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Isolating the causal genes from numerous genetic association signals in genome-wide association studies (GWASs) of complex phenotypes remains an open and challenging question. In the present study, we proposed a statistical approach, the effective-median-based Mendelian randomization (MR) framework, for inferring the causal genes of complex phenotypes with the GWAS summary statistics (named EMIC). The effective-median method solved the high false-positive issue in the existing MR methods due to either correlation among instrumental variables or noises in approximated linkage disequilibrium (LD). EMIC can further perform a pleiotropy fine-mapping analysis to remove possible false-positive estimates. With the usage of multiple cis-expression quantitative trait loci (eQTLs), EMIC was also more powerful than the alternative methods for the causal gene inference in the simulated datasets. Furthermore, EMIC rediscovered many known causal genes of complex phenotypes (schizophrenia, bipolar disorder, and total cholesterol) and reported many new and promising candidate causal genes. In sum, this study provided an efficient solution to discriminate the candidate causal genes from vast amounts of GWAS signals with eQTLs. EMIC has been implemented in our integrative software platform KGGSEE.

Background: Recent genome-wide association studies (GWASs) have suggested several susceptibility loci of hepatitis B virus (HBV)-related hepatocellular carcinoma (HCC) by statistical analysis at individual single-nucleotide polymorphisms (SNPs). However, these loci only explain a small fraction of HBV-related HCC heritability. Methods: In the present study, we aimed to identify additional susceptibility loci in two existing HBV-related HCC GWAS datasets using advanced gene- and gene-set-based association tests. Findings: The gene-based association analysis suggested that five genes are associated with HBV-related HCC risk: RNY4, GOLGA8M, LINC01207, WHAMMP2 and SLC39A8 with statistical significance. Through gene-set-based association analysis, we found that the genes in systemic lupus erythematosus pathway may be relevant to development of HBV-related HCC. Three previously reported genes, NAT2, GSTA1 and GSTA2, were also highlighted when genes were stratified in a liver-specific expression set. Furthermore, our analyses suggested that susceptibility loci of HBV-related HCC are unlikely to be enriched in several functional gene sets of HCC defined by our current knowledge. However, our failure to replicate significance at individual SNPs selected from the knowledge-based association analyses in independent cohorts calls for larger replication studies. Interpretation: This comprehensive knowledge-based association mining study suggested several promising genes significantly associated with HBV-related HCC risk, which may shed insights into the pathogenic mechanism of this fatal disorder. Funding Statement: This study was supported by Hong Kong Health and the Medical Research Fund (01121436 and 02132236 to M.X.L.), the National Natural Science Foundation of China (31100895, 81472618 and 81670535 to D.K.J., 81402297 to Q.L.X.), the National Science and Technology Major Project (No. 2018ZX10301202 to D.K.J. and J.H.), the Local Innovative and Research Teams Project of Guangdong Pearl River Talents Program (No. 2017BT01S131 to D.K.J. and J.H.), the Grant for Recruited Talents to Start Scientific Research from Nanfang Hospital (to D.K.J.), and the Distinguished Youth Scholars Incubation Project of Nanfang Hospital (No. 2017J001 to D.K.J.) Declaration of Interests: The authors declare that they have no conflict of interest. Ethics Approval Statement: The study was performed in accordance with guidelines approved by the local ethical committees from all participating centers involved in both the GWAS stage and the replication stage. An informed consent to participate in the study was obtained from each subject in accordance with the declaration of Helsinki principles. All study participants approved the storage of their frozen DNA specimens, for research purposes, in our laboratory.

Background: Schistosomiasis (japonica) is a neglected infectious disease, influencing millions of people at risk of infection worldwide. The patients are at high risk of gradually developing hepatic fibrosis. Immune regulation is recognized to contribute to schistosomal liver fibrosis. However, we still lack appropriate preventive and therapeutic modalities. Previous evidence points out that there is an interaction between lipid regulation and inflammation which moderates the homeostasis after parasitic infection. Moreover, while immune response to Schistosoma infection is considered affected by genetic diversity; yet so far little is known regarding the mechanism of action. To explore the association between lipid metabolism-related genes and the hepatic fibrosis induced by Schistosoma japonicum infection, we conducted the following study. Methods: This study combines epidemiological investigation, in-vitro studies, and animal experiment. First, we conducted a whole-genome sequencing in the epidemic area of China and established a S. japonicum-infected mice model and liver tissue morphology and mRNA analysis of PLA2G2D and PPARG were conducted. Then we expanded the sample size and collected biological information under epidemiological investigation. This was followed with genotyping of the candidate genes, the serum protein expression, as well as the level of three inflammation-related lipid mediators, which were measured and compared in different groups. Finally, we evaluated whether the allelic changes alter PLA2G2D enzymatic activity in vitro and compared the Pro and Ala PPARγ forms concerning the ability to activate transcription via dimerizing with the retinoid X receptor α (RXRα) and response element (PPRE). Findings: A group of lipid metabolism-related genes in schistosomiasis patients were identified. We found schistosome immunoregulation accompanied by the development of lipid metabolism in the murine model. We confirmed the genetic variation of arachidonic acid metabolic pathway related genes (PLA2G2D rs584367 and PPARG rs1801282) associated with a reduced risk of high grades of schistosomiasis induced hepatic fibrosis in a large sample size. Moreover, the levels of serum PLA2G2D and the 15d-PGJ2、PGE2 and TXB2 showed significant differences due to grades of fibrosis. Besides, the level of TXB2 significantly correlated with PLA2G2D. The enzyme activity of the PLA2G2D was increased approximately four-fold in the variant relative to the wild-type. The PPARγ 12Ala allele showed 18.7%-fold reduction in the ability to transactivate responsive promoters. Interpretation: This study raises a novel perspective conclusion from whole-genome sequencing that lipid metabolism particularly arachidonic acid metabolic pathway may play a regulatory role in the balance of inflammatory microenvironment which is essential for the development of Schistosoma liver fibrosis. Patients with risk polymorphism have more probability to develop uncontrollable inflammation, which eventually progress to hepatic fibrosis. The significant markers we found in this investigation may be used to facilitate diagnosis. Funding Statement: This study was supported by National Natural Science Foundation of China (Grant Number: 81601781) and the China Postdoctoral Science Foundation (Grant Number: 2016M591605), Science and Technology Program of Guangzhou (Grant Number: 201803010116). Declaration of Interests: The authors have no conflicts of interest to disclose. Ethics Approval Statement: Epidemiological studies were approved by the Ethics Committees of Fudan University (IRB#2016-TYSQ-03-17), and all participants gave informed written consent. Animals were cared for by the guidelines developed by the China Council on Animal care, and all animal experiments were performed according to the procedures approved by the Human Research Ethics Committee of the Sun Yat-sen University (No·2016-104).

The extended Simes' test (known as GATES) and scaled chi-square test were proposed to combine a set of dependent genome-wide association signals at multiple single-nucleotide polymorphisms (SNPs) for assessing the overall significance of association at the gene or pathway levels. The two tests use different strategies to combine association p values and can outperform each other when the number of and linkage disequilibrium between SNPs vary. In this paper, we introduce a hybrid set-based test (HYST) combining the two tests for genome-wide association studies (GWASs). We describe how HYST can be used to evaluate statistical significance for association at the protein-protein interaction (PPI) level in order to increase power for detecting disease-susceptibility genes of moderate effect size. Computer simulations demonstrated that HYST had a reasonable type 1 error rate and was generally more powerful than its parents and other alternative tests to detect a PPI pair where both genes are associated with the disease of interest. We applied the method to three complex disease GWAS data sets in the public domain; the method detected a number of highly connected significant PPI pairs involving multiple confirmed disease-susceptibility genes not found in the SNP- and gene-based association analyses. These results indicate that HYST can be effectively used to examine a collection of predefined SNP sets based on prior biological knowledge for revealing additional disease-predisposing genes of modest effects in GWASs. © 2012 The American Society of Human Genetics., link_to_subscribed_fulltext

Alzheimer's disease (AD) is the most common neurodegenerative disorders in the elderly. To identify rare genetic factors other than apolipoprotein E ɛ4 allele (ApoE ɛ4) contributing to the pathogenesis of late-onset AD (LOAD), we conducted a whole-exome analysis of 246 ApoE ɛ4-negative LOAD cases and 172 matched controls in Hong Kong Chinese population. LOAD patients showed a significantly higher burden of rare loss-of-function variants in genes related to immune function than healthy controls. Among the genes involved in immune function, we identified a rare stop-gain variant (p.Q48X) in mixed lineage kinase domain like pseudokinase (MLKL) gene present exclusively in 6 LOAD cases. MLKL is expressed in neurons, and the its expression levels in the p.Q48X carriers were significantly lower than that in age-matched wild-type controls. The ratio of Aβ42 to Aβ40 significantly increased in MLKL knockdown cells compared to scramble controls. MLKL loss-of-function mutation might contribute to late-onset ApoE ɛ4-negative AD in the Hong Kong Chinese population.

In the present study, we simultaneously test linkage and/or association of the collagen type I alpha 2 (COL1A2) gene with bone mineral density (BMD) and bone area. A total of 1280 subjects from 407 Chinese nuclear families (including both parents and their daughters) were genotyped for an intragenic marker MspI in the COL1A2 gene. BMD and bone area at the lumbar spine and hip were measured by dual-energy X-ray absorptiometry. Applying the QTDT (quantitative transmission disequilibrium test) program, we performed tests for population stratification, within-family association (via transmission disequilibrium test), total association, linkage, and linkage while modeling association. Significant or marginal within-family associations were found with BMD at the lumbar spine (P = 0.013), trochanter (P = 0.004), and total hip (P = 0.053) and with bone area at the intertrochanteric region (P = 0.024) and total hip (P = 0.048). The positive associations were confirmed in permutations except for bone area at total hip (P0.10). A small proportion (1%) of the population variance of bone phenotypes can be explained by the MspI polymorphism; however, it may be underestimated given the significant population stratification detected in our sample. Due to the limited number of sib pairs in this sample, we did not find evidence of linkage. In summary, the MspI polymorphism is likely to be in linkage disequilibrium with a nearby functional mutation affecting BMD and bone area.