title: A Burden of Rare Variants Associated with Extremes of Gene Expression in Human Peripheral Blood.
abstract: In order to evaluate whether rare regulatory variants in the vicinity of promoters are likely to impact gene expression, we conducted a novel burden test for enrichment of rare variants at the extremes of expression. After sequencing 2-kb promoter regions of 472 genes in 410 healthy adults, we performed a quadratic regression of rare variant count on bins of peripheral blood transcript abundance from microarrays, summing over ranks of all genes. After adjusting for common eQTLs and the major axes of gene expression covariance, a highly significant excess of variants with minor allele frequency less than 0.05 at both high and low extremes across individuals was observed. Further enrichment was seen in sites annotated as potentially regulatory by RegulomeDB, but a deficit of effects was associated with known metabolic disease genes. The main result replicates in an independent sample of 75 individuals with RNA-seq and whole-genome sequence information. Three of four predicted large-effect sites were validated by CRISPR/Cas9 knockdown in K562 cells, but simulations indicate that effect sizes need not be unusually large to produce the observed burden. Unusually divergent low-frequency promoter haplotypes were observed at 31 loci, at least 9 of which appear to be derived from Neandertal admixture, but these were not associated with divergent gene expression in blood. The overall burden test results are consistent with rare and private regulatory variants driving high or low transcription at specific loci, potentially contributing to disease.
authors: School of Biology and Center for Integrative Genomics, Georgia Institute of Technology, Atlanta, GA 30332, USA.
authors: Jing
authors: J
authors: Zhao
authors: School of Biology and Center for Integrative Genomics, Georgia Institute of Technology, Atlanta, GA 30332, USA.
authors: Idowu
authors: I
authors: Akinsanmi
authors: School of Biology and Center for Integrative Genomics, Georgia Institute of Technology, Atlanta, GA 30332, USA.
authors: Dalia
authors: D
authors: Arafat
authors: Wallace H. Coulter Department of Biomedical Engineering, Laboratory of Biomolecular Engineering and Nanomedicine, Georgia Institute of Technology, Atlanta, GA 30332, USA.
authors: T J
authors: TJ
authors: Cradick
authors: Wallace H. Coulter Department of Biomedical Engineering, Laboratory of Biomolecular Engineering and Nanomedicine, Georgia Institute of Technology, Atlanta, GA 30332, USA; Department of Bioengineering, Rice University, Texas Medical Center, Houston, TX 77030, USA.
authors: Ciaran M
authors: CM
authors: Lee
authors: School of Biology and Center for Integrative Genomics, Georgia Institute of Technology, Atlanta, GA 30332, USA.
authors: Samridhi
authors: S
authors: Banskota
authors: School of Biology and Center for Integrative Genomics, Georgia Institute of Technology, Atlanta, GA 30332, USA.
authors: Urko M
authors: UM
authors: Marigorta
authors: Wallace H. Coulter Department of Biomedical Engineering, Laboratory of Biomolecular Engineering and Nanomedicine, Georgia Institute of Technology, Atlanta, GA 30332, USA; Department of Bioengineering, Rice University, Texas Medical Center, Houston, TX 77030, USA.
authors: Gang
authors: G
authors: Bao
authors: School of Biology and Center for Integrative Genomics, Georgia Institute of Technology, Atlanta, GA 30332, USA. Electronic address: greg.gibson@biology.gatech.edu.
authors: Greg
authors: G
authors: Gibson
mesh_terms: D000328:Adult; D000368:Aged; D000369:Aged, 80 and over; D005260:Female; D015870:Gene Expression; D020869:Gene Expression Profiling; D005787:Gene Frequency; D056426:Genetic Loci; D023281:Genomics; D060005:Genotyping Techniques; D006239:Haplotypes; D006801:Humans; D016014:Linear Models; D008297:Male; D008875:Middle Aged; D020641:Polymorphism, Single Nucleotide; D011401:Promoter Regions, Genetic; D015203:Reproducibility of Results; D017422:Sequence Analysis, DNA; D055815:Young Adult