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Gustafson JA, Gibson SB, Damaraju N, Zalusky MPG, Hoekzema K, Twesigomwe D, Yang L, Snead AA, Richmond PA, De Coster W, Olson ND, Guarracino A, Li Q, Miller AL, Goffena J, Anderson Z, Storz SHR, Ward SA, Sinha M, Gonzaga-Jauregui C, Clarke WE, Basile AO, Corvelo A, Reeves C, Helland A, Musunuri RL, Revsine M, Patterson KE, Paschal CR, Zakarian C, Goodwin S, Jensen TD, Robb E, McCombie WR, Sedlazeck FJ, Zook JM, Montgomery SB, Garrison E, Kolmogorov M, Schatz MC, McLaughlin RN, Dashnow H, Zody MC, Loose M, Jain M, Eichler EE, Miller DE. Nanopore sequencing of 1000 Genomes Project samples to build a comprehensive catalog of human genetic variation. medRxiv 2024:2024.03.05.24303792. [PMID: 38496498 PMCID: PMC10942501 DOI: 10.1101/2024.03.05.24303792] [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] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/19/2024]
Abstract
Less than half of individuals with a suspected Mendelian condition receive a precise molecular diagnosis after comprehensive clinical genetic testing. Improvements in data quality and costs have heightened interest in using long-read sequencing (LRS) to streamline clinical genomic testing, but the absence of control datasets for variant filtering and prioritization has made tertiary analysis of LRS data challenging. To address this, the 1000 Genomes Project ONT Sequencing Consortium aims to generate LRS data from at least 800 of the 1000 Genomes Project samples. Our goal is to use LRS to identify a broader spectrum of variation so we may improve our understanding of normal patterns of human variation. Here, we present data from analysis of the first 100 samples, representing all 5 superpopulations and 19 subpopulations. These samples, sequenced to an average depth of coverage of 37x and sequence read N50 of 54 kbp, have high concordance with previous studies for identifying single nucleotide and indel variants outside of homopolymer regions. Using multiple structural variant (SV) callers, we identify an average of 24,543 high-confidence SVs per genome, including shared and private SVs likely to disrupt gene function as well as pathogenic expansions within disease-associated repeats that were not detected using short reads. Evaluation of methylation signatures revealed expected patterns at known imprinted loci, samples with skewed X-inactivation patterns, and novel differentially methylated regions. All raw sequencing data, processed data, and summary statistics are publicly available, providing a valuable resource for the clinical genetics community to discover pathogenic SVs.
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Affiliation(s)
- Jonas A. Gustafson
- Division of Genetic Medicine, Department of Pediatrics, University of Washington, Seattle, WA, USA
- Molecular and Cellular Biology Program, University of Washington, Seattle, WA, USA
| | - Sophia B. Gibson
- Division of Genetic Medicine, Department of Pediatrics, University of Washington, Seattle, WA, USA
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Nikhita Damaraju
- Division of Genetic Medicine, Department of Pediatrics, University of Washington, Seattle, WA, USA
- Institute for Public Health Genetics, University of Washington, Seattle, WA, USA
| | - Miranda PG Zalusky
- Division of Genetic Medicine, Department of Pediatrics, University of Washington, Seattle, WA, USA
| | - Kendra Hoekzema
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - David Twesigomwe
- Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Lei Yang
- Pacific Northwest Research Institute, Seattle, WA, USA
| | | | | | - Wouter De Coster
- Applied and Translational Neurogenomics Group, VIB Center for Molecular Neurology, VIB, Antwerp, Belgium
- Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
| | - Nathan D. Olson
- Material Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, MD, USA
| | - Andrea Guarracino
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN, USA
- Human Technopole, Milan, Italy
| | - Qiuhui Li
- Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA
| | - Angela L. Miller
- Division of Genetic Medicine, Department of Pediatrics, University of Washington, Seattle, WA, USA
| | - Joy Goffena
- Division of Genetic Medicine, Department of Pediatrics, University of Washington, Seattle, WA, USA
| | - Zachery Anderson
- Division of Genetic Medicine, Department of Pediatrics, University of Washington, Seattle, WA, USA
| | - Sophie HR Storz
- Division of Genetic Medicine, Department of Pediatrics, University of Washington, Seattle, WA, USA
| | - Sydney A. Ward
- Division of Genetic Medicine, Department of Pediatrics, University of Washington, Seattle, WA, USA
| | - Maisha Sinha
- Division of Genetic Medicine, Department of Pediatrics, University of Washington, Seattle, WA, USA
| | - Claudia Gonzaga-Jauregui
- International Laboratory for Human Genome Research, Laboratorio Internacional de Investigación sobre el Genoma Humano, Universidad Nacional Autónoma de México
| | - Wayne E. Clarke
- New York Genome Center, New York, NY, USA
- Outlier Informatics Inc., Saskatoon, SK, Canada
| | | | | | | | | | | | - Mahler Revsine
- Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA
| | | | - Cate R. Paschal
- Department of Laboratories, Seattle Children’s Hospital, Seattle, WA, USA
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
| | - Christina Zakarian
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Sara Goodwin
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | | | - Esther Robb
- Department of Computer Science, Stanford University, Stanford, CA, USA
| | | | | | | | | | - Fritz J. Sedlazeck
- Human Genome Sequencing Center Baylor College of Medicine, Houston, TX, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Department of Computer Science, Rice University, Houston, TX, USA
| | - Justin M. Zook
- Material Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, MD, USA
| | | | - Erik Garrison
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Mikhail Kolmogorov
- Cancer Data Science Laboratory, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Michael C. Schatz
- Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA
| | - Richard N. McLaughlin
- Molecular and Cellular Biology Program, University of Washington, Seattle, WA, USA
- Pacific Northwest Research Institute, Seattle, WA, USA
| | - Harriet Dashnow
- Department of Human Genetics, University of Utah, Salt Lake City, UT, USA
- Department of Biomedical Informatics, University of Colorado School of Medicine, Aurora, CO, USA
| | | | - Matt Loose
- Deep Seq, School of Life Sciences, University of Nottingham, Nottingham, England
| | - Miten Jain
- Department of Bioengineering, Department of Physics, Khoury College of Computer Sciences, Northeastern University, Boston, MA
| | - Evan E. Eichler
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
- Brotman Baty Institute for Precision Medicine, University of Washington, Seattle, WA, USA
- Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA
| | - Danny E. Miller
- Division of Genetic Medicine, Department of Pediatrics, University of Washington, Seattle, WA, USA
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
- Brotman Baty Institute for Precision Medicine, University of Washington, Seattle, WA, USA
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Quiat D, Timberlake AT, Curran JJ, Cunningham ML, McDonough B, Artunduaga MA, DePalma SR, Duenas-Roque MM, Gorham JM, Gustafson JA, Hamdan U, Hing AV, Hurtado-Villa P, Nicolau Y, Osorno G, Pachajoa H, Porras-Hurtado GL, Quintanilla-Dieck L, Serrano L, Tumblin M, Zarante I, Luquetti DV, Eavey RD, Heike CL, Seidman JG, Seidman CE. Damaging variants in FOXI3 cause microtia and craniofacial microsomia. Genet Med 2023; 25:143-150. [PMID: 36260083 PMCID: PMC9885525 DOI: 10.1016/j.gim.2022.09.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Revised: 09/11/2022] [Accepted: 09/12/2022] [Indexed: 11/05/2022] Open
Abstract
PURPOSE Craniofacial microsomia (CFM) represents a spectrum of craniofacial malformations, ranging from isolated microtia with or without aural atresia to underdevelopment of the mandible, maxilla, orbit, facial soft tissue, and/or facial nerve. The genetic causes of CFM remain largely unknown. METHODS We performed genome sequencing and linkage analysis in patients and families with microtia and CFM of unknown genetic etiology. The functional consequences of damaging missense variants were evaluated through expression of wild-type and mutant proteins in vitro. RESULTS We studied a 5-generation kindred with microtia, identifying a missense variant in FOXI3 (p.Arg236Trp) as the cause of disease (logarithm of the odds = 3.33). We subsequently identified 6 individuals from 3 additional kindreds with microtia-CFM spectrum phenotypes harboring damaging variants in FOXI3, a regulator of ectodermal and neural crest development. Missense variants in the nuclear localization sequence were identified in cases with isolated microtia with aural atresia and found to affect subcellular localization of FOXI3. Loss of function variants were found in patients with microtia and mandibular hypoplasia (CFM), suggesting dosage sensitivity of FOXI3. CONCLUSION Damaging variants in FOXI3 are the second most frequent genetic cause of CFM, causing 1% of all cases, including 13% of familial cases in our cohort.
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Affiliation(s)
- Daniel Quiat
- Department of Cardiology, Boston Children’s Hospital, Boston, MA,Department of Pediatrics, Harvard Medical School, Boston, MA,Department of Genetics, Harvard Medical School, Boston, MA
| | - Andrew T. Timberlake
- Hansjörg Wyss Department of Plastic and Reconstructive Surgery, NYU Langone Medical Center, New York, NY
| | | | - Michael L. Cunningham
- Division of Craniofacial Medicine, Department of Pediatrics, University of Washington, Seattle, WA,Center for Developmental Biology and Regenerative Medicine, Seattle Children’s Research Institute, Seattle, WA
| | | | | | | | | | | | - Jonas A. Gustafson
- Division of Craniofacial Medicine, Department of Pediatrics, University of Washington, Seattle, WA
| | | | - Anne V. Hing
- Division of Craniofacial Medicine, Department of Pediatrics, University of Washington, Seattle, WA,Center for Developmental Biology and Regenerative Medicine, Seattle Children’s Research Institute, Seattle, WA
| | | | | | - Gabriel Osorno
- Facultad de Medicina, Universidad Nacional de Colombia, Bogotá, Colombia
| | - Harry Pachajoa
- Servicio de Genética Médica, Fundación Valle del Lili, Cali, Colombia,Centro de Investigación en Anomalías Congénitas y Enfermedades Raras (CIACER), Universidad Icesi, Cali, Colombia
| | | | - Lourdes Quintanilla-Dieck
- Department of Otolaryngology Head and Neck Surgery, Oregon Health & Science University, Portland, OR
| | | | | | - Ignacio Zarante
- Human Genomics Institute, Pontificia Universidad Javeriana, Bogotá, Colombia,Hospital Universitario San Ignacio, Bogotá, Colombia
| | - Daniela V. Luquetti
- Division of Craniofacial Medicine, Department of Pediatrics, University of Washington, Seattle, WA,Center for Developmental Biology and Regenerative Medicine, Seattle Children’s Research Institute, Seattle, WA
| | - Roland D. Eavey
- Department of Otolaryngology–Head & Neck Surgery, Vanderbilt University Medical Center, Nashville, TN,Correspondence and requests for materials should be addressed to Roland D. Eavey, Department of Otolaryngology Head and Neck Surgery, Vanderbilt University Medical Center; Nashville, TN 37232. OR Carrie L. Heike, Department of Pediatrics, Division of Craniofacial Medicine, University of Washington, Seattle, WA 98105. OR Jonathan G. Seidman, Department of Genetics, Harvard Medical School, 77 Avenue Louis, Pasteur, Boston, MA 02115. OR Christine Seidman, Department of Genetics, Harvard Medical School, 77 Avenue Louis, Pasteur, Boston, MA 02115. c
| | - Carrie L. Heike
- Division of Craniofacial Medicine, Department of Pediatrics, University of Washington, Seattle, WA,Center for Developmental Biology and Regenerative Medicine, Seattle Children’s Research Institute, Seattle, WA,Correspondence and requests for materials should be addressed to Roland D. Eavey, Department of Otolaryngology Head and Neck Surgery, Vanderbilt University Medical Center; Nashville, TN 37232. OR Carrie L. Heike, Department of Pediatrics, Division of Craniofacial Medicine, University of Washington, Seattle, WA 98105. OR Jonathan G. Seidman, Department of Genetics, Harvard Medical School, 77 Avenue Louis, Pasteur, Boston, MA 02115. OR Christine Seidman, Department of Genetics, Harvard Medical School, 77 Avenue Louis, Pasteur, Boston, MA 02115. c
| | - Jonathan G. Seidman
- Department of Genetics, Harvard Medical School, Boston, MA,Correspondence and requests for materials should be addressed to Roland D. Eavey, Department of Otolaryngology Head and Neck Surgery, Vanderbilt University Medical Center; Nashville, TN 37232. OR Carrie L. Heike, Department of Pediatrics, Division of Craniofacial Medicine, University of Washington, Seattle, WA 98105. OR Jonathan G. Seidman, Department of Genetics, Harvard Medical School, 77 Avenue Louis, Pasteur, Boston, MA 02115. OR Christine Seidman, Department of Genetics, Harvard Medical School, 77 Avenue Louis, Pasteur, Boston, MA 02115. c
| | - Christine E. Seidman
- Department of Genetics, Harvard Medical School, Boston, MA,Cardiovascular Division, Brigham and Women’s Hospital, Boston, MA,Howard Hughes Medical Institute, Chevy Chase, MD,Correspondence and requests for materials should be addressed to Roland D. Eavey, Department of Otolaryngology Head and Neck Surgery, Vanderbilt University Medical Center; Nashville, TN 37232. OR Carrie L. Heike, Department of Pediatrics, Division of Craniofacial Medicine, University of Washington, Seattle, WA 98105. OR Jonathan G. Seidman, Department of Genetics, Harvard Medical School, 77 Avenue Louis, Pasteur, Boston, MA 02115. OR Christine Seidman, Department of Genetics, Harvard Medical School, 77 Avenue Louis, Pasteur, Boston, MA 02115. c
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Calpena E, Wurmser M, McGowan SJ, Atique R, Bertola DR, Cunningham ML, Gustafson JA, Johnson D, Morton JEV, Passos-Bueno MR, Timberlake AT, Lifton RP, Wall SA, Twigg SRF, Maire P, Wilkie AOM. Unexpected role of SIX1 variants in craniosynostosis: expanding the phenotype of SIX1-related disorders. J Med Genet 2022; 59:165-169. [PMID: 33436522 PMCID: PMC8273188 DOI: 10.1136/jmedgenet-2020-107459] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Revised: 12/07/2020] [Accepted: 12/09/2020] [Indexed: 01/19/2023]
Abstract
BACKGROUND Pathogenic heterozygous SIX1 variants (predominantly missense) occur in branchio-otic syndrome (BOS), but an association with craniosynostosis has not been reported. METHODS We investigated probands with craniosynostosis of unknown cause using whole exome/genome (n=628) or RNA (n=386) sequencing, and performed targeted resequencing of SIX1 in 615 additional patients. Expression of SIX1 protein in embryonic cranial sutures was examined in the Six1nLacZ/+ reporter mouse. RESULTS From 1629 unrelated cases with craniosynostosis we identified seven different SIX1 variants (three missense, including two de novo mutations, and four nonsense, one of which was also present in an affected twin). Compared with population data, enrichment of SIX1 loss-of-function variants was highly significant (p=0.00003). All individuals with craniosynostosis had sagittal suture fusion; additionally four had bilambdoid synostosis. Associated BOS features were often attenuated; some carrier relatives appeared non-penetrant. SIX1 is expressed in a layer basal to the calvaria, likely corresponding to the dura mater, and in the mid-sagittal mesenchyme. CONCLUSION Craniosynostosis is associated with heterozygous SIX1 variants, with possible enrichment of loss-of-function variants compared with classical BOS. We recommend screening of SIX1 in craniosynostosis, particularly when sagittal±lambdoid synostosis and/or any BOS phenotypes are present. These findings highlight the role of SIX1 in cranial suture homeostasis.
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Affiliation(s)
- Eduardo Calpena
- Clinical Genetics Group, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Maud Wurmser
- Institut Cochin, INSERM, CNRS, Université de Paris, Paris, France
| | - Simon J McGowan
- Centre for Computational Biology, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Rodrigo Atique
- Centro de Estudos do Genoma Humano, Universidade de São Paulo, São Paulo, Brazil
| | - Débora R Bertola
- Unidade de Genética Clínica, Instituto da Criança do Hospital das Clínicas, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
- Instituto de Biociências, Universidade de São Paulo, São Paulo, São Paulo, Brazil
| | - Michael L Cunningham
- Center for Developmental Biology and Regenerative Medicine, Seattle Children's Research Institute, Seattle, Washington, USA
- Seattle Children's Craniofacial Center, Seattle Children's Hospital, and Department of Pediatrics, Division of Craniofacial Medicine, University of Washington, Seattle, Washington, USA
| | - Jonas A Gustafson
- Center for Developmental Biology and Regenerative Medicine, Seattle Children's Research Institute, Seattle, Washington, USA
| | - David Johnson
- Craniofacial Unit, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Jenny E V Morton
- West Midlands Regional Clinical Genetics Service and Birmingham Health Partners, Birmingham Women's and Children's Hospitals NHS Foundation Trust, Birmingham, UK
| | | | - Andrew T Timberlake
- Hansjörg Wyss Department of Plastic Surgery, New York University Langone Medical Center, New York, New York, USA
| | | | - Steven A Wall
- Craniofacial Unit, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Stephen R F Twigg
- Clinical Genetics Group, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Pascal Maire
- Institut Cochin, INSERM, CNRS, Université de Paris, Paris, France
| | - Andrew O M Wilkie
- Clinical Genetics Group, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
- Craniofacial Unit, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
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4
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Clarke CM, Fok VT, Gustafson JA, Smyth MD, Timms AE, Frazar CD, Smith JD, Birgfeld CB, Lee A, Ellenbogen RG, Gruss JS, Hopper RA, Cunningham ML. Single suture craniosynostosis: Identification of rare variants in genes associated with syndromic forms. Am J Med Genet A. 2018 Feb;176(2):290-300. Am J Med Genet A 2018; 176:2522. [PMID: 30537273 DOI: 10.1002/ajmg.a.38846] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Accepted: 04/21/2018] [Indexed: 11/06/2022]
Affiliation(s)
- C M Clarke
- Center for Developmental Biology and Regenerative Medicine, Seattle Children's Research Institute, Seattle, Washington
| | - V T Fok
- Center for Developmental Biology and Regenerative Medicine, Seattle Children's Research Institute, Seattle, Washington
| | - J A Gustafson
- Center for Developmental Biology and Regenerative Medicine, Seattle Children's Research Institute, Seattle, Washington
| | - M D Smyth
- Washington University Department of Neurosurgery, St. Louis, Missouri.,St. Louis Children's Hospital, St. Louis, Missouri
| | - A E Timms
- Center for Developmental Biology and Regenerative Medicine, Seattle Children's Research Institute, Seattle, Washington
| | - C D Frazar
- Department of Genome Sciences, University of Washington, Seattle, Washington
| | - J D Smith
- Department of Genome Sciences, University of Washington, Seattle, Washington
| | - C B Birgfeld
- Division of Plastic Surgery, Department of Surgery, University of Washington School of Medicine, Seattle, Washington.,Division of Craniofacial and Plastic Surgery, Seattle Children's Hospital, Seattle, Washington.,Seattle Children's Craniofacial Center, Seattle Children's Hospital, Seattle, Washington
| | - A Lee
- Seattle Children's Craniofacial Center, Seattle Children's Hospital, Seattle, Washington.,Department of Neurological Surgery, University of Washington School of Medicine, Seattle, Washington.,Department of Pediatric Neurosurgery, Seattle Children's Hospital, Seattle, Washington
| | - R G Ellenbogen
- Seattle Children's Craniofacial Center, Seattle Children's Hospital, Seattle, Washington.,Department of Neurological Surgery, University of Washington School of Medicine, Seattle, Washington.,Department of Pediatric Neurosurgery, Seattle Children's Hospital, Seattle, Washington
| | - J S Gruss
- Division of Plastic Surgery, Department of Surgery, University of Washington School of Medicine, Seattle, Washington.,Division of Craniofacial and Plastic Surgery, Seattle Children's Hospital, Seattle, Washington.,Seattle Children's Craniofacial Center, Seattle Children's Hospital, Seattle, Washington
| | - R A Hopper
- Division of Plastic Surgery, Department of Surgery, University of Washington School of Medicine, Seattle, Washington.,Division of Craniofacial and Plastic Surgery, Seattle Children's Hospital, Seattle, Washington.,Seattle Children's Craniofacial Center, Seattle Children's Hospital, Seattle, Washington
| | - M L Cunningham
- Center for Developmental Biology and Regenerative Medicine, Seattle Children's Research Institute, Seattle, Washington.,Seattle Children's Craniofacial Center, Seattle Children's Hospital, Seattle, Washington.,Division of Craniofacial Medicine, Department of Pediatrics, University of Washington, Seattle, Washington
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Gustafson JA. Science in General (X). Science 1963; 139:664-5. [PMID: 17788343 DOI: 10.1126/science.139.3555.664-a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
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