Project description:Immune thrombocytopenia (ITP) is an autoimmnue bleeding disorder characterized by low platelet count. To identify susceptibility loci for disease progression of ITP, we performed this genome-wide association study using DNA pools of 200 ITP cases and 200 controsl in Han Chinese. Performing GWAS on pools of DNA samples is an effective strategy to reduce the costs of studies and pooling DNA has been shown to be an efficient method to select candidate susceptibility loci for follow-up by individual genotyping.
Project description:Leprosy is a chronic granulomatous disease caused by infection with Mycobacterium leprae. Genetic association studies indicated that leprosy risk is strongly associated with variation within the major histocompatibility complex (MHC) region, but the full number of variants in this region has yet to be elucidated. To identify further susceptibility loci or loss of function variants for this disease, we performed fine-mapping analysis of the MHC region using a Han Chinese reference panel (n= 10,689 patients, 29,948 genetic markers) in the data sets from our previous leprosy studies. Then, a fixed-effect meta-analysis was carried out separately for Chinese (case=2,901, control=3,801) and North Chinese (case=1,983, control=2,635) participants. The meta-analysis of Chinese participants identified 10 HLA-type or amino acid variants with lower than the genome-wide significant susceptibility signal. Next, gene-by-gene step-wise conditional analysis was performed in the combined dataset of these cohorts. Finally, we identified four new independent susceptibility loci (HLA-DQA1, HLA-C, rs3129063, and rs58327373) and confirmed one previously reported locus (HLA-DRB1) that significantly associated with leprosy in the Chinese Han population. Thus the results of this study increase knowledge about leprosy risk variants and illustrate the value of HLA imputation for fine mapping of causal variants in the MHC.
Project description:Tetralogy of Fallot (TOF), the most frequent cyanotic congenital heart disease, occurs as a simplex trait of unknown etiology in the majority of cases. Studies of non-Asian populations suggest that approximately 10% of TOF cases carry a de novo rare copy number variant (CNV) thought to underlie the malformation. A genome-wide CNV analysis was performed in 303 TOF and 302 controls of Han Chinese as well as compared to 1,000 common Chinese database and revealed 166 rare CNVs identified in TOF patients with 119 CNVs further evaluated as potential “TOF-specific CNVs”; 98 were validated by qPCR, and 44 CNVs showed positive results on validation (positive rate 46.9%, 44/98). The genes related to the clinical phenotypes (subpulmonary VSD, bicuspid pulmonary valve, aortic valve overriding more than 75%, and right aortic arch) and the specific CNVs were included in integrating gene-gene interaction network analysis that identified the genes covering the specific CNVs directly or indirectly correlated to TOF and the signaling pathways. Thus, this study identified novel TOF-specific/associate CNVs in the Han Chinese that occurring at higher frequency in the Han Chinese (28.4% in Chr 1-20 and 42.9% in all chromosomes) is reflective of the increased prevalence of TOF in China. These novel CNVs identify new candidate genes for TOF. Our findings provide new insight into the contribution of CNVs to the genetic basis of TOF and identify new genetic loci potentially important to the pathogenesis of TOF
Project description:Genome wide DNA methylation profiling of blood samples from eight female identical twins of Han Chinese for forensic age prediction, age 21 to 32. The Illumina Infinium HumanMethylation450 BeadChip was used to obtain DNA methylation profiles across approximately 485,000 CpGs at a single-nucleotide resolution. Samples included 8 pairs of identical female twins of Han Chinese.
Project description:We compared standard human reference genome GRCh38 and de novo assembled reference genome HX1 in precision medicine applications for specific ethnics. In order to quantify the HX1 misassembled genes and HX1-specific contigs, we performed RNA-seq and RNC-seq on hepatocellular carcinoma cell lines (MHCC97H, MHCCLM3 and MHCCLM6) which were derived from Chinese Han individuals. In which, RNC-seq datasets of MHCC97H and MHCCLM3 had been published. We found that a considerable fraction of HX1 misassembled genes was expressed in the Chinese Han samples. Furthermore, we found no HX1-specific contigs yielded more than 2.27 FPKM (minimun FPKM of 1 copy/cell transcript) in the Chinese Han sampels.
Project description:Elucidating the genetic basis underlying the variation in hepatic gene expression is of importance to understand disease etiology and drug metabolism variances. To date, no genome-wide eQTL analysis has been conducted in the Han Chinese, the largest ethnic group in the world. We performed a genome-wide eQTL mapping in a set of Han Chinese liver tissue (n=64).
Project description:Elucidating the genetic basis underlying the variation in hepatic gene expression is of importance to understand disease etiology and drug metabolism variances. To date, no genome-wide eQTL analysis has been conducted in the Han Chinese, the largest ethnic group in the world. We performed a genome-wide eQTL mapping in a set of Han Chinese liver tissue (n=64).
Project description:The genes had different expression between healthy people and acute myocardial infarction.We aimed to identify the differentially expressed genes involved in acute myocardial infarction in Northeast Chinese Han people. We used microarrays to detail the global programme of gene expression to identify the differentially gene between the patients with acute myocardial infarction and healthy people in Northeast Chinese Han people
Project description:By analyse the tissue/blood variant spectrum model using NGS, the present clinical trial aims to elucidate the genetic basis of CRC in Chinese; to establish of CRC genetic map in Chinese patients; to identification new genetic biomarkers, drug and pathways; and to subtyping for precision treatment and management for Chinese CRC patients.
