High prevalence of multilocus pathogenic variation in neurodevelopmental disorders in the Turkish population

Neurodevelopmental disorders (NDDs) are clinically and genetically heterogenous; many such disorders are secondary to perturbation in brain development and/or function. The prevalence of NDDs is > 3%, resulting in significant sociocultural and economic challenges to society. With recent advances...

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Published inAmerican journal of human genetics Vol. 108; no. 10; pp. 1981 - 2005
Main Authors Mitani, Tadahiro, Isikay, Sedat, Gezdirici, Alper, Gulec, Elif Yilmaz, Punetha, Jaya, Fatih, Jawid M., Herman, Isabella, Akay, Gulsen, Du, Haowei, Calame, Daniel G., Ayaz, Akif, Tos, Tulay, Yesil, Gozde, Aydin, Hatip, Geckinli, Bilgen, Elcioglu, Nursel, Candan, Sukru, Sezer, Ozlem, Erdem, Haktan Bagis, Gul, Davut, Demiral, Emine, Elmas, Muhsin, Yesilbas, Osman, Kilic, Betul, Gungor, Serdal, Ceylan, Ahmet C., Bozdogan, Sevcan, Ozalp, Ozge, Cicek, Salih, Aslan, Huseyin, Yalcintepe, Sinem, Topcu, Vehap, Bayram, Yavuz, Grochowski, Christopher M., Jolly, Angad, Dawood, Moez, Duan, Ruizhi, Jhangiani, Shalini N., Doddapaneni, Harsha, Hu, Jianhong, Muzny, Donna M., Marafi, Dana, Akdemir, Zeynep Coban, Karaca, Ender, Carvalho, Claudia M.B., Gibbs, Richard A., Posey, Jennifer E., Lupski, James R., Pehlivan, Davut
Format Journal Article
LanguageEnglish
Published United States Elsevier Inc 07.10.2021
Elsevier
Subjects
Adolescent
Adult
Alu-Alu mediated rearrangement (AAMR)
Child
Child, Preschool
Cohort Studies
exome reanalysis
Exome Sequencing
Female
Genomics - methods
Humans
identity-by-descent (IBD)
Infant
Infant, Newborn
Male
Middle Aged
multilocus pathogenic variation
Mutation
neurodevelopmental disorders
Neurodevelopmental Disorders - epidemiology
Neurodevelopmental Disorders - genetics
Neurodevelopmental Disorders - pathology
Pedigree
Phenotype
Prevalence
runs of homozygosity (ROH)
Turkey - epidemiology
whole-genome sequencing
Young Adult
Turkey
exome reanalysis
Alu-Alu mediated rearrangement (AAMR)
identity-by-descent (IBD)
whole-genome sequencing
runs of homozygosity (ROH)
multilocus pathogenic variation
neurodevelopmental disorders
Online AccessGet full text
ISSN0002-9297
1537-6605
1537-6605
DOI10.1016/j.ajhg.2021.08.009

Cover

Abstract Neurodevelopmental disorders (NDDs) are clinically and genetically heterogenous; many such disorders are secondary to perturbation in brain development and/or function. The prevalence of NDDs is > 3%, resulting in significant sociocultural and economic challenges to society. With recent advances in family-based genomics, rare-variant analyses, and further exploration of the Clan Genomics hypothesis, there has been a logarithmic explosion in neurogenetic “disease-associated genes” molecular etiology and biology of NDDs; however, the majority of NDDs remain molecularly undiagnosed. We applied genome-wide screening technologies, including exome sequencing (ES) and whole-genome sequencing (WGS), to identify the molecular etiology of 234 newly enrolled subjects and 20 previously unsolved Turkish NDD families. In 176 of the 234 studied families (75.2%), a plausible and genetically parsimonious molecular etiology was identified. Out of 176 solved families, deleterious variants were identified in 218 distinct genes, further documenting the enormous genetic heterogeneity and diverse perturbations in human biology underlying NDDs. We propose 86 candidate disease-trait-associated genes for an NDD phenotype. Importantly, on the basis of objective and internally established variant prioritization criteria, we identified 51 families (51/176 = 28.9%) with multilocus pathogenic variation (MPV), mostly driven by runs of homozygosity (ROHs) – reflecting genomic segments/haplotypes that are identical-by-descent. Furthermore, with the use of additional bioinformatic tools and expansion of ES to additional family members, we established a molecular diagnosis in 5 out of 20 families (25%) who remained undiagnosed in our previously studied NDD cohort emanating from Turkey.
AbstractList Neurodevelopmental disorders (NDDs) are clinically and genetically heterogenous; many such disorders are secondary to perturbation in brain development and/or function. The prevalence of NDDs is > 3%, resulting in significant sociocultural and economic challenges to society. With recent advances in family-based genomics, rare-variant analyses, and further exploration of the Clan Genomics hypothesis, there has been a logarithmic explosion in neurogenetic "disease-associated genes" molecular etiology and biology of NDDs; however, the majority of NDDs remain molecularly undiagnosed. We applied genome-wide screening technologies, including exome sequencing (ES) and whole-genome sequencing (WGS), to identify the molecular etiology of 234 newly enrolled subjects and 20 previously unsolved Turkish NDD families. In 176 of the 234 studied families (75.2%), a plausible and genetically parsimonious molecular etiology was identified. Out of 176 solved families, deleterious variants were identified in 218 distinct genes, further documenting the enormous genetic heterogeneity and diverse perturbations in human biology underlying NDDs. We propose 86 candidate disease-trait-associated genes for an NDD phenotype. Importantly, on the basis of objective and internally established variant prioritization criteria, we identified 51 families (51/176 = 28.9%) with multilocus pathogenic variation (MPV), mostly driven by runs of homozygosity (ROHs) - reflecting genomic segments/haplotypes that are identical-by-descent. Furthermore, with the use of additional bioinformatic tools and expansion of ES to additional family members, we established a molecular diagnosis in 5 out of 20 families (25%) who remained undiagnosed in our previously studied NDD cohort emanating from Turkey.
Neurodevelopmental disorders (NDDs) are clinically and genetically heterogenous; many such disorders are secondary to perturbation in brain development and/or function. The prevalence of NDDs is > 3%, resulting in significant sociocultural and economic challenges to society. With recent advances in family-based genomics, rare-variant analyses, and further exploration of the Clan Genomics hypothesis, there has been a logarithmic explosion in neurogenetic "disease-associated genes" molecular etiology and biology of NDDs; however, the majority of NDDs remain molecularly undiagnosed. We applied genome-wide screening technologies, including exome sequencing (ES) and whole-genome sequencing (WGS), to identify the molecular etiology of 234 newly enrolled subjects and 20 previously unsolved Turkish NDD families. In 176 of the 234 studied families (75.2%), a plausible and genetically parsimonious molecular etiology was identified. Out of 176 solved families, deleterious variants were identified in 218 distinct genes, further documenting the enormous genetic heterogeneity and diverse perturbations in human biology underlying NDDs. We propose 86 candidate disease-trait-associated genes for an NDD phenotype. Importantly, on the basis of objective and internally established variant prioritization criteria, we identified 51 families (51/176 = 28.9%) with multilocus pathogenic variation (MPV), mostly driven by runs of homozygosity (ROHs) - reflecting genomic segments/haplotypes that are identical-by-descent. Furthermore, with the use of additional bioinformatic tools and expansion of ES to additional family members, we established a molecular diagnosis in 5 out of 20 families (25%) who remained undiagnosed in our previously studied NDD cohort emanating from Turkey.Neurodevelopmental disorders (NDDs) are clinically and genetically heterogenous; many such disorders are secondary to perturbation in brain development and/or function. The prevalence of NDDs is > 3%, resulting in significant sociocultural and economic challenges to society. With recent advances in family-based genomics, rare-variant analyses, and further exploration of the Clan Genomics hypothesis, there has been a logarithmic explosion in neurogenetic "disease-associated genes" molecular etiology and biology of NDDs; however, the majority of NDDs remain molecularly undiagnosed. We applied genome-wide screening technologies, including exome sequencing (ES) and whole-genome sequencing (WGS), to identify the molecular etiology of 234 newly enrolled subjects and 20 previously unsolved Turkish NDD families. In 176 of the 234 studied families (75.2%), a plausible and genetically parsimonious molecular etiology was identified. Out of 176 solved families, deleterious variants were identified in 218 distinct genes, further documenting the enormous genetic heterogeneity and diverse perturbations in human biology underlying NDDs. We propose 86 candidate disease-trait-associated genes for an NDD phenotype. Importantly, on the basis of objective and internally established variant prioritization criteria, we identified 51 families (51/176 = 28.9%) with multilocus pathogenic variation (MPV), mostly driven by runs of homozygosity (ROHs) - reflecting genomic segments/haplotypes that are identical-by-descent. Furthermore, with the use of additional bioinformatic tools and expansion of ES to additional family members, we established a molecular diagnosis in 5 out of 20 families (25%) who remained undiagnosed in our previously studied NDD cohort emanating from Turkey.
Author Dawood, Moez
Candan, Sukru
Grochowski, Christopher M.
Muzny, Donna M.
Aslan, Huseyin
Yalcintepe, Sinem
Yesilbas, Osman
Bozdogan, Sevcan
Aydin, Hatip
Ceylan, Ahmet C.
Jhangiani, Shalini N.
Lupski, James R.
Duan, Ruizhi
Akdemir, Zeynep Coban
Gezdirici, Alper
Calame, Daniel G.
Topcu, Vehap
Gibbs, Richard A.
Posey, Jennifer E.
Punetha, Jaya
Jolly, Angad
Isikay, Sedat
Cicek, Salih
Gul, Davut
Elcioglu, Nursel
Doddapaneni, Harsha
Marafi, Dana
Pehlivan, Davut
Yesil, Gozde
Fatih, Jawid M.
Karaca, Ender
Tos, Tulay
Erdem, Haktan Bagis
Gulec, Elif Yilmaz
Akay, Gulsen
Elmas, Muhsin
Ayaz, Akif
Geckinli, Bilgen
Gungor, Serdal
Hu, Jianhong
Ozalp, Ozge
Du, Haowei
Herman, Isabella
Bayram, Yavuz
Kilic, Betul
Sezer, Ozlem
Demiral, Emine
Mitani, Tadahiro
Carvalho, Claudia M.B.
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BackLink https://www.ncbi.nlm.nih.gov/pubmed/34582790$$D View this record in MEDLINE/PubMed
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2021 American Society of Human Genetics. 2021 American Society of Human Genetics
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Issue 10
Keywords exome reanalysis
Alu-Alu mediated rearrangement (AAMR)
identity-by-descent (IBD)
whole-genome sequencing
runs of homozygosity (ROH)
multilocus pathogenic variation
neurodevelopmental disorders
Language English
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content type line 23
Present address: Department of Pediatrics, Faculty of Medicine, Kuwait University, PO Box 24923, 13110 Safat, Kuwait
Present address: Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA
Present address: Pacific Northwest Research Institute, Seattle, Washington, 98122, USA
Present address: Sanford Molecular Genetics Laboratory, Sioux Falls, 57105, South Dakota, USA
Present address: Division of Genomic Diagnostics, Department of Pathology and Laboratory Medicine, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, 19104, USA and Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, 19104, USA
Present address: Human Genetics Center, Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, Texas, USA
Present address: Department of Pediatrics, Jichi Medical University, 3311-1 Yakushiji, Shimotsuke, Tochigi 329-0498, Japan
Lead contact
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Snippet Neurodevelopmental disorders (NDDs) are clinically and genetically heterogenous; many such disorders are secondary to perturbation in brain development and/or...
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StartPage 1981
SubjectTerms Adolescent
Adult
Alu-Alu mediated rearrangement (AAMR)
Child
Child, Preschool
Cohort Studies
exome reanalysis
Exome Sequencing
Female
Genomics - methods
Humans
identity-by-descent (IBD)
Infant
Infant, Newborn
Male
Middle Aged
multilocus pathogenic variation
Mutation
neurodevelopmental disorders
Neurodevelopmental Disorders - epidemiology
Neurodevelopmental Disorders - genetics
Neurodevelopmental Disorders - pathology
Pedigree
Phenotype
Prevalence
runs of homozygosity (ROH)
Turkey - epidemiology
whole-genome sequencing
Young Adult
Title High prevalence of multilocus pathogenic variation in neurodevelopmental disorders in the Turkish population
URI https://dx.doi.org/10.1016/j.ajhg.2021.08.009
https://www.ncbi.nlm.nih.gov/pubmed/34582790
https://www.proquest.com/docview/2577729016
https://pubmed.ncbi.nlm.nih.gov/PMC8546040
Volume 108
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