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Kim W, Hecker J, Barr RG, Boerwinkle E, Cade B, Correa A, Dupuis J, Gharib SA, Lange L, London SJ, Morrison AC, O'Connor GT, Oelsner EC, Psaty BM, Vasan RS, Redline S, Rich SS, Rotter JI, Yu B, Lange C, Manichaikul A, Zhou JJ, Sofer T, Silverman EK, Qiao D, Cho MH. Assessing the contribution of rare genetic variants to phenotypes of chronic obstructive pulmonary disease using whole-genome sequence data. Hum Mol Genet 2022; 31:3873-3885. [PMID: 35766891 PMCID: PMC9652112 DOI: 10.1093/hmg/ddac117] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Revised: 04/13/2022] [Accepted: 05/16/2021] [Indexed: 01/04/2023] Open
Abstract
RATIONALE Genetic variation has a substantial contribution to chronic obstructive pulmonary disease (COPD) and lung function measurements. Heritability estimates using genome-wide genotyping data can be biased if analyses do not appropriately account for the nonuniform distribution of genetic effects across the allele frequency and linkage disequilibrium (LD) spectrum. In addition, the contribution of rare variants has been unclear. OBJECTIVES We sought to assess the heritability of COPD and lung function using whole-genome sequence data from the Trans-Omics for Precision Medicine program. METHODS Using the genome-based restricted maximum likelihood method, we partitioned the genome into bins based on minor allele frequency and LD scores and estimated heritability of COPD, FEV1% predicted and FEV1/FVC ratio in 11 051 European ancestry and 5853 African-American participants. MEASUREMENTS AND MAIN RESULTS In European ancestry participants, the estimated heritability of COPD, FEV1% predicted and FEV1/FVC ratio were 35.5%, 55.6% and 32.5%, of which 18.8%, 19.7%, 17.8% were from common variants, and 16.6%, 35.8%, and 14.6% were from rare variants. These estimates had wide confidence intervals, with common variants and some sets of rare variants showing a statistically significant contribution (P-value < 0.05). In African-Americans, common variant heritability was similar to European ancestry participants, but lower sample size precluded calculation of rare variant heritability. CONCLUSIONS Our study provides updated and unbiased estimates of heritability for COPD and lung function, and suggests an important contribution of rare variants. Larger studies of more diverse ancestry will improve accuracy of these estimates.
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Affiliation(s)
- Wonji Kim
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Julian Hecker
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - R Graham Barr
- Departments of Medicine and Epidemiology, Columbia University Medical Center, New York, NY 10032, USA
| | - Eric Boerwinkle
- Department of Epidemiology, Human Genetics and Environmental Sciences, School of Public Health, University of Texas Health Science Center at Houston, Houston, TX 77030, USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Brian Cade
- Division of Sleep and Circadian Disorders, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Adolfo Correa
- Department of Medicine, University of Mississippi Medical Center, Jackson, MS 39216, USA
| | - Josée Dupuis
- Department of Biostatistics, Boston University of Public Health, Boston, MA 02118, USA
| | - Sina A Gharib
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA 98101, USA
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, University of Washington, Seattle, WA 98109, USA
| | - Leslie Lange
- Department of Medicine, University of Colorado Denver, Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Stephanie J London
- Epidemiology Branch, National Institute of Environmental Health Sciences, Department of Health and Human Services, National Institutes of Health, Research Triangle Park, NC 27709, USA
| | - Alanna C Morrison
- Human Genetics Center, School of Public Health, University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - George T O'Connor
- Pulmonary Center, Boston University School of Medicine, Boston, MA 02118, USA
| | - Elizabeth C Oelsner
- Departments of Medicine and Epidemiology, Columbia University Medical Center, New York, NY 10032, USA
| | - Bruce M Psaty
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA 98101, USA
- Departments of Epidemiology and Health Services, University of Washington, Seattle, WA 98101, USA
| | - Ramachandran S Vasan
- Lung and Blood Institute Framingham Heart Study, Boston University and National Heart, Framingham, MA 01702, USA
- Department of Preventive Medicine and Epidemiology, School of Medicine and Public Health, Boston University, Boston, MA 02118, USA
| | - Susan Redline
- Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Stephen S Rich
- Center for Public Health Genomics, University of Virginia School of Medicine, Charlottesville, VA 22908, USA
| | - Jerome I Rotter
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA 90502, USA
| | - Bing Yu
- Department of Epidemiology, Human Genetics and Environmental Sciences, School of Public Health, University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Christoph Lange
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | - Ani Manichaikul
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA 22908, USA
| | - Jin J Zhou
- Department of Epidemiology and Biostatistics, University of Arizona, Tucson, AZ 85721, USA
| | - Tamar Sofer
- Division of Sleep and Circadian Disorder, Brigham and Women’s Hospital, Boston, MA 02115, USA
| | - Edwin K Silverman
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Dandi Qiao
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Michael H Cho
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
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Marafi D, Fatih JM, Kaiyrzhanov R, Ferla MP, Gijavanekar C, Al-Maraghi A, Liu N, Sites E, Alsaif HS, Al-Owain M, Zakkariah M, El-Anany E, Guliyeva U, Guliyeva S, Gaba C, Haseeb A, Alhashem AM, Danish E, Karageorgou V, Beetz C, Subhi AA, Mullegama SV, Torti E, Sebastin M, Breilyn MS, Duberstein S, Abdel-Hamid MS, Mitani T, Du H, Rosenfeld JA, Jhangiani SN, Coban Akdemir Z, Gibbs RA, Taylor JC, Fakhro KA, Hunter JV, Pehlivan D, Zaki MS, Gleeson JG, Maroofian R, Houlden H, Posey JE, Sutton VR, Alkuraya FS, Elsea SH, Lupski JR. Biallelic variants in SLC38A3 encoding a glutamine transporter cause epileptic encephalopathy. Brain 2022; 145:909-924. [PMID: 34605855 PMCID: PMC9050560 DOI: 10.1093/brain/awab369] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [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: 03/17/2021] [Revised: 07/13/2021] [Accepted: 08/26/2021] [Indexed: 11/14/2022] Open
Abstract
The solute carrier (SLC) superfamily encompasses >400 transmembrane transporters involved in the exchange of amino acids, nutrients, ions, metals, neurotransmitters and metabolites across biological membranes. SLCs are highly expressed in the mammalian brain; defects in nearly 100 unique SLC-encoding genes (OMIM: https://www.omim.org) are associated with rare Mendelian disorders including developmental and epileptic encephalopathy and severe neurodevelopmental disorders. Exome sequencing and family-based rare variant analyses on a cohort with neurodevelopmental disorders identified two siblings with developmental and epileptic encephalopathy and a shared deleterious homozygous splicing variant in SLC38A3. The gene encodes SNAT3, a sodium-coupled neutral amino acid transporter and a principal transporter of the amino acids asparagine, histidine, and glutamine, the latter being the precursor for the neurotransmitters GABA and glutamate. Additional subjects with a similar developmental and epileptic encephalopathy phenotype and biallelic predicted-damaging SLC38A3 variants were ascertained through GeneMatcher and collaborations with research and clinical molecular diagnostic laboratories. Untargeted metabolomic analysis was performed to identify novel metabolic biomarkers. Ten individuals from seven unrelated families from six different countries with deleterious biallelic variants in SLC38A3 were identified. Global developmental delay, intellectual disability, hypotonia, and absent speech were common features while microcephaly, epilepsy, and visual impairment were present in the majority. Epilepsy was drug-resistant in half. Metabolomic analysis revealed perturbations of glutamate, histidine, and nitrogen metabolism in plasma, urine, and CSF of selected subjects, potentially representing biomarkers of disease. Our data support the contention that SLC38A3 is a novel disease gene for developmental and epileptic encephalopathy and illuminate the likely pathophysiology of the disease as perturbations in glutamine homeostasis.
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Affiliation(s)
- Dana Marafi
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Department of Pediatrics, Faculty of Medicine, Kuwait University, P.O. Box 24923, 13110 Safat, Kuwait
- Correspondence to: Dana Marafi, MD, MSc Department of Pediatrics, Faculty of Medicine, Kuwait University P.O. Box 24923, 13110 Safat, Kuwait E-mail:
| | - Jawid M Fatih
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Rauan Kaiyrzhanov
- Department of Neuromuscular Disorders Institute of Neurology, University College London, Queen Square, London, UK
| | - Matteo P Ferla
- NIHR Oxford Biomedical Research Centre, Oxford OX4 2PG, UK
- Wellcome Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
| | - Charul Gijavanekar
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Baylor Genetics Laboratory, Houston, TX 77030, USA
| | | | - Ning Liu
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Baylor Genetics Laboratory, Houston, TX 77030, USA
| | - Emily Sites
- Division of Molecular and Human Genetics, Nationwide Children's Hospital, Columbus, OH 43205, USA
| | - Hessa S Alsaif
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh 11211, Saudi Arabia
| | - Mohammad Al-Owain
- Department of Medical Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh 11211, Saudi Arabia
- Department of Anatomy and Cell Biology, College of Medicine, Alfaisal University 11533, Riyadh, Saudi Arabia
| | - Mohamed Zakkariah
- Section of Child Neurology, Department of Pediatrics, Al-adan Hospital, Riqqa, Kuwait
| | - Ehab El-Anany
- Section of Child Neurology, Department of Pediatrics, Al-adan Hospital, Riqqa, Kuwait
| | | | | | - Colette Gaba
- Department of Pediatrics, Bon Secours Mercy Health, Toledo, OH 43608, USA
| | - Ateeq Haseeb
- Mercy Children’s Hospital, Toledo, OH 43608, USA
| | - Amal M Alhashem
- Division of Medical Genetic and Metabolic Medicine, Department of Pediatrics, Prince Sultan Medical Military City, Riyadh, Saudi Arabia
| | - Enam Danish
- Department of Ophthalmology, King Fahad Armed Forces Hospital, Jeddah, Saudi Arabia
| | | | | | - Alaa A Subhi
- Neurosciences Department, King Faisal Specialist Hospital and Research Center, Jeddah, Saudi Arabia
| | | | | | - Monisha Sebastin
- Albert Einstein College of Medicine and the Children's Hospital at Montefiore, Bronx, New York 10467, USA
- Division of Genetics, Department of Pediatrics, Montefiore Medical Center and Albert Einstein College of Medicine, Bronx, New York, 10467, USA
| | - Margo Sheck Breilyn
- Albert Einstein College of Medicine and the Children's Hospital at Montefiore, Bronx, New York 10467, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Susan Duberstein
- Isabelle Rapin Division of Child Neurology in the Saul R Korey Department of Neurology, Montefiore Medical Center, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Mohamed S Abdel-Hamid
- Department of Medical Molecular Genetics, Human Genetics and Genome Research Division, National Research Centre, Cairo, Egypt
| | - Tadahiro Mitani
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Haowei Du
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Jill A Rosenfeld
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Baylor Genetics Laboratory, Houston, TX 77030, USA
| | - Shalini N Jhangiani
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Zeynep Coban Akdemir
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Human Genetics Center, University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Richard A Gibbs
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Jenny C Taylor
- NIHR Oxford Biomedical Research Centre, Oxford OX4 2PG, UK
- Wellcome Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
| | - Khalid A Fakhro
- Department of Human Genetics, Sidra Medicine, Doha 26999, Qatar
- Department of Genetic Medicine, Weill Cornell Medical College, Doha, Qatar
- College of Health and Life Sciences, Hamad Bin Khalifa University, Doha 34110, Qatar
| | - Jill V Hunter
- E.B. Singleton Department of Pediatric Radiology, Texas Children’s Hospital, Houston, TX 77030, USA
- Department of Radiology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Davut Pehlivan
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Texas Children's Hospital, Houston, TX 77030, USA
- Section of Pediatric Neurology and Developmental Neuroscience, Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Maha S Zaki
- Department of Clinical Genetics, Human Genetics and Genome Research Division, National Research Centre, Cairo, Egypt
| | - Joseph G Gleeson
- Rady Children's Institute for Genomic Medicine, Howard Hughes Medical Institute, University of California, San Diego, CA 92123, USA
| | - Reza Maroofian
- Department of Neuromuscular Disorders Institute of Neurology, University College London, Queen Square, London, UK
| | - Henry Houlden
- Department of Neuromuscular Disorders Institute of Neurology, University College London, Queen Square, London, UK
| | - Jennifer E Posey
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - V Reid Sutton
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Baylor Genetics Laboratory, Houston, TX 77030, USA
- Texas Children's Hospital, Houston, TX 77030, USA
| | - Fowzan S Alkuraya
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh 11211, Saudi Arabia
| | - Sarah H Elsea
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Baylor Genetics Laboratory, Houston, TX 77030, USA
| | - James R Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
- Texas Children's Hospital, Houston, TX 77030, USA
- Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA
- Correspondence may also be addressed to: James R. Lupski, MD, PhD, DSc (hon) Department of Molecular and Human Genetics, Baylor College of Medicine One Baylor Plaza, Room 604B, Houston, TX 77030, USA E-mail:
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3
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Saad AK, Marafi D, Mitani T, Jolly A, Du H, Elbendary HM, Jhangiani SN, Akdemir ZC, Gibbs RA, Hunter JV, Carvalho CMBC, Pehlivan D, Posey JE, Zaki MS, Lupski JR. Biallelic in-frame deletion in TRAPPC4 in a family with developmental delay and cerebellar atrophy. Brain 2020; 143:e83. [PMID: 33011761 PMCID: PMC7586085 DOI: 10.1093/brain/awaa256] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Affiliation(s)
- Ahmed K Saad
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030, USA
- Department of Medical Molecular Genetics, Human Genetics and Genome Research Division, National Research Centre, Cairo, Egypt
| | - Dana Marafi
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030, USA
- Department of Pediatrics, Faculty of Medicine, Kuwait University, P.O. Box 24923, 13110 Safat, Kuwait
| | - Tadahiro Mitani
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030, USA
| | - Angad Jolly
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030, USA
- MD/PhD Medical Scientist Training Program, Baylor College of Medicine, Houston, Texas, 77030, USA
| | - Haowei Du
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030, USA
| | - Hasnaa M Elbendary
- Department of Clinical Genetics, Human Genetics and Genome Research Division, National Research Centre, Cairo, Egypt
| | - Shalini N Jhangiani
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, 77030, USA
| | - Zeynep C Akdemir
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030, USA
| | | | - Richard A Gibbs
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030, USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, 77030, USA
| | - Jill V Hunter
- Department of Radiology, Baylor College of Medicine, Houston, Texas, 77030, USA
- E.B. Singleton Department of Pediatric Radiology, Texas Children's Hospital, Houston, Texas, 77030, USA
| | - Claudia M B C Carvalho
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030, USA
| | - Davut Pehlivan
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030, USA
- Texas Children's Hospital, Houston, Texas, 77030, USA
- Section of Pediatric Neurology and Developmental Neuroscience, Department of Pediatrics, Baylor College of Medicine, Houston, Texas, 77030, USA
| | - Jennifer E Posey
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030, USA
| | - Maha S Zaki
- Department of Clinical Genetics, Human Genetics and Genome Research Division, National Research Centre, Cairo, Egypt
| | - James R Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030, USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, 77030, USA
- Texas Children's Hospital, Houston, Texas, 77030, USA
- Department of Pediatrics, Baylor College of Medicine, Houston, Texas, 77030, USA
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