Dissecting the genetic basis of comorbid epilepsy phenotypes in neurodevelopmental disorders

Julie Chow, Matthew Jensen, Hajar Amini, Farhad Hormozdiari, Osnat Penn, Sagiv Shifman, Santhosh Girirajan, Fereydoun Hormozdiari

Research output: Contribution to journalArticle

Abstract

Background: Neurodevelopmental disorders (NDDs) such as autism spectrum disorder, intellectual disability, developmental disability, and epilepsy are characterized by abnormal brain development that may affect cognition, learning, behavior, and motor skills. High co-occurrence (comorbidity) of NDDs indicates a shared, underlying biological mechanism. The genetic heterogeneity and overlap observed in NDDs make it difficult to identify the genetic causes of specific clinical symptoms, such as seizures. Methods: We present a computational method, MAGI-S, to discover modules or groups of highly connected genes that together potentially perform a similar biological function. MAGI-S integrates protein-protein interaction and co-expression networks to form modules centered around the selection of a single "seed" gene, yielding modules consisting of genes that are highly co-expressed with the seed gene. We aim to dissect the epilepsy phenotype from a general NDD phenotype by providing MAGI-S with high confidence NDD seed genes with varying degrees of association with epilepsy, and we assess the enrichment of de novo mutation, NDD-associated genes, and relevant biological function of constructed modules. Results: The newly identified modules account for the increased rate of de novo non-synonymous mutations in autism, intellectual disability, developmental disability, and epilepsy, and enrichment of copy number variations (CNVs) in developmental disability. We also observed that modules seeded with genes strongly associated with epilepsy tend to have a higher association with epilepsy phenotypes than modules seeded at other neurodevelopmental disorder genes. Modules seeded with genes strongly associated with epilepsy (e.g., SCN1A, GABRA1, and KCNB1) are significantly associated with synaptic transmission, long-term potentiation, and calcium signaling pathways. On the other hand, modules found with seed genes that are not associated or weakly associated with epilepsy are mostly involved with RNA regulation and chromatin remodeling. Conclusions: In summary, our method identifies modules enriched with de novo non-synonymous mutations and can capture specific networks that underlie the epilepsy phenotype and display distinct enrichment in relevant biological processes.

Original languageEnglish (US)
Article number65
JournalGenome Medicine
Volume11
Issue number1
DOIs
StatePublished - Oct 25 2019

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Epilepsy
Phenotype
Genes
Developmental Disabilities
Seeds
Intellectual Disability
Mutation
Biological Phenomena
Neurodevelopmental Disorders
Motor Skills
Chromatin Assembly and Disassembly
Calcium Signaling
Genetic Heterogeneity
Long-Term Potentiation
Gene Regulatory Networks
Protein S
Autistic Disorder
Synaptic Transmission
Cognition
Comorbidity

All Science Journal Classification (ASJC) codes

  • Molecular Medicine
  • Molecular Biology
  • Genetics
  • Genetics(clinical)

Cite this

Chow, J., Jensen, M., Amini, H., Hormozdiari, F., Penn, O., Shifman, S., ... Hormozdiari, F. (2019). Dissecting the genetic basis of comorbid epilepsy phenotypes in neurodevelopmental disorders. Genome Medicine, 11(1), [65]. https://doi.org/10.1186/s13073-019-0678-y
Chow, Julie ; Jensen, Matthew ; Amini, Hajar ; Hormozdiari, Farhad ; Penn, Osnat ; Shifman, Sagiv ; Girirajan, Santhosh ; Hormozdiari, Fereydoun. / Dissecting the genetic basis of comorbid epilepsy phenotypes in neurodevelopmental disorders. In: Genome Medicine. 2019 ; Vol. 11, No. 1.
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Chow, J, Jensen, M, Amini, H, Hormozdiari, F, Penn, O, Shifman, S, Girirajan, S & Hormozdiari, F 2019, 'Dissecting the genetic basis of comorbid epilepsy phenotypes in neurodevelopmental disorders', Genome Medicine, vol. 11, no. 1, 65. https://doi.org/10.1186/s13073-019-0678-y

Dissecting the genetic basis of comorbid epilepsy phenotypes in neurodevelopmental disorders. / Chow, Julie; Jensen, Matthew; Amini, Hajar; Hormozdiari, Farhad; Penn, Osnat; Shifman, Sagiv; Girirajan, Santhosh; Hormozdiari, Fereydoun.

In: Genome Medicine, Vol. 11, No. 1, 65, 25.10.2019.

Research output: Contribution to journalArticle

TY - JOUR

T1 - Dissecting the genetic basis of comorbid epilepsy phenotypes in neurodevelopmental disorders

AU - Chow, Julie

AU - Jensen, Matthew

AU - Amini, Hajar

AU - Hormozdiari, Farhad

AU - Penn, Osnat

AU - Shifman, Sagiv

AU - Girirajan, Santhosh

AU - Hormozdiari, Fereydoun

PY - 2019/10/25

Y1 - 2019/10/25

N2 - Background: Neurodevelopmental disorders (NDDs) such as autism spectrum disorder, intellectual disability, developmental disability, and epilepsy are characterized by abnormal brain development that may affect cognition, learning, behavior, and motor skills. High co-occurrence (comorbidity) of NDDs indicates a shared, underlying biological mechanism. The genetic heterogeneity and overlap observed in NDDs make it difficult to identify the genetic causes of specific clinical symptoms, such as seizures. Methods: We present a computational method, MAGI-S, to discover modules or groups of highly connected genes that together potentially perform a similar biological function. MAGI-S integrates protein-protein interaction and co-expression networks to form modules centered around the selection of a single "seed" gene, yielding modules consisting of genes that are highly co-expressed with the seed gene. We aim to dissect the epilepsy phenotype from a general NDD phenotype by providing MAGI-S with high confidence NDD seed genes with varying degrees of association with epilepsy, and we assess the enrichment of de novo mutation, NDD-associated genes, and relevant biological function of constructed modules. Results: The newly identified modules account for the increased rate of de novo non-synonymous mutations in autism, intellectual disability, developmental disability, and epilepsy, and enrichment of copy number variations (CNVs) in developmental disability. We also observed that modules seeded with genes strongly associated with epilepsy tend to have a higher association with epilepsy phenotypes than modules seeded at other neurodevelopmental disorder genes. Modules seeded with genes strongly associated with epilepsy (e.g., SCN1A, GABRA1, and KCNB1) are significantly associated with synaptic transmission, long-term potentiation, and calcium signaling pathways. On the other hand, modules found with seed genes that are not associated or weakly associated with epilepsy are mostly involved with RNA regulation and chromatin remodeling. Conclusions: In summary, our method identifies modules enriched with de novo non-synonymous mutations and can capture specific networks that underlie the epilepsy phenotype and display distinct enrichment in relevant biological processes.

AB - Background: Neurodevelopmental disorders (NDDs) such as autism spectrum disorder, intellectual disability, developmental disability, and epilepsy are characterized by abnormal brain development that may affect cognition, learning, behavior, and motor skills. High co-occurrence (comorbidity) of NDDs indicates a shared, underlying biological mechanism. The genetic heterogeneity and overlap observed in NDDs make it difficult to identify the genetic causes of specific clinical symptoms, such as seizures. Methods: We present a computational method, MAGI-S, to discover modules or groups of highly connected genes that together potentially perform a similar biological function. MAGI-S integrates protein-protein interaction and co-expression networks to form modules centered around the selection of a single "seed" gene, yielding modules consisting of genes that are highly co-expressed with the seed gene. We aim to dissect the epilepsy phenotype from a general NDD phenotype by providing MAGI-S with high confidence NDD seed genes with varying degrees of association with epilepsy, and we assess the enrichment of de novo mutation, NDD-associated genes, and relevant biological function of constructed modules. Results: The newly identified modules account for the increased rate of de novo non-synonymous mutations in autism, intellectual disability, developmental disability, and epilepsy, and enrichment of copy number variations (CNVs) in developmental disability. We also observed that modules seeded with genes strongly associated with epilepsy tend to have a higher association with epilepsy phenotypes than modules seeded at other neurodevelopmental disorder genes. Modules seeded with genes strongly associated with epilepsy (e.g., SCN1A, GABRA1, and KCNB1) are significantly associated with synaptic transmission, long-term potentiation, and calcium signaling pathways. On the other hand, modules found with seed genes that are not associated or weakly associated with epilepsy are mostly involved with RNA regulation and chromatin remodeling. Conclusions: In summary, our method identifies modules enriched with de novo non-synonymous mutations and can capture specific networks that underlie the epilepsy phenotype and display distinct enrichment in relevant biological processes.

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