Genome-wide association studies (GWAS) detect common genetic variants associated with complex disorders. With their comprehensive coverage of common single nucleotide polymorphisms and comparatively ...low cost, GWAS are an attractive tool in the clinical and commercial genetic testing. This review introduces the pipeline of statistical methods used in GWAS analysis, from data quality control, association tests, population structure control, interaction effects and results visualization, through to post-GWAS validation methods and related issues.
The genetic epistasis effect has been widely acknowledged as an essential contributor to genetic variation in complex diseases. In this chapter, we introduce a powerful and efficient statistical ...method, called W-test, for genetic epistasis testing. A wtest R package is developed for the implementation of the W-test method, which provides various functions to measure the main effect, pairwise interaction, higher-order interaction, and cis-regulation of SNP-CpG pairs in genetic and epigenetic data. It allows flexible stagewise and exhaustive association testing as well as diagnostic checking on the probability distributions in a user-friendly interface. The wtest package is available in CRAN at https://CRAN.R-project.org/package=wtest .
A recent mutation analysis suggested that Non-Structural Protein 6 (NSP6) of the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) is a key determinant of the viral pathogenicity. Here, by ...transcriptome analysis, we demonstrated that the inflammasome-related NOD-like receptor signaling was activated in SARS-CoV-2-infected lung epithelial cells and Coronavirus Disease 2019 (COVID-19) patients' lung tissues. The induction of inflammasomes/pyroptosis in patients with severe COVID-19 was confirmed by serological markers. Overexpression of NSP6 triggered NLRP3/ASC-dependent caspase-1 activation, interleukin-1β/18 maturation, and pyroptosis of lung epithelial cells. Upstream, NSP6 impaired lysosome acidification to inhibit autophagic flux, whose restoration by 1α,25-dihydroxyvitamin D
, metformin or polydatin abrogated NSP6-induced pyroptosis. NSP6 directly interacted with ATP6AP1, a vacuolar ATPase proton pump component, and inhibited its cleavage-mediated activation. L37F NSP6 variant, which was associated with asymptomatic COVID-19, exhibited reduced binding to ATP6AP1 and weakened ability to impair lysosome acidification to induce pyroptosis. Consistently, infection of cultured lung epithelial cells with live SARS-CoV-2 resulted in autophagic flux stagnation, inflammasome activation, and pyroptosis. Overall, this work supports that NSP6 of SARS-CoV-2 could induce inflammatory cell death in lung epithelial cells, through which pharmacological rectification of autophagic flux might be therapeutically exploited.
Studies in general population reported a positive association between tobacco smoking and airflow obstruction (AFO), a hallmark of chronic obstructive pulmonary disease (COPD). However, this attempt ...was less addressed in silica dust-exposed workers.
This retrospective cohort study consisted of 4481 silicotic workers attending the Pneumoconiosis Clinic during 1981-2019. The lifelong work history and smoking habits of these workers were extracted from medical records. Spirometry was carried out at the diagnosis of silicosis (n = 4177) and reperformed after an average of 9.4 years of follow-up (n = 2648). AFO was defined as forced expiratory volume in one second (FEV1)/force vital capacity (FVC) less than lower limit of normal (LLN). The association of AFO with smoking status was determined using multivariate logistics regression, and the effect of smoking cessation on the development of AFO was evaluated Cox regression.
Smoking was significantly associated with AFO (current smokers: OR = 1.92, 95% CI 1.51-2.44; former smokers: OR = 2.09, 95% CI 1.65-2.66). The risk of AFO significantly increased in the first 3 years of quitting smoking (OR = 1.23, 95% CI 1.02-1.47) but decreased afterwards with increasing years of cessation. Smoking cessation reduced the risk of developing AFO no matter before or after the confirmation of silicosis (pre-silicosis cessation: HR = 0.58, 95% CI 0.46-0.74; post-silicosis cessation: HR = 0.62, 95% CI 0.48-0.79).
Smoking cessation significantly reduced the risk of AFO in the workers with silicosis, although the health benefit was not observed until 3 years of abstinence. These findings highlight the importance of early and long-term smoking cessation among silicotic or silica dust-exposed workers.
Multi-population cohorts offer unprecedented opportunities for profiling disease risk in large samples, however, heterogeneous risk effects underlying complex traits across populations make ...integrative prediction challenging. In this study, we propose a novel Bayesian probability framework, the Prism Vote (PV), to construct risk predictions in heterogeneous genetic data. The PV views the trait of an individual as a composite risk from subpopulations, in which stratum-specific predictors can be formed in data of more homogeneous genetic structure. Since each individual is described by a composition of subpopulation memberships, the framework enables individualized risk characterization. Simulations demonstrated that the PV framework applied with alternative prediction methods significantly improved prediction accuracy in mixed and admixed populations. The advantage of PV enlarges as genetic heterogeneity and sample size increase. In two real genome-wide association data consists of multiple populations, we showed that the framework considerably enhanced prediction accuracy of the linear mixed model in five-group cross validations. The proposed method offers a new aspect to analyze individual's disease risk and improve accuracy for predicting complex traits in genotype data.
Recently, a number of single nucleotide polymorphisms (SNPs) were identified to be associated with late-onset Alzheimer disease (LOAD) through genome-wide association study data. Identification of ...SNP-SNP interaction played an important role in better understanding genetic basis of LOAD. In this study, fifty-eight SNPs were screened in a cohort of 229 LOAD cases and 318 controls from mainland China, and their interaction was evaluated by a series of analysis methods. Seven risk SNPs and six protective SNPs were identified to be associated with LOAD. Risk SNPs included rs9331888 (CLU), rs6691117 (CR1), rs4938933 (MS4A), rs9349407 (CD2AP), rs1160985 (TOMM40), rs4945261 (GAB2) and rs5984894 (PCDH11X); Protective SNPs consisted of rs744373 (BIN1), rs1562990 (MS4A), rs597668 (EXOC3L2), rs9271192 (HLA-DRB5/DRB1), rs157581 and rs11556505 (TOMM40). Among positive SNPs presented above, we found the interaction between rs4938933 (risk) and rs1562990 (protective) in MS4A weakened their each effect for LOAD; for three significant SNPs in TOMM40, their cumulative interaction induced the two protective SNPs effects lost and made the risk SNP effect aggravate for LOAD. Finally, we found rs6656401-rs3865444 (CR1-CD33) pairs were significantly associated with decreasing LOAD risk, while rs28834970-rs6656401 (PTK2B-CR1), and rs28834970-rs6656401 (PTK2B-CD33) were associated with increasing LOAD risk. In a word, our study indicates that SNP-SNP interaction existed in the same gene or cross different genes, which could weaken or aggravate their initial single effects for LOAD.
Routine immunizations and supplementary immunization activities (SIAs) have significantly improved measles control over the past two decades in China. Progress towards eliminating measles currently ...faces multiple challenges as the infection age increases, and adult-targeted SIA strategies are being considered. This study developed an age-stratified susceptible-exposed-infectious-recovered model using a recently published contact matrix to depict measles transmissions between individuals in seven age groups. Hubei, a high measles-incidence province in central China, was the selected setting. The baseline scenario was calibrated by fitting with the 2012-2015 age-stratified incidence data. SIAs targeting multiple age groups were simulated. Adult-targeted (>29 years) two-year SIA cycles produced the greatest annual incidence rate decrease, reducing incidences by half over a long timespan with 90% coverage levels. Incidences could remain below 10/100,000 until 2030 if SIAs were provided to individuals ≥6 years old with at least 50% coverage. These findings will help officials prioritize supplementary vaccination strategies. Public health officials in China should consider adult-to-adult transmissions and provide adult-targeted SIAs. Although officials have reported approximately 90% SIA coverage in the past, SIAs for the adult population should be provided on shorter intervals, particularly for the aging population with decreased immunity.
Altered microbiome composition and aberrant promoter hypermethylation of tumor suppressor genes (TSGs) are two important hallmarks of colorectal cancer (CRC). Here we performed concurrent 16S rRNA ...gene sequencing and methyl-CpG binding domain-based capture sequencing in 33 tissue biopsies (5 normal colonic mucosa tissues, 4 pairs of adenoma and adenoma-adjacent tissues, and 10 pairs of CRC and CRC-adjacent tissues) to identify significant associations between TSG promoter hypermethylation and CRC-associated bacteria, followed by functional validation of the methylation-associated bacteria.
Fusobacterium nucleatum and Hungatella hathewayi were identified as the top two methylation-regulating bacteria. Targeted analysis on bona fide TSGs revealed that H. hathewayi and Streptococcus spp. significantly correlated with CDX2 and MLH1 promoter hypermethylation, respectively. Mechanistic validation with cell-line and animal models revealed that F. nucleatum and H. hathewayi upregulated DNA methyltransferase. H. hathewayi inoculation also promoted colonic epithelial cell proliferation in germ-free and conventional mice.
Our integrative analysis revealed previously unknown epigenetic regulation of TSGs in host cells through inducing DNA methyltransferase by F. nucleatum and H. hathewayi, and established the latter as CRC-promoting bacteria. Video abstract.
Animal studies have suggested that Mn might be associated with some components of the metabolic syndrome (MetS). A few epidemiological studies have assessed dietary Mn intake and its association with ...the risk of the MetS and its components among Chinese adults. In this study, we assessed daily dietary Mn intake and its relationship with MetS risk among Chinese adults in Zhejiang Province using data from the 5th Chinese National Nutrition and Health Survey (2010–2012). A total of 2111 adults were included. Dietary Mn intake was assessed using 3-d 24-h dietary recalls; health-related data were obtained by questionnaire surveys, physical examinations and laboratory assessments. The mean intake of Mn was 6·07 (sd 2·94) mg/d for men (n 998) and 5·13 (sd 2·65) mg/d for women (n 1113). Rice (>42 %) was the main food source of Mn. The prevalence of the MetS was 28·0 % (590/2111). Higher Mn intake was associated with a decreased risk of the MetS in men (Q4 v. Q1 OR 0·62; 95 % CI 0·42, 0·92; P
trend=0·043) but an increased risk in women (Q4 v. Q1 OR 1·56; 95 % CI 1·02, 2·45; P
trend=0·078). In addition, Mn intake was inversely associated with abdominal obesity (P
trend=0·016) and hypertriacylglycerolaemia (P
trend=0·029) in men, but positively associated with low HDL-cholesterol in both men (P
trend=0·003) and women (P
trend<0·001). Our results suggest that higher Mn intakes may be protective against the MetS in men. The inverse association between Mn intake and the MetS in women might be due to the increased risk for low HDL-cholesterol.
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