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ABSTRACT: Genome-wide analysis confirms the independent origin of the Japanese and Korean Adonis amurensis (Ranunculaceae)

PROVIDER: PRJNA1227022 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR32456486_1.fastq.gz	Fastqsanger.gz
	SRR32456486_2.fastq.gz	Fastqsanger.gz
	SRR32456487_1.fastq.gz	Fastqsanger.gz
	SRR32456487_2.fastq.gz	Fastqsanger.gz
	SRR32456488_1.fastq.gz	Fastqsanger.gz

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Project description:More than 200 asthma-associated genetic variants have been identified in genome-wide association studies (GWASs). Expression quantitative trait loci (eQTL) data resources can help identify causal genes of the GWAS signals, but it can be difficult to find an eQTL that reflects the disease state because most eQTL data are obtained from normal healthy subjects. We performed a blood eQTL analysis using transcriptomic and genotypic data from 436 Korean asthma patients. To identify asthma-related genes, we carried out colocalization and Summary-based Mendelian Randomization (SMR) analysis using the results of asthma GWASs and eQTL data. In addition, we compared the results of disease eQTL data and asthma-related genes with two normal blood eQTL data from Genotype-Tissue Expression (GTEx) project and a Japanese study. We identified 342,054 cis-eQTL and 2,931 eGenes from asthmatic eQTL analysis. We compared the disease eQTL results with GTEx and a Japanese study and found that 63.2 % of the 2,931 eGenes overlapped with the GTEx eGenes and 38.5 % with the Japanese eGenes. Following the integrated analysis of the asthmatic eQTL data with asthma GWASs, using colocalization and SMR methods, we identified 13 asthma-related genes specific to the Korean asthmatic eQTL data. We provided Korean asthmatic cis-eQTL data and identified asthma-related genes by integrating them with GWAS data. In addition, we suggested these asthma-related genes as therapeutic targets for asthma. We envisage that our findings will contribute to understanding the etiological mechanisms of asthma and provide novel therapeutic targets.

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Affymetrix SNP array data for Japanese schizophrenia samples

Project description:Genome-wide association study (GWAS) was performed in 120 patient-parents trio samples from Japanese schizophrenia pedigrees ABSTRACT: Schizophrenia is a devastating neuropsychiatric disorder with genetically complex traits. Genetic variants should explain a considerable portion of the risk for schizophrenia, and genome-wide association study (GWAS) is a potentially powerful tool for identifying the risk variants that underlie the disease. Here, we report the results of a three-stage analysis of three independent cohorts consisting of a total of 2,535 samples from Japanese and Chinese populations for searching schizophrenia susceptibility genes using a GWAS approach. Firstly, we examined 115,770 single nucleotide polymorphisms (SNPs) in 120 patient-parents trio samples from Japanese schizophrenia pedigrees. In stage II, we evaluated 1,632 SNPs (1,159 SNPs of p < 0.01 and 473 SNPs of p < 0.05 that located in previously reported linkage regions). The second sample consisted of 1,012 case-control samples of Japanese origin. The most significant p value was obtained for the SNP in the ELAVL2 [(embryonic lethal, abnormal vision, Drosophila)-like 2] gene located on 9p21.3 (p = 0.00087). In stage III, we scrutinized the ELAVL2 gene by genotyping gene-centric tagSNPs in the third sample set of 293 family samples (1,163 individuals) of Chinese descent and the SNP in the gene showed a nominal association with schizophrenia in Chinese population (p = 0.026). The current data in Asian population would be helpful for deciphering ethnic diversity of schizophrenia etiology.

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