Loci nominally associated with autism from genome-wide analysis show enrichment of brain expression quantitative trait loci but not lymphoblastoid cell line expression quantitative trait loci
Open accessAbstract
BACKGROUND: Autism spectrum disorder is a severe early onset neurodevelopmental disorder with high heritability but significant heterogeneity. Traditional genome-wide approaches to test for an association of common variants with autism susceptibility risk have met with limited success. However, novel methods to identify moderate risk alleles in attainable sample sizes are now gaining momentum. METHODS: In this study, we utilized publically available genome-wide association study data from the Autism Genome Project and annotated the results (P <0.001) for expression quantitative trait loci present in the parietal lobe (GSE35977), cerebellum (GSE35974) and lymphoblastoid cell lines (GSE7761). We then performed a test of enrichment by comparing these results to simulated data conditioned on minor allele frequency to generate an empirical P-value indicating statistically significant enrichment of expression quantitative trait loci in top results from the autism genome-wide association study. RESULTS: Our findings show a global enrichment of brain expression quantitative trait loci, but not lymphoblastoid cell line expression quantitative trait loci, among top single nucleotide polymorphisms from an autism genome-wide association study. Additionally, the data implicates individual genes SLC25A12, PANX1 and PANX2 as well as pathways previously implicated in autism. CONCLUSIONS: These findings provide supportive rationale for the use of annotation-based approaches to genome-wide association studies.
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Gene-set enrichment and related analyses for AGP and other ASD data sets have found significant evidence for common variants affecting risk.
“gene-set enrichment and related analyses for AGP and other ASD data sets have found significant evidence for common variants affecting risk (54–57)”
From Individual common variants exert weak effects on the risk for autism spectrum disorders (2012) · cites this paper as [57]
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- Authors
- Davis, L. K., Gamazon, E. R., Kistner-Griffin, E., Badner, J. A., Liu, C., Cook, E. H., Sutcliffe, J. S., & Cox, N. J.
- Affiliations
- University of Chicago (US)
- University of Illinois Chicago (US)
- Vanderbilt University (US)
- Corresponding author
- Davis, Lea K
- Venue
- Molecular Autism
- Published
- 2012
- Volume
- 3
- Issue
- 1
- Pages
- 3
- ISSN
- 2040-2392 (ISSN-L)
- PMC
- PMC3484025
- OpenAlex
- W2163068701
- Cited by
- 40
- References
- 34
- Citations by year
- 2026: 1 · 2024: 3 · 2023: 3 · 2022: 3 · 2021: 3 · 2020: 3 · 2019: 2 · 2018: 2 · 2017: 5 · 2016: 2 · 2015: 4 · 2014: 4 · 2013: 3 · 2012: 2
- FWCI
- 2.13
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- cc-by
- Locations
- Molecular Autism (publishedVersion, cc-by)
- Europe PMC (PubMed Central) (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion)
- Funders
- National Institute of Child Health and Human Development (HD055751)
- Eunice Kennedy Shriver National Institute of Child Health and Human Development (P50HD055751)
- Topics
- Life Sciences › Neuroscience › Cognitive Neuroscience › Autism Spectrum Disorder Research
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic Associations and Epidemiology
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetics and Neurodevelopmental Disorders
- Keywords
- autism spectrum disorder, expression quantitative trait loci, brain gene expression, lymphoblastoid cell lines, enrichment analysis, SLC25A12, pannexin 1, PANX2, parietal lobe, cerebellum
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