ArticleEuropean journal of human genetics : EJHG2015
Effects of copy number variable regions on local gene expression in white blood cells of Mexican Americans.
Article in European journal of human genetics : EJHG, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 5 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
5 citing papers in PubMed, 9 citations in OpenAlex.
- Deciphering the genomic, epigenomic, and transcriptomic landscapes of pre-invasive lung cancer lesions.Nature medicine · 2019Article
- Characterizing functional consequences of DNA copy number alterations in breast and ovarian tumors by spaceMap.Journal of genetics and genomics = Yi chuan xue bao · 2018Article
- Inferring gene regulatory relationships with a high-dimensional robust approach.Genetic epidemiology · 2017Article
- Copy Number Variations in Tilapia Genomes.Marine biotechnology (New York, N.Y.) · 2017Article
- Analysing multiple types of molecular profiles simultaneously: connecting the needles in the haystack.BMC bioinformatics · 2016Article
Corrections and comments
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Authors and funding
17 authors at 4 institutions in 2 countries.
Funding
Abstract
Only few systematic studies on the contribution of copy number variation to gene expression variation have been published to date. Here we identify effects of copy number variable regions (CNVRs) on nearby gene expression by investigating 909 CNVRs and expression levels of 12059 nearby genes in white blood cells from Mexican-American participants of the San Antonio Family Heart Study. We empirically evaluate our ability to detect the contribution of CNVs to proximal gene expression (presumably in cis) at various window sizes (up to a 10 Mb distance) between the gene and CNV. We found a ~1-Mb window size to be optimal for capturing cis effects of CNVs. Up to 10% of the CNVs in this study were found to be significantly associated with the expression of at least one gene within their vicinity. As expected, we find that CNVs that directly overlap gene sequences have the largest effects on gene expression (compared with non-overlapping CNVRs located nearby), with positive correlation (except for a few exceptions) between estimated genomic dosage and expression level. We find that genes whose expression level is significantly influenced by nearby CNVRs are enriched for immunity and autoimmunity related genes. These findings add to the currently limited catalog of CNVRs that are recognized as expression quantitative trait loci, and have implications for future study designs as well as for prioritizing candidate causal variants in genomic regions associated with disease.
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