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Series GSE83708 Query DataSets for GSE83708
Status Public on Dec 30, 2016
Title CSF pQTL study in the Japanese population [genotyping Q17]
Organism Homo sapiens
Experiment type Genome variation profiling by SNP array
SNP genotyping by SNP array
Summary Cerebrospinal fluid (CSF) is virtually the only one accessible source of proteins derived from the central nervous system (CNS) of living humans and possibly reflects the pathophysiology of a variety of neuropsychiatric diseases. However, little is known regarding the genetic basis of variation in protein levels of human CSF. We examined CSF levels of 1,126 proteins in 133 subjects and performed genome-wide association analysis of 514,227 single nucleotide polymorphisms (SNPs) to detect protein quantitative trait loci (pQTLs). Spearman’s correlation was used to identify association between genotypes of SNPs and protein levels. A total of 421 cis and 25 trans SNP-protein pairs were significantly correlated at a false discovery rate (FDR) of less than 0.01 (nominal P < 7.66 x 10 −9). Cis-only analysis revealed additional 580 significant cis SNP-protein pairs with FDR < 0.01 (nominal P < 2.13 x 10 −5). pQTL SNPs were more likely, compared to non-pQLT SNPs, to be disease/trait-associated variants identified by previous genome-wide association studies. The present findings suggest that genetic variations play a major role in the regulation of protein expression in the CNS. The obtained database will serve as a valuable resource for future neuropsychiatric research.
Overall design CSF levels of 1,126 proteins in 133 subjects were examined. Genome-wide association analysis was performed to detect protein quantitative trait loci (pQTLs) affecting CSF protein levels.
Contributor(s) Sasayama D, Hattori K, Ogawa S, Yokota Y, Matsumura R, Teraishi T, Hori H, Ota M, Yoshida S, Kunugi H
Citation(s) 28031287, 32426945
Submission date Jun 24, 2016
Last update date Dec 15, 2020
Contact name Daimei Sasayama
Organization name National Center of Neurology and Psychiatry
Street address 4-1-1 Ogawahigashi-machi
City Kodaira
ZIP/Postal code 187-8551
Country Japan
Platforms (1)
GPL18224 Infinium HumanOmniExpressExome BeadChip
Samples (90)
GSM2213649 blood_Q17_1
GSM2213650 blood_Q17_2
GSM2213651 blood_Q17_3
This SubSeries is part of SuperSeries:
GSE83711 CSF pQTL study in the Japanese population
BioProject PRJNA326775

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE83708_Matrix_processed_Q17.csv.gz 1.4 Gb (ftp)(http) CSV
GSE83708_Matrix_signal_intensities_Q17.csv.gz 1.1 Gb (ftp)(http) CSV
Processed data are available on Series record

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