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Series GSE131663 Query DataSets for GSE131663
Status Public on May 24, 2019
Title Exome-wide rare loss-of-function variant enrichment study in 21,347 Han Chinese individuals identifies four new susceptibility genes for psoriasis [psoriasis patients]
Organism Homo sapiens
Experiment type Genome variation profiling by array
SNP genotyping by SNP array
Summary Most psoriasis-related genes or loci identified through genome-wide association studies (GWASs) represent common clusters and are located in non-coding regions of the human genome, providing only limited evidence for the role of coding variants in psoriasis. Two exome-wide case-control genotyping data sets were obtained from our previous study. Quality control was established for each data set, and the remaining markers in each were annotated using ANNOVAR. Gene-based analysis was performed on the annotation results. A total of 250 and 35 genes in the Exome_Fine and Exome_Asian Array cohorts, respectively, exceeded the threshold (P < 4.43 × 10-6). Merged gene-based analysis was then conducted on the same set of SNPs from seven genes common to both arrays, and the chi-square test was used to confirm all gene-based results. Ultimately, four new susceptibility genes were identified: BBS7 (Pcombine = 1.38 × 10−29), GSTCD (Pcombine = 8.35 × 10−47), LIPK (Pcombine = 1.02 × 10−19) and PPP4R3B (Pcombine = 1.79 × 10−33). This study identified four new susceptibility genes for psoriasis through a gene-based method using rare variants, contributing to our understanding of the pathogenesis of psoriasis.
Overall design To contributing to our understanding of the pathogenesis of psoriasis, we performed gene-based analysis in cohorts genotyped using Exome_Fine Array and Exome_Asian Array in the data sets from our previous psoriasis studies. The following data included 8,949 samples (4,179 cases and 4,770 controls) in Exome_Asian Array.
Contributor(s) Yang C
Citation(s) 31376382
Submission date May 22, 2019
Last update date Aug 23, 2019
Contact name Chao Yang
Organization name First Affiliated Hospital of Anhui Medical University
Street address #69 Meishan Road, Hefei230032, Anhui, China
City Hefei
ZIP/Postal code 230023
Country China
Platforms (1)
GPL26698 Illumina Human Exome Asian BeadChip (Exome_Asian_30K_ExomePlus_15031624_A)
Samples (8949)
GSM3792022 7785496042_R02C01
GSM3792023 7785496042_R02C02
GSM3792024 7785496042_R03C01
BioProject PRJNA544462

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
GSE131663_RAW.tar 77.5 Gb (http)(custom) TAR (of TXT)
Processed data provided as supplementary file

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