The discovery of integrated gene networks for autism and related disorders
Open accessAbstract
Despite considerable genetic heterogeneity underlying neurodevelopmental diseases, there is compelling evidence that many disease genes will map to a much smaller number of biological subnetworks. We developed a computational method, termed MAGI (m erging a ffected g enes into i ntegrated networks), that simultaneously integrates protein–protein interactions and RNA-seq expression profiles during brain development to discover “modules” enriched for de novo mutations in probands. We applied this method to recent exome sequencing of 1116 patients with autism and intellectual disability, discovering two distinct modules that differ in their properties and associated phenotypes. The first module consists of 80 genes associated with Wnt, Notch, SWI/SNF, and NCOR complexes and shows the highest expression early during embryonic development (8–16 post-conception weeks [pcw]). The second module consists of 24 genes associated with synaptic function, including long-term potentiation and calcium signaling with higher levels of postnatal expression. Patients with de novo mutations in these modules are more significantly intellectually impaired and carry more severe missense mutations when compared to probands with de novo mutations outside of these modules. We used our approach to define subsets of the network associated with higher functioning autism as well as greater severity with respect to IQ. Finally, we applied MAGI independently to epilepsy and schizophrenia exome sequencing cohorts and found significant overlap as well as expansion of these modules, suggesting a core set of integrated neurodevelopmental networks common to seemingly diverse human diseases.
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M1 consists of 47 genes associated with Wnt, Notch, SWI/SNF, and NCOR signaling, and showing high expression during embryonic development (8-16 pcw).
“M1 consists of 47 genes associated with Wnt, Notch, SWI/SNF, and NCOR signaling, and showing high expression during embryonic development (8–16 pcw) (Fig. 1, Supplementary Table S1).”
From Distinct selective forces and Neanderthal introgression shaped genetic diversity at genes involved in neurodevelopmental disorders (2017) · cites this paper as [29]
The Results section reports 48 genes in M1_Best and 80 in M1_Extended, not 47. It associates the M1 modules with Wnt and Notch signaling and SWI/SNF and NCOR complexes; the Results and Discussion place M1_Extended’s peak expression at 8–16 pcw. The pathway and expression descriptions are supported, but the gene count is not. (LLM, conf=0.91)
Experimental — accuracy not yet measuredM2 includes 21 genes associated with synaptic function and mainly expressed at postnatal stages.
“M2 includes 21 genes associated with synaptic function and mainly expressed at postnatal stages (Fig. 1, Supplementary Table S1).”
From Distinct selective forces and Neanderthal introgression shaped genetic diversity at genes involved in neurodevelopmental disorders (2017) · cites this paper as [29]
The Results section describes M2_Extended as enriched for synaptic plasticity genes and reports a sharp rise in their expression after birth; the Discussion says their expression peaks postnatally. The gene count does not match: the paper reports 24 genes in M2_Extended, not 21. (LLM, conf=0.90)
Experimental — accuracy not yet measuredThe modules were built through exome sequencing data of 1116 patients affected by ASD and ID.
“These modules were built through the exome sequencing data of 1116 patients affected by ASD and ID29.”
From Distinct selective forces and Neanderthal introgression shaped genetic diversity at genes involved in neurodevelopmental disorders (2017) · cites this paper as [29]
The Results (Algorithm) say MAGI used exome de novo mutation data, and the Results (Autism and intellectual disability) say it identified two ASD and ID modules. But that section gives the input for those modules as 877 autism and ID probands, not 1116. No page number is available for these passages. (LLM, conf=0.85)
Experimental — accuracy not yet measuredThe 68 genes were previously shown to represent functional modules enriched of de novo mutations in probands.
“We focused in particular on 68 genes which, despite not being an exhaustive catalog of genetic risk loci for ASD and ID, were previously shown to represent functional modules enriched of de novo mutations in probands29.”
From Distinct selective forces and Neanderthal introgression shaped genetic diversity at genes involved in neurodevelopmental disorders (2017) · cites this paper as [29]
The Results (Autism and intellectual disability; page unavailable) describe connected, coexpressed gene modules enriched for de novo mutations in ASD and ID probands. They report 80 genes in M1_Extended and 24 in M2_Extended, however, and do not identify the citing document’s specific set of 68 genes as those modules. (LLM, conf=0.85)
Experimental — accuracy not yet measuredModule 1 includes genes associated with transcriptional regulation during brain development.
“Module 1 includes genes associated to transcriptional regulation during brain development, whereas module 2 is composed of synaptic genes involved in long-term potentiation and calcium signaling29.”
From Distinct selective forces and Neanderthal introgression shaped genetic diversity at genes involved in neurodevelopmental disorders (2017) · cites this paper as [29]
Module 2 is composed of synaptic genes involved in long-term potentiation and calcium signaling.
“Module 1 includes genes associated to transcriptional regulation during brain development, whereas module 2 is composed of synaptic genes involved in long-term potentiation and calcium signaling29.”
From Distinct selective forces and Neanderthal introgression shaped genetic diversity at genes involved in neurodevelopmental disorders (2017) · cites this paper as [29]
MAGI identified modules containing functionally related genes enriched for deleterious mutations in ASD, many under strong purifying selection, and also found in epilepsy, schizophrenia, and intellectual disability.
“MAGI identified modules containing functionally related genes enriched for deleterious mutations in ASD, many of which are under strong purifying selection, and are also found in epilepsy, schizophrenia and intellectual disability133.”
From Systems biology and gene networks in neurodevelopmental and neurodegenerative disorders (2015) · cites this paper as [133]
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- Authors
- Hormozdiari, F., Penn, O., Borenstein, E., & Eichler, E. E.
- Affiliations
- University of Washington (US)
- Howard Hughes Medical Institute (US)
- Venue
- Genome Research
- Publisher
- Cold Spring Harbor Laboratory
- Published
- 2014-11-05
- Volume
- 25
- Issue
- 1
- Pages
- 142-154
- ISSN
- 1088-9051 (ISSN-L)
- 1549-5469
- PMC
- PMC4317170
- OpenAlex
- W2106870542
- Cited by
- 249
- References
- 53
- Citations by year
- 2026: 5 · 2025: 11 · 2024: 11 · 2023: 16 · 2022: 20 · 2021: 20 · 2020: 29 · 2019: 27 · 2018: 23 · 2017: 27 · 2016: 43 · 2015: 16 · 2014: 1
- Type
- posted content
- Language
- en
- Open access
- bronze
- doi.org
- Locations
- Genome Research (publishedVersion)
- PubMed Central (publishedVersion, cc-by-nc)
- PubMed (publishedVersion)
- eScholarship (California Digital Library) (submittedVersion, cc-by-nc)
- Funders
- Simons Foundation (303241)
- NIH/NIMH (R01MH101221)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetics and Neurodevelopmental Disorders
- Life Sciences › Neuroscience › Cognitive Neuroscience › Autism Spectrum Disorder Research
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Bioinformatics and Genomic Networks
- Keywords
- autism spectrum disorder, intellectual disability, de novo mutations, gene regulatory networks, Three Kings, protein-protein interaction, RNA-seq expression, brain development, Wnt signaling, Notch signaling, SWI/SNF complex, synaptic function, long-term potentiation, calcium signaling, epilepsy, schizophrenia, neurodevelopmental disorders, missense mutations, disease severity
- MeSH terms
- Algorithms, Autistic Disorder, Epilepsy, Humans, Phenotype, Schizophrenia, Cohort Studies, Cluster Analysis, Databases, Factual, Sequence Analysis, RNA, Genetic Heterogeneity, Mutation, Missense, Gene Regulatory Networks, Exome
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