA, Tossing G, Mulroe F, Simmons C, Butler KM, Schreiber A, Alsadah A, Neilson DE, Naess K, Wedell A, Wredenberg A, Sorlin A, McCann E, Burghel GJ, Menendez B, Hoganson GE, Botto LD, Filloux FM, Aledo-Serrano Á, Gil-Nagel A, Tatton-Brown K, Verbeek NE, van der Zwaag B, Aleck KA, Fazenbaker AC, Balciuniene J, Dubbs HA, Marsh ED, Garber K, Ek J, Duno M, Hoei-Hansen CE, Deardorff MA, Raca G, Quindipan C, van Hirtum-Das M, Breckpot J, Hammer TB, Møller RS, Whitney A, Douglas AGL, Kharbanda M, Brunetti-Pierri N, Morleo M, Nigro V, May HJ, Tao JX, Argilli E, Sherr EH, Dobyns WB, Baines RA, Warwicker J, Parker JA, Banka S, Campeau PM, Escayg A. ATP6V0C variants impair V-ATPase function causing a neurodevelopmental disorder often associated with epilepsy. Brain 2023; 146:1357-1372. [PMID: 36074901 PMCID: PMC10319782 DOI: 10.1093/brain/awac330] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Revised: 07/29/2022] [Accepted: 08/14/2022] [Indexed: 11/14/2022] Open
Abstract
The vacuolar H+-ATPase is an enzymatic complex that functions in an ATP-dependent manner to pump protons across membranes and acidify organelles, thereby creating the proton/pH gradient required for membrane trafficking by several different types of transporters. We describe heterozygous point variants in ATP6V0C, encoding the c-subunit in the membrane bound integral domain of the vacuolar H+-ATPase, in 27 patients with neurodevelopmental abnormalities with or without epilepsy. Corpus callosum hypoplasia and cardiac abnormalities were also present in some patients. In silico modelling suggested that the patient variants interfere with the interactions between the ATP6V0C and ATP6V0A subunits during ATP hydrolysis. Consistent with decreased vacuolar H+-ATPase activity, functional analyses conducted in Saccharomyces cerevisiae revealed reduced LysoSensor fluorescence and reduced growth in media containing varying concentrations of CaCl2. Knockdown of ATP6V0C in Drosophila resulted in increased duration of seizure-like behaviour, and the expression of selected patient variants in Caenorhabditis elegans led to reduced growth, motor dysfunction and reduced lifespan. In summary, this study establishes ATP6V0C as an important disease gene, describes the clinical features of the associated neurodevelopmental disorder and provides insight into disease mechanisms.
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Affiliation(s)
- Kari A Mattison
- Genetics and Molecular Biology Graduate Program, Graduate Division of Biological and Biomedical Sciences, Laney Graduate School, Emory University, Atlanta, GA, USA
- Department of Human Genetics, Emory University, Atlanta, GA, USA
| | - Gilles Tossing
- Department of Neuroscience, University of Montreal, Montreal, QC, Canada
| | - Fred Mulroe
- Division of Neuroscience and Experimental Psychology, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Center, Manchester, UK
| | - Callum Simmons
- Division of Neuroscience and Experimental Psychology, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Center, Manchester, UK
| | - Kameryn M Butler
- Department of Human Genetics, Emory University, Atlanta, GA, USA
- Greenwood Genetics Center, Greenwood, SC, USA
| | - Alison Schreiber
- Center for Personalized Genetic Healthcare, Cleveland Clinic, Cleveland, OH, USA
| | - Adnan Alsadah
- Center for Personalized Genetic Healthcare, Cleveland Clinic, Cleveland, OH, USA
| | - Derek E Neilson
- Division of Genetics and Metabolism, Department of Child Health, The University of Arizona College of Medicine, Phoenix, AZ, USA
- Department of Genetics and Metabolism, Phoenix Children’s Hospital, Phoenix Children’s Medical Group, Phoenix, AZ, USA
| | - Karin Naess
- Center for Inherited Metabolic Diseases, Karolinska University Hospital, Stockholm, Sweden
- Department of Medical Biochemistry and Biophysics, Karolinska Institute, Stockholm, Sweden
| | - Anna Wedell
- Center for Inherited Metabolic Diseases, Karolinska University Hospital, Stockholm, Sweden
- Deparment of Molecular Medicine and Surgery, Karolinska Institute, Stockholm, Sweden
| | - Anna Wredenberg
- Center for Inherited Metabolic Diseases, Karolinska University Hospital, Stockholm, Sweden
- Department of Medical Biochemistry and Biophysics, Karolinska Institute, Stockholm, Sweden
| | - Arthur Sorlin
- National Center of Genetics, Laboratoire National de Santé, Dudelange, Luxembourg
| | - Emma McCann
- Liverpool Center for Genomic Medicine, Liverpool Women’s Hospital, Liverpool, UK
| | - George J Burghel
- Genomic Diagnostic Laboratory, St. Mary’s Hospital, Manchester University NHS Foundation Trust, Manchester, UK
| | | | - George E Hoganson
- Division of Genetics, Department of Pediatrics, University of Illinois College of Medicine, Chicago, IL, USA
| | - Lorenzo D Botto
- Division of Medical Genetics, Department of Pediatrics, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Francis M Filloux
- Division of Pediatric Neurology, Department of Pediatrics, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Ángel Aledo-Serrano
- Genetic Epilepsy Program, Department of Neurology, Ruber International Hospital, Madrid, Spain
| | - Antonio Gil-Nagel
- Genetic Epilepsy Program, Department of Neurology, Ruber International Hospital, Madrid, Spain
| | - Katrina Tatton-Brown
- Medical Genetics, St. George’s University Hospitals NHS Foundation Trust and Institute for Molecular and Cell Sciences, St. George’s, University of London, London, UK
| | - Nienke E Verbeek
- Department of Genetics, University Medical Center Utrecht, Member of the ERN EpiCARE, Utrecht, The Netherlands
| | - Bert van der Zwaag
- Department of Genetics, University Medical Center Utrecht, Member of the ERN EpiCARE, Utrecht, The Netherlands
| | - Kyrieckos A Aleck
- Division of Genetics and Metabolism, Department of Child Health, The University of Arizona College of Medicine, Phoenix, AZ, USA
- Department of Genetics and Metabolism, Phoenix Children’s Hospital, Phoenix Children’s Medical Group, Phoenix, AZ, USA
| | - Andrew C Fazenbaker
- Department of Genetics and Metabolism, Phoenix Children’s Hospital, Phoenix Children’s Medical Group, Phoenix, AZ, USA
| | - Jorune Balciuniene
- Divison of Genomic Diagnostics, Department of Pathology and Laboratory Medicine, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- PerkinElmer Genomics, Pittsburgh, PA, USA
| | - Holly A Dubbs
- Division of Neurology, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - Eric D Marsh
- Division of Neurology, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - Kathryn Garber
- Department of Human Genetics, Emory University, Atlanta, GA, USA
| | - Jakob Ek
- Department of Clinical Genetics, University Hospital of Copenhagen, Copenhagen, Denmark
| | - Morten Duno
- Department of Clinical Genetics, University Hospital of Copenhagen, Copenhagen, Denmark
| | - Christina E Hoei-Hansen
- Department of Pediatrics, University Hospital of Copenhagen, Copenhagen, Denmark
- Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Matthew A Deardorff
- Department of Pathology and Laboratory Medicine, Children’s Hospital Los Angeles, Los Angeles, CA, USA
- Department of Pediatrics, Division of Medical Genetics, Children’s Hospital Los Angeles, Los Angeles, CA, USA
- Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Gordana Raca
- Department of Pathology and Laboratory Medicine, Children’s Hospital Los Angeles, Los Angeles, CA, USA
- Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Catherine Quindipan
- Center for Personalized Medicine, Children’s Hospital Los Angeles, Los Angeles, CA, USA
| | - Michele van Hirtum-Das
- Department of Pediatrics, Division of Medical Genetics, Children’s Hospital Los Angeles, Los Angeles, CA, USA
- Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Jeroen Breckpot
- Center for Human Genetics, University Hospitals Leuven, Leuven, Belgium
| | - Trine Bjørg Hammer
- Department of Epilepsy Genetics and Personalized Medicine, Danish Epilepsy Center, Fildelfia, Dianalund, Denmark
| | - Rikke S Møller
- Department of Epilepsy Genetics and Personalized Medicine, Danish Epilepsy Center, Fildelfia, Dianalund, Denmark
- Insititue for Regional Health Services Research, University of Southern Denmark, Odense, Denmark
| | - Andrea Whitney
- Pediatric Neurology, University Hospital Southampton NHS Foundation Trust, Southampton, UK
| | - Andrew G L Douglas
- Wessex Clinical Genetics Service, University of Southampton, Southampton, UK
- Human Development and Health, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Mira Kharbanda
- Human Development and Health, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Nicola Brunetti-Pierri
- Telethon Institute of Genetics and Medicine (TIGEM), Pozzuoli, Italy
- Department of Translational Medicine, Federico II University of Naples, Naples, Italy
| | - Manuela Morleo
- Telethon Institute of Genetics and Medicine (TIGEM), Pozzuoli, Italy
- Department of Precision Medicine, University of Campania ‘Luigi Vanvitelli’, Naples, Italy
| | - Vincenzo Nigro
- Telethon Institute of Genetics and Medicine (TIGEM), Pozzuoli, Italy
- Department of Precision Medicine, University of Campania ‘Luigi Vanvitelli’, Naples, Italy
| | - Halie J May
- Institute for Genomic Medicine, Columbia University Irving Medical Center, New York, NY, USA
| | - James X Tao
- Department of Neurology, University of Chicago, Chicago, IL, USA
| | - Emanuela Argilli
- Department of Neurology, University of California, San Francisco, San Francisco, CA, USA
- Pediatrics Institute of Human Genetics and Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA
| | - Elliot H Sherr
- Department of Neurology, University of California, San Francisco, San Francisco, CA, USA
- Pediatrics Institute of Human Genetics and Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA
| | - William B Dobyns
- Department of Pediatrics, Division of Genetics and Metabolism, University of Minnesota, Minneapolis, MN, USA
| | | | - Richard A Baines
- Division of Neuroscience and Experimental Psychology, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Center, Manchester, UK
| | - Jim Warwicker
- School of Biological Sciences, Faculty of Biology, Medicine and Health, Manchester Institute of Biotechnology, University of Manchester, Manchester, UK
| | - J Alex Parker
- Department of Neuroscience, University of Montreal, Montreal, QC, Canada
| | - Siddharth Banka
- Division of Evolution, Infection, and Genomics, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
| | | | - Andrew Escayg
- Department of Human Genetics, Emory University, Atlanta, GA, USA
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4
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Odgis JA, Gallagher KM, Rehman AU, Marathe P, Bonini KE, Sebastin M, Di Biase M, Brown K, Kelly NR, Ramos MA, Thomas-Wilson A, Guha S, Okur V, Ganapathi M, Elkhoury L, Edelmann L, Zinberg RE, Abul-Husn NS, Diaz GA, Greally JM, Suckiel SA, Jobanputra V, Horowitz CR, Kenny EE, Wasserstein MP, Gelb BD. Detection of mosaic variants using genome sequencing in a large pediatric cohort. Am J Med Genet A 2023; 191:699-710. [PMID: 36563179 PMCID: PMC10266700 DOI: 10.1002/ajmg.a.63062] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Revised: 11/07/2022] [Accepted: 11/18/2022] [Indexed: 12/24/2022]
Abstract
The increased use of next-generation sequencing has expanded our understanding of the involvement and prevalence of mosaicism in genetic disorders. We describe a total of eleven cases: nine in which mosaic variants detected by genome sequencing (GS) and/or targeted gene panels (TGPs) were considered to be causative for the proband's phenotype, and two of apparent parental mosaicism. Variants were identified in the following genes: PHACTR1, SCN8A, KCNT1, CDKL5, NEXMIF, CUX1, TSC2, GABRB2, and SMARCB1. In addition, we identified one large duplication including three genes, UBE3A, GABRB3, and MAGEL2, and one large deletion including deletion of ARFGAP1, EEF1A2, CHRNA4, and KCNQ2. All patients were enrolled in the NYCKidSeq study, a research program studying the communication of genomic information in clinical care, as well as the clinical utility and diagnostic yield of GS for children with suspected genetic disorders in diverse populations in New York City. We observed variability in the correlation between reported variant allele fraction and the severity of the patient's phenotype, although we were not able to determine the mosaicism percentage in clinically relevant tissue(s). Although our study was not sufficiently powered to assess differences in mosaicism detection between the two testing modalities, we saw a trend toward better detection by GS as compared with TGP testing. This case series supports the importance of mosaicism in childhood-onset genetic conditions and informs guidelines for laboratory and clinical interpretation of mosaic variants detected by GS.
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Affiliation(s)
- Jacqueline A. Odgis
- The Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Katie M. Gallagher
- Department of Pediatrics, Division of Pediatric Genetic Medicine, Children’s Hospital at Montefiore/Montefiore Medical Center/Albert Einstein College of Medicine, Bronx, NY, USA
| | - Atteeq U. Rehman
- Molecular Diagnostics, New York Genome Center, New York, NY, USA
| | - Priya Marathe
- The Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Katherine E. Bonini
- The Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Monisha Sebastin
- Department of Pediatrics, Division of Pediatric Genetic Medicine, Children’s Hospital at Montefiore/Montefiore Medical Center/Albert Einstein College of Medicine, Bronx, NY, USA
| | - Miranda Di Biase
- Department of Pediatrics, Division of Pediatric Genetic Medicine, Children’s Hospital at Montefiore/Montefiore Medical Center/Albert Einstein College of Medicine, Bronx, NY, USA
| | - Kaitlyn Brown
- Department of Pediatrics, Division of Pediatric Genetic Medicine, Children’s Hospital at Montefiore/Montefiore Medical Center/Albert Einstein College of Medicine, Bronx, NY, USA
| | - Nicole R. Kelly
- Department of Pediatrics, Division of Pediatric Genetic Medicine, Children’s Hospital at Montefiore/Montefiore Medical Center/Albert Einstein College of Medicine, Bronx, NY, USA
| | - Michelle A. Ramos
- Department of Population Health Science and Policy, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Institute for Health Equity Research, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | | | - Saurav Guha
- Molecular Diagnostics, New York Genome Center, New York, NY, USA
| | - Volkan Okur
- Molecular Diagnostics, New York Genome Center, New York, NY, USA
| | | | | | | | - Randi E. Zinberg
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Obstetrics, Gynecology and Reproductive Science, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Noura S. Abul-Husn
- The Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - George A. Diaz
- Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Pediatrics, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - John M. Greally
- Department of Pediatrics, Division of Pediatric Genetic Medicine, Children’s Hospital at Montefiore/Montefiore Medical Center/Albert Einstein College of Medicine, Bronx, NY, USA
| | - Sabrina A. Suckiel
- The Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Vaidehi Jobanputra
- Molecular Diagnostics, New York Genome Center, New York, NY, USA
- Department of Pathology and Cell Biology, Columbia University Medical Center, New York, NY, USA
| | - Carol R. Horowitz
- Department of Population Health Science and Policy, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Institute for Health Equity Research, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Eimear E. Kenny
- The Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Melissa P. Wasserstein
- Department of Pediatrics, Division of Pediatric Genetic Medicine, Children’s Hospital at Montefiore/Montefiore Medical Center/Albert Einstein College of Medicine, Bronx, NY, USA
| | - Bruce D. Gelb
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Pediatrics, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
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