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| 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
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| 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.
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| 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.
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| Contributor(s) |
Yang C |
| Citation(s) |
31376382 |
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| Submission date |
May 22, 2019 |
| Last update date |
Aug 23, 2019 |
| Contact name |
Chao Yang |
| E-mail(s) |
chenmengyun888@163.com
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| Organization name |
First Affiliated Hospital of Anhui Medical University
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| Street address |
#69 Meishan Road, Hefei230032, Anhui, China
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| City |
Hefei |
| ZIP/Postal code |
230023 |
| Country |
China |
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| Platforms (1) |
| GPL26698 |
Illumina Human Exome Asian BeadChip (Exome_Asian_30K_ExomePlus_15031624_A) |
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| Samples (8949)
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| Relations |
| BioProject |
PRJNA544462 |
| 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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