ArticleBMC medical genomics2020
Sensitivity to gene dosage and gene expression affects genes with copy number variants observed among neuropsychiatric diseases.
Article in BMC medical genomics, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers, 2 of them syntheses that pooled it.
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Who cites it
10 citing papers in PubMed, 2 syntheses or guidelines pooled it, 16 citations in OpenAlex.
- Fully exploiting SNP arrays: a systematic review on the tools to extract underlying genomic structure.Briefings in bioinformatics · 2022Pooled it
- Guidelines for bioinformatics of single-cell sequencing data analysis in Alzheimer's disease: review, recommendation, implementation and application.Molecular neurodegeneration · 2022Pooled it
- Article
- Improving CNV Detection Performance in Microarray Data Using a Machine Learning-Based Approach.Diagnostics (Basel, Switzerland) · 2023Article
- A case of complex balanced chromosomal translocations associated with adverse pregnancy outcomes.Molecular cytogenetics · 2022Article
- Polyploidy as a Fundamental Phenomenon in Evolution, Development, Adaptation and Diseases.International journal of molecular sciences · 2022Review
- Keeping the balance: Trade-offs between human brain evolution, autism, and schizophrenia.Frontiers in genetics · 2022Review
- Position effects at the FGF8 locus are associated with femoral hypoplasia.American journal of human genetics · 2021Article
- 7p21.3 Together With a 12p13.32 Deletion in a Patient With Microcephaly-Does 12p13.32 Locus Possibly Comprises a Candidate Gene Region for Microcephaly?Frontiers in molecular neuroscience · 2021Article
- Loop Interrupted: Dysfunctional Chromatin Relations in Neurological Diseases.Frontiers in genetics · 2021Review
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Authors and funding
24 authors at 14 institutions in 1 country.
Funding
Abstract
backgroundCopy number variants (CNVs) have been reported to be associated with diseases, traits, and evolution. However, it is hard to determine which gene should have priority as a target for further functional experiments if a CNV is rare or a singleton. In this study, we attempted to overcome this issue by using two approaches: by assessing the influences of gene dosage sensitivity and gene expression sensitivity. Dosage sensitive genes derived from two-round whole-genome duplication in previous studies. In addition, we proposed a cross-sectional omics approach that utilizes open data from GTEx to assess the effect of whole-genome CNVs on gene expression.
methodsAffymetrix Genome-Wide SNP Array 6.0 was used to detect CNVs by PennCNV and CNV Workshop. After quality controls for population stratification, family relationship and CNV detection, 287 patients with narcolepsy, 133 patients with essential hypersomnia, 380 patients with panic disorders, 164 patients with autism, 784 patients with Alzheimer disease and 1280 healthy individuals remained for the enrichment analysis.
resultsOverall, significant enrichment of dosage sensitive genes was found across patients with narcolepsy, panic disorders and autism. Particularly, significant enrichment of dosage-sensitive genes in duplications was observed across all diseases except for Alzheimer disease. For deletions, less or no enrichment of dosage-sensitive genes with deletions was seen in the patients when compared to the healthy individuals. Interestingly, significant enrichments of genes with expression sensitivity in brain were observed in patients with panic disorder and autism. While duplications presented a higher burden, deletions did not cause significant differences when compared to the healthy individuals. When we assess the effect of sensitivity to genome dosage and gene expression at the same time, the highest ratio of enrichment was observed in the group including dosage-sensitive genes and genes with expression sensitivity only in brain. In addition, shared CNV regions among the five neuropsychiatric diseases were also investigated.
conclusionsThis study contributed the evidence that dosage-sensitive genes are associated with CNVs among neuropsychiatric diseases. In addition, we utilized open data from GTEx to assess the effect of whole-genome CNVs on gene expression. We also investigated shared CNV region among neuropsychiatric diseases.
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