Phosphorylated AKT (p-AKT), constitutive activation of AKT, is a potentially interesting prognostic marker and therapeutic target in non-small cell lung cancer (NSCLC). However, the available results of p-AKT expression in NSCLC are heterogeneous. Therefore, a meta-analysis of published researches investigating the prognostic relevance of p-AKT expression in patients with NSCLC was performed.
Materials and Methods
A literature search via PubMed, EMBASE and CNKI (China National Knowledge Infrastructure) databases was conducted. Data from eligible studies were extracted and included into meta-analysis using a random effects model.
A total of 1049 patients from nine studies were included in the meta-analysis. Nine studies investigated the relationship between p-AKT expression and overall survival using univariate analysis, and five of these undertook multivariate analysis. The pooled hazard ratio (HR) for overall survival was 1.49 (95% confidence interval (CI): 1.01-2.20) by univariate analysis and 1.02 (95% CI: 0.54-1.95) by multivariate analysis.
Our study shows that positive expression of p-AKT is associated with poor prognosis in patients with NSCLC. However, adequately designed prospective studies need to perform.
The scavenger receptor class B type 1 (SCARB1) gene is a key component in the reverse cholesterol transport pathway and thus plays an important role in lipid metabolism. Studies suggested that the SCARB1 gene may contribute to variation in plasma lipid levels at the fasting; however, the results have been inconsistent and it is unclear if SCARB1 may also influence lipid response to dietary and pharmacologic interventions. In this study, we examined genetic variation in the SCARB1 gene in participants of the Genetics of Lipid Lowering Drugs and Diet Network (GOLDN) study for associations with basal lipid levels, changes in lipid measures after dietary fat intake and fenofibrate treatment. We found that the exon 1 variant SCARB1_G2S was significantly associated with post-fenofibrate change for triglyceride (TG) (P = 0.004). Subjects bearing SCARB1_G2S minor allele A tend to have higher responsiveness to fenofibrate in lowering TG. In summary, our study suggested that the SCARB1 gene may serve as a useful marker that predicts variation in baseline lipid levels, postprandial lipid response as well as response to fenofibrate intervention.
Scavenger receptor class B type 1; lipid; genetics; fenofibrate; postprandial
Populations of African ancestry continue to account for a disproportionate burden of human immunodeficiency virus type 1 (HIV-1) epidemic in the US. We investigated the effects of human leukocyte antigen (HLA) class I markers in association with virologic and immunologic control of HIV-1 infection among 338 HIV-1 subtype B-infected African Americans in two cohorts: REACH (Reaching for Excellence in Adolescent Care and Health) and HERS (HIV Epidemiology Research Study). One-year treatment-free interval measurements of HIV-1 RNA viral loads and CD4+ T-cells were examined both separately and combined to represent three categories of HIV-1 disease control (76 “controllers,” 169 “intermediates,” and 93 “non-controllers”). Certain previously or newly implicated HLA class I alleles (A*32, A*36, A*74, B*14, B*1510, B*3501, B*45, B*53, B*57, Cw*04, Cw*08, Cw*12, and Cw*18) were associated with one or more of the endpoints in univariate analyses. After multivariable adjustments for other genetic and non-genetic risk factors of HIV-1 progression, the subset of alleles more strongly or consistently associated with HIV-1 disease control included A*32, A*74, B*14, B*45, B*53, B*57, and Cw*08. Carriage of infrequent HLA-B but not HLA-A alleles was associated with more favorable disease outcomes. Certain HLA class I associations with control of HIV-1 infection span the boundaries of race and viral subtype; while others appear confined within one or the other of those boundaries.
HLA class I; Allele frequency; HIV-1 control; African American
To determine the prevalence of male circumcision (MC) among men in the western region of Jamaica, and to identify factors associated with acceptability of MC for self, infants (<1 year) and older sons (1-17 years).
A cross-sectional, interviewer-administered questionnaire survey of 549 men aged 19-54 years was conducted in the western region of Jamaica. The survey included questions about the acceptance of MC for self, infants, and sons before and after an information session about the benefits of MC in preventing HIV/STI transmission. Logistic regression models were used to identify factors that were associated with acceptability of MC. Adjusted odds ratios (AOR) and 95% confidence intervals (CI) were calculated from the models.
Fourteen percent of the men reported that they were circumcised. In the multivariable model, which adjusted for age, education, religion and income, there were increased odds of accepting MC for infants/sons among uncircumcised men who accepted MC for self (AOR=8.1; 95% CI = 4.1-15.9), believed they would experience more pleasure during sex if circumcised (AOR=4.0; 95% CI = 2.0-8.2), and reported having no concerns regarding MC (AOR=3.0; 95% CI = 1.8-4.8). Similarly, uncircumcised men who reported no concerns about MC or who believed that they would experience more pleasure during sex if circumcised were more likely to accept MC for self.
Providing men with information about MC increased acceptance of MC for self, infants (<17 years) and sons (1-17 years). Since targeted education on the benefits of male circumcision for prevention of HIV/STI can be effective in increasing acceptability of MC, health professionals should be trained, and willing to discuss MC with men in healthcare facilities and in the community.
Rationale: DNA methylation is an important epigenetic mechanism, which often occurs in response to environmental stimuli and is crucial in regulating gene expression. It is likely that epigenetic alterations contribute to pathogenesis in idiopathic pulmonary fibrosis (IPF).
Objectives: To determine the DNA methylation changes in IPF and their effects on gene expression.
Methods: Total DNA methylation and DNA methyltransferase expression were compared in IPF and normal control lung tissues. IPF and normal tissues were subjected to comparative analysis of genome-wide DNA methylation and RNA expression using DNA hybridization to the Illumina HumanMethylation27 BeadChip and RNA hybridization to Illumina HumanHT-12 BeadChip. Functional analyses of differentially expressed and differentially methylated genes were done. Selected genes were validated at DNA, RNA, and protein levels.
Measurements and Main Results: DNA methylation status was altered in IPF. IPF samples demonstrated higher DNA methyltransferase expression without observed alterations in global DNA methylation. Genome-wide differences in DNA methylation status and RNA expression were demonstrated by array hybridization. Among the genes whose DNA methylation status and RNA expression were both significantly altered, 16 genes were hypermethylated in DNA associated with decreased mRNA expression or vice versa. We validated CLDN5, ZNF467, TP53INP1, and DDAH1 genes at the level of DNA methylation status, RNA, and protein-level expression.
Conclusions: Changes in DNA methylation correspond to altered mRNA expression of a number of genes, some with known and others with previously uncharacterized roles in IPF, suggesting that DNA methylation is important in the pathogenesis of IPF.
idiopathic pulmonary fibrosis; DNA methylation; gene expression; microarray
Detecting uncommon causal variants (minor allele frequency (MAF) < 5%) is difficult with commercial single-nucleotide polymorphism (SNP) arrays that are designed to capture common variants (MAF > 5%). Haplotypes can provide insights into underlying linkage disequilibrium (LD) structure and can tag uncommon variants that are not well tagged by common variants. In this work, we propose a wei-SIMc-matching test that inversely weights haplotype similarities with the estimated standard deviation of haplotype counts, to boost the power of similarity-based approaches for detecting uncommon causal variants. We then compare the power of the wei-SIMc-matching test with that of several popular haplotype-based tests, including four other similarity-based tests, a global score test for haplotypes (global), a test based on the maximum score statistic over all haplotypes (max), and two newly proposed haplotype-based tests for rare variant detection. With systematic simulations under a wide range of LD patterns, the results show that wei-SIMc-matching and global are the two most powerful tests. Among these two tests, wei-SIMc-matching has reliable asymptotic P values, whereas global needs permutations to obtain reliable P values when the frequencies of some haplotype categories are low or when the trait is skewed. Therefore, we recommend wei-SIMc-matching for detecting uncommon causal variants with surrounding common SNPs, in light of its power and computational feasibility.
Haplotype; Similarity; Linkage disequilibrium; Rare variants
Growing studies have revealed the association between polymorphisms in the Toll-like receptor 9 (TLR9) and susceptibility to cancer, however, the results remained inconsistent.
To assess the effect of three selected SNPs (rs352140, rs5743836 and rs187084) in TLR9 on cancer, we performed a meta-analysis based on 11 case-control studies, including a total of 6,585 cancer cases and 7,506 controls. Summary odds ratios (OR) and corresponding 95% confidence intervals (CIs) for polymorphisms in TLR9 and cancer risk were estimated. Our meta-analysis indicated that rs352140 was associated with an increased cancer risk, especially in Caucasian. However, no significantly increased cancer risk was detected to be associated with rs187084 and rs5743836 either the overall or subgroup estimation.
These meta-analysis results indicate that polymorphisms in TLR9 may play a role in cancer development.
Vascular calcification is a hallmark of atherosclerosis, a major cause of morbidity and mortality in the United States. We have previously reported that the osteogenic transcription factor Runx2 is an essential and sufficient regulator of calcification of vascular smooth muscle cells (VSMC) in vitro.
To determine the contribution of osteogenic differentiation of VSMC to the pathogenesis of vascular calcification and the function of VSMC-derived Runx2 in regulating calcification in vivo.
Methods and Results
SMC-specific Runx2 deficient mice, generated by breeding SM22α-Cre mice with the Runx2 exon 8 floxed mice, exhibited normal aortic gross anatomy and expression levels of SMC-specific marker genes. Runx2 deficiency did not affect basal SMC markers, but inhibited oxidative stress-reduced expression of SMC markers. High-fat diet-induced vascular calcification in vivo was markedly inhibited in the Runx2-deficient mice compared with their control littermates. Runx2 deficiency inhibited the expression of receptor activator of nuclear factor κB ligand, which was accompanied by decreased macrophage infiltration and formation of osteoclast-like cells in the calcified lesions. Co-culture of VSMC with bone marrow-derived macrophages demonstrated that the Runx2 deficient VSMC failed to promote differentiation of macrophages into osteoclast-like cells.
These data have determined the importance of osteogenic differentiation of VSMC in the pathogenesis of vascular calcification in mice and defined the functional role of SMC-derived Runx2 in regulating vascular calcification and promoting infiltration of macrophages into the calcified lesion to form osteoclast-like cells. Our studies suggest that the development of vascular calcification is coupled with the formation of osteoclast-like cells, paralleling the bone remodeling process.
vascular smooth muscle cells; osteogenic differentiation; Runx2; vascular calcification; vascular osteoclasts; smooth muscle cells; vascular disease
Background Drinking alcohol has a long tradition in Chinese culture. However, data on the prevalence and patterns of alcohol consumption in China, and its main correlates, are limited.
Methods During 2004–08 the China Kadoorie Biobank recruited 512 891 men and women aged 30–79 years from 10 urban and rural areas of China. Detailed information on alcohol consumption was collected using a standardized questionnaire, and related to socio-demographic, physical and behavioural characteristics in men and women separately.
Results Overall, 76% of men and 36% of women reported drinking some alcohol during the past 12 months, with 33% of men and 2% of women drinking at least weekly; the prevalence of weekly drinking in men varied from 7% to 51% across the 10 study areas. Mean consumption was 286 g/week and was higher in those with less education. Most weekly drinkers habitually drank spirits, although this varied by area, and beer consumption was highest among younger drinkers; 37% of male weekly drinkers (12% of all men) reported weekly heavy drinking episodes, with the prevalence highest in younger men. Drinking alcohol was positively correlated with regular smoking, blood pressure and heart rate. Among male weekly drinkers, each 20 g/day alcohol consumed was associated with 2 mmHg higher systolic blood pressure. Potential indicators of problem drinking were reported by 24% of male weekly drinkers.
Conclusion The prevalence and patterns of drinking in China differ greatly by age, sex and geographical region. Alcohol consumption is associated with a number of unfavourable health behaviours and characteristics.
Alcohol; drinking; cohort study; descriptive analysis; China
Adaptation to a sustained stimulus is an important phenomenon in psychophysical experiments. When studying the response to an experimental task, the investigator has to account for the change in perceived stimulus intensity with repeated stimulus application and, if the stimulus is sustained, for the change in intensity during the presentation. An example of a sustained stimulus is the cold pressor task (CPT). The task has been used both as an experimental pain task and to study cardiovascular physiology. In functional imaging research, the CPT has been used to evaluate cognitive processing of a noxious stimulus. Investigators typically model the stimulus in a block design as a categorical (on-off) stimulus and do not account for a temporal change in stimulus perception. If the perceived stimulus changes over time, the results may be misleading.
Therefore, we characterized the time course of cold pain in human volunteers and developed a model of the temporal characteristics of perceived cold pain. Fifteen healthy participants underwent cold pain testing by immersing their right foot into a container filled with ice water (2 °C) for 30 seconds alternating with a 30 seconds immersion into a container filled with tepid water 32°C (control). Participants rated the pain intensity using an electronic slide algometer.
Using a mixed general linear model (effectively a polynomial regression model), we determined that pain ratings follow a crescendo-decrescendo pattern that can be described well using a quadratic model. We conclude that the time course of quantitative perception differs fundamentally from the time course of stimulus presentation. This may be important when looking for the physiological correlates of perception as opposed to the presence of a stimulus per se.
Pain; Rating; Cold; Sensory Adaptation; Imaging
Testing multiple markers simultaneously not only can capture the linkage disequilibrium patterns but also can decrease the number of tests and thus alleviate the multiple-testing penalty. If a gene is associated with a phenotype, subjects with similar genotypes in this gene should also have similar phenotypes. Based on this concept, we have developed a general framework that is applicable to continuous traits. Two similarity-based tests (namely, SIMc and SIMp tests) were derived as special cases of the general framework. In our simulation study, we compared the power of the two tests with that of the single-marker analysis, a standard haplotype regression, and a popular and powerful kernel machine regression. Our SIMc test outperforms other tests when the average r-square (a measure of linkage disequilibrium) between the causal variant and the surrounding markers is larger than 0.3 or when the causal allele is common (say, frequency = 0.3). Our SIMp test outperforms other tests when the causal variant was introduced at common haplotypes (the maximum frequency of risk haplotypes > 0.4). We also applied our two tests to an adiposity data set to show their utility.
Haplotype; Similarity; Genomic distance; Linkage disequilibrium; Multi-marker test; Body-mass index; CPE gene
Motivation: Low coverage sequencing provides an economic strategy for whole genome sequencing. When sequencing a set of individuals, genotype calling can be challenging due to low sequencing coverage. Linkage disequilibrium (LD) based refinement of genotyping calling is essential to improve the accuracy. Current LD-based methods use read counts or genotype likelihoods at individual potential polymorphic sites (PPSs). Reads that span multiple PPSs (jumping reads) can provide additional haplotype information overlooked by current methods.
Results: In this article, we introduce a new Hidden Markov Model (HMM)-based method that can take into account jumping reads information across adjacent PPSs and implement it in the HapSeq program. Our method extends the HMM in Thunder and explicitly models jumping reads information as emission probabilities conditional on the states of adjacent PPSs. Our simulation results show that, compared to Thunder, HapSeq reduces the genotyping error rate by 30%, from 0.86% to 0.60%. The results from the 1000 Genomes Project show that HapSeq reduces the genotyping error rate by 12 and 9%, from 2.24% and 2.76% to 1.97% and 2.50% for individuals with European and African ancestry, respectively. We expect our program can improve genotyping qualities of the large number of ongoing and planned whole genome sequencing projects.
Availability: The software package HapSeq and its manual can be found and downloaded at www.ssg.uab.edu/hapseq/.
Supplementary data are available at Bioinformatics online.
The marriage of energy transfer with electrochemiluminescence has produced a new technology named electrochemiluminescence energy transfer (ECL-ET), which can realize effective and sensitive detection of biomolecules. To obtain optimal ECL-ET efficiency, perfect energy overlapped donor/acceptor pair is of great importance. Herein, we present a sensitive ECL-ET based immunosensor for the detection of tumor markers, using energy tunable CdSeTe/CdS/ZnS double shell quantum dots (QDs) and gold nanorods (GNRs) as the donor and acceptor, respectively. Firstly a facile microwave-assisted strategy for the synthesis of green- to near-infrared-emitting CdSeTe/CdS/ZnS QDs with time- and component-tunable photoluminescence was proposed. And, on the basis of the adjustable optical properties of both CdSeTe/CdS/ZnS QDs and GNRs, excellent overlap between donor emission and acceptor absorption can be obtained to ensure effective ECL-ET quenching, thus improving the sensing sensitivity. This method represents a novel approach for versatile detection of biomolecules at low concentrations.
Uterine leiomyomas (or fibroids) are the most common tumors in women of reproductive age. Early studies of two familial cancer syndromes, the multiple cutaneous and uterine leiomyomatosis (MCUL1), and the hereditary leiomyomatosis and renal cell cancer (HLRCC), implicated FH, a gene on chromosome 1q43 encoding the tricarboxylic acid cycle fumarate hydratase enzyme. The role of this metabolic housekeeping gene in tumorigenesis is still a matter of debate and pseudo-hypoxia has been suggested as a pathological mechanism. Inactivating FH mutations have rarely been observed in the nonsyndromic and common form of fibroids; however, loss of heterozygosity across FH appeared as a significant event in the pathogenesis of a subset of these tumors. To assess the role of FH and the linked genes in nonsyndromic uterine fibroids, we explored a two-megabase interval spanning FH in the NIEHS Uterine fibroid study, a cross-sectional study of fibroids in 1152 premenopausal women. Association mapping with a dense set of single nucleotide polymorphisms revealed several peaks of association (p = 10−2–8.10−5) with the risk and/or growth of fibroids. In particular, genes encoding factors suspected (cytosolic FH) or known (EXO1 - exonuclease 1) to be involved in DNA mismatch repair emerged as candidate susceptibility genes whereas those acting in the autophagy/apoptosis (MAP1LC3C - microtubule-associated protein) or signal transduction (RGS7 - Regulator of G-protein and PLD5– Phospoholipase D) appeared to affect tumor growth. Furthermore, body mass index, a suspected confounder altered significantly but unpredictably the association with the candidate genes in the African and European American populations, suggesting the presence of a major obesity gene in the studied region. With the high potential for occult tumors in common conditions such as fibroids, validation of our data in family-based studies is needed.
Within heterogeneous tumors, subpopulations often labeled cancer stem cells (CSCs) have been identified that have enhanced tumorigenicity and chemoresistance in ex vivo models. However, whether these populations are more capable of surviving chemotherapy in de novo tumors is unknown.
We examined 45 matched primary/recurrent tumor pairs of high grade ovarian adenocarcinomas for expression of CSC markers ALDH1A1, CD44 and CD133 using immunohistochemistry. Tumors collected immediately after completion of primary therapy were then laser-capture microdissected and subjected to a quantitative PCR array examining stem cell biology pathways (Hedgehog, Notch, TGF-β and Wnt). Select genes of interest were validated as important targets using siRNA-mediated downregulation.
Primary samples were composed of low densities of ALDH1A1, CD44 and CD133. Tumors collected immediately after primary therapy were more densely composed of each marker, while samples collected at first recurrence, before initiating secondary therapy, were composed of similar percentages of each marker as their primary tumor. In tumors collected from recurrent platinum-resistant patients, only CD133 was significantly increased. Of stem cell pathway members examined, 14% were significantly overexpressed in recurrent compared to matched primary tumors. Knockdown of genes of interest, including endoglin/CD105 and the hedgehog mediators Gli1 and Gli2, led to decreased ovarian cancer cell viability, with Gli2 demonstrating a novel contribution to cisplatin resistance.
These data indicate that ovarian tumors are enriched with CSCs and stem cell pathway mediators, especially at the completion of primary therapy. This suggests that stem cell subpopulations contribute to tumor chemoresistance and ultimately recurrent disease.
CD133; CD44; aldehyde dehydrogenase; ALDH1A1; endoglin; CD105; gli1; gli2; cancer stem cell; ovarian cancer
Previous observational studies have reported associations between prostate cancer and alpha-linolenic acid (ALA). However, few investigations have been able to study this relationship prospectively and in well-controlled settings. Moreover, no studies have determined whether single nucleotide polymorphisms (SNPs) that influence ALA metabolism are associated with this common cancer. The purpose of this study was to explore associations between prostatic levels of ALA, SNPs and prostate cancer-specific biomarkers in samples collected from a previous randomized clinical trial conducted using a presurgical model and which tested the effects of flaxseed supplementation, a rich source of ALA, prior to prostatectomy (n = 134). Serum prostate-specific antigen (PSA) was determined and immunohistochemistry was used to assess tumor proliferation rate (Ki67). Prostatic ALA was determined with gas chromatography. Seven previously identified SNPs associated with delta-6 desaturase activity (rs99780, rs174537, rs174545, rs174572, rs498793, rs3834458 and rs968567) were tested for associations with prostatic ALA, PSA and Ki67. Despite consuming seven times more ALA per day, men in the flaxseed arm had similar amounts of prostatic ALA relative to men not consuming flaxseed. In unadjusted analysis, there were significant positive associations between prostatic ALA and PSA (ρ = 0.191, p = 0.028) and Ki67 (ρ = 0.186, p = 0.037). After adjusting for covariates (flaxseed, age, race, BMI and statin-use) the association between ALA and PSA remained (p = 0.004) but was slightly attenuated for Ki67 (p = 0.051). We did not observe associations between any of the SNPs studied and prostatic ALA; however, in models for PSA there was a significant interaction between rs498793 and ALA and for Ki67 there were significant interactions with ALA and rs99780 and rs174545. Independent and inverse associations were observed between rs174572 and Ki67. This study provides evidence that prostatic ALA, independent of the amount of ALA consumed, is positively associated with biomarkers of aggressive prostate cancer and that genetic variation may modify this relationship.
RNA interference via exogenous small interference RNAs (siRNA) is a powerful tool in gene function study and disease treatment. Designing efficient and specific siRNA on target gene remains the key issue in RNAi. Although various in silico models have been proposed for rational siRNA design, most of them focus on the efficiencies of selected siRNAs, while limited effort has been made to improve their specificities targeted on specific mRNAs, which is related to reducing off-target effects (OTEs) in RNAi. In our study, we propose for the first time that the enhancement of target specificity of siRNA design can be achieved computationally by domain transfer in heterogeneous data sources from different siRNA targets. A transfer learning based method i.e., heterogeneous regression (HEGS) is presented for target-specific siRNA efficacy modeling and feature selection. Based on the model, (1) the target regression model can be built by extracting information from related data in other targets/experiments, thus increasing the target specificity in siRNA design with the help of information from siRNAs binding to other homologous genes, and (2) the potential features correlated to the current siRNA design can be identified even when there is lack of experimental validated siRNA affinity data on this target. In summary, our findings present useful instructions for a better target-specific siRNA design, with potential applications in genome-wide high-throughput screening of effective siRNA, and will provide further insights on the mechanism of RNAi.
Studies have linked prostate cancer risk with insulin resistance and obesity. Circulating levels of adiponectin, a protein involved in insulin resistance and obesity, have been associated with prostate cancer risk. We studied the association of prostate cancer risk with haplotype tagging single nucleotide polymorphisms (SNPs) of the adiponectin (ADIPOQ) and adiponectin receptor 1 (ADIPOR1) chosen based on their functional relevance or association with other types of cancer.
DNA samples from 465 cases and 441 healthy volunteers from New York City were genotyped for ADIPOQ rs266729, rs822395, rs822396, rs1501299 and rs2241766 SNPs and ADIPOR1 rs12733285, rs1342387, rs7539542, rs2232853 and rs10920531 SNPs. We performed both single and multiple SNP analyses.
We found that rs12733285, rs7539452, rs266729, rs822395, rs822396 and rs1501299 were significantly associated with prostate cancer risk. Haplotype analysis confirmed these results and identified five ADIPOQ 4-SNP haplotypes and one ADIPOR1 2-SNP haplotype tightly associated with prostate cancer risk. Importantly two ADIPOQ SNPs, rs266729 and rs1501299 have been previously associated with colon and breast cancer risk, respectively, in the same direction as in this study.
These findings suggest that variants of the adiponectin pathway may be associated with susceptibility to various forms of common cancers and warrant validation studies.
Genetic association studies based on haplotypes are powerful in the discovery and characterization of the genetic basis of complex human diseases. However, statistical methods for detecting haplotype-haplotype and haplotype-environment interactions have not yet been fully developed owing to the difficulties encountered: large numbers of potential haplotypes and unknown haplotype pairs. Furthermore, methods for detecting the association between rare haplotypes and disease have not kept pace with their counterpart of common haplotypes.
We herein propose an efficient and robust method to tackle these problems based on a Bayesian hierarchical generalized linear model. Our model simultaneously fits environmental effects, main effects of numerous common and rare haplotypes, and haplotype-haplotype and haplotype-environment interactions. The key to the approach is the use of a continuous prior distribution on coefficients that favors sparseness in the fitted model and facilitates computation. We develop a fast expectation-maximization algorithm to fit models by estimating posterior modes of coefficients. We incorporate our algorithm into the iteratively weighted least squares for classical generalized linear models as implemented in the R package glm. We evaluate the proposed method and compare its performance to existing methods on extensive simulated data.
The results show that the proposed method performs well under all situations and is more powerful than existing approaches.
Bayesian methods; Generalized linear models; Genetic associations; Hierarchical models; Haplotype; Haplotype-haplotype interactions; Haplotype-environment interactions
Vitamin D deficiency has been associated with markers for allergy and asthma severity in children with asthma. However, its association with Chinese adult asthmatics has not been studied.
To examine whether vitamin D status is associated with lung function and total serum IgE in Chinese adults with newly diagnosed asthma.
We conducted a cross-sectional study including 435 Chinese patients aged >18 years with newly diagnosed asthma. Vitamin D status was assessed by measuring serum 25 hydroxyvitamin D (25OHD) concentrations. The primary outcomes included airflow limitation, as measured by the forced expiratory volume in 1 s (FEV1), FEV1 % predicted, and FEV1/forced vital capacity (FVC), and serum total IgE concentration.
Vitamin D deficiency was prevalent in Chinese adults with asthma, with 88.9% of the subjects having 25OHD <50 nmol/l. Serum 25OHD concentration was positively correlated with FEV1 % predicted (p = 0.02, r = 0.12). After adjusting for age, sex, body mass index, smoking, month of blood collection, and symptom duration, we found significant positive associations between 25OHD concentrations and FEV1 (in liters), FEV1 % predicted, and FEV1/FVC (p for trend < 0.05 for all). The adjusted odds ratios for the highest versus the lowest 25OHD quartile were 0.50 (0.26–0.96) for FEV1 <75% predicted and 0.44 (0.20–0.95) for FEV1/FVC% <0.75. There was no significant association between 25OHD concentrations and total IgE.
Vitamin D deficiency was highly prevalent in Chinese asthma patients, and vitamin D status was associated with lung function.
Vitamin D; Asthma; Lung function; FEV1; IgE
Host genetic variation, particularly within the human leukocyte antigen (HLA) loci, reportedly mediates heterogeneity in immune response to certain vaccines; however, no large study of genetic determinants of anthrax vaccine response has been described. We searched for associations between the IgG antibody to protective antigen (AbPA) response to Anthrax Vaccine Adsorbed (AVA) in humans and polymorphisms at HLA class I (HLA-A, -B, and -C) and class II (HLA-DRB1, -DQA1, -DQB1, -DPB1) loci. The study included 794 European-Americans and 200 African-Americans participating in a 43-month, double-blind, placebo-controlled, clinical trial of AVA (clinicaltrials.gov identifier NCT00119067). Among European-Americans, genes from tightly linked HLA-DRB1-DQA1-DQB1 haplotypes displayed significant overall associations with longitudinal variation in AbPA levels at 4, 8, 26, and 30 weeks from baseline in response to vaccination with 3 or 4 doses of AVA (global p=6.53×10−4). In particular, carriage of the DRB1-DQA1-DQB1 haplotypes *1501-*0102-*0602 (p=1.17×10−5), *0101-*0101-*0501 (p=0.009), and *0102-*0101-*0501 (p=0.006) was associated with significantlylower AbPA levels. In carriers of two copies of these haplotypes, lower AbPA levels persisted following subsequent vaccinations. No significant associations were observed amongst African-Americans or for any HLA class I allele/haplotype. Further studies will be required to replicate these findings and to explore the role of host genetic variation outside of the HLA region.
Anthrax vaccines; Bacillus anthracis; Bacterial vaccines; Vaccination; HLA Antigens
Motivation: Next-generation sequencing technologies are being rapidly applied to quantifying transcripts (RNA-seq). However, due to the unique properties of the RNA-seq data, the differential expression of longer transcripts is more likely to be identified than that of shorter transcripts with the same effect size. This bias complicates the downstream gene set analysis (GSA) because the methods for GSA previously developed for microarray data are based on the assumption that genes with same effect size have equal probability (power) to be identified as significantly differentially expressed. Since transcript length is not related to gene expression, adjusting for such length dependency in GSA becomes necessary.
Results: In this article, we proposed two approaches for transcript-length adjustment for analyses based on Poisson models: (i) At individual gene level, we adjusted each gene's test statistic using the square root of transcript length followed by testing for gene set using the Wilcoxon rank-sum test. (ii) At gene set level, we adjusted the null distribution for the Fisher's exact test by weighting the identification probability of each gene using the square root of its transcript length. We evaluated these two approaches using simulations and a real dataset, and showed that these methods can effectively reduce the transcript-length biases. The top-ranked GO terms obtained from the proposed adjustments show more overlaps with the microarray results.
Availability: R scripts are at http://www.soph.uab.edu/Statgenetics/People/XCui/r-codes/.
Supplementary information:Supplementary data are available at Bioinformatics online.
Imputation offers a promising way to infer the missing and/or untyped genotypes in genetic studies. In practice, however, many factors may affect the quality of imputation. In this study, we evaluated the influence of untyped rate, sizes of the study sample and the reference sample, window size, and reference choice (for admixed population), as the factors affecting the quality of imputation. The results show that in order to obtain good imputation quality, it is necessary to have an untyped rate less than 50%, a reference sample size greater than 50, and a window size of greater than 500 SNPs (roughly 1 MB in base pairs). Compared with the whole-region imputation, piecewise imputation with large-enough window sizes provides improved efficacy. For an admixed study sample, if only an external reference panel is used, it should include samples from the ancestral populations that represent the admixed population under investigation. Internal references are strongly recommended. When internal references are limited, however, augmentation by external references should be used carefully. More specifically, augmentation with samples from the major source populations of the admixture can lower the quality of imputation; augmentation with seemingly genetically unrelated cohorts may improve the quality of imputation.
genotype imputation; genetic study; admixed population; untyped rate; window size; reference
Interleukin-6 (IL6) is a pleiotropic inflammatory cytokine, which is implicated in the development and progression of several types of cancer. The -174G/C polymorphism of the IL6 gene controls serum levels of IL6 and may be associated with cancer risk, but the results from the published studies on the association between this polymorphism and cancer risk are conflicting. A comprehensive meta-analysis was conducted to assess the association of IL6 -174G/C with cancer risk. Studies were identified by searches of MEDLINE and HuGE Published Literature databases, with no restrictions. An eligible 83 articles involving 44,735 cancer patients and 60,747 controls were included. Combined odds ratios (ORs) and 95% confidence intervals (CIs) were used to assess the strength of the association between the IL6 -174 G/C polymorphism and cancer risk. Potential sources of heterogeneity were explored by meta-regression and sensitivity analysis. Overall, the IL6 -174G/C polymorphism was not significantly associated with cancer risk. However, cancer risk was increased for individuals with the CC genotype compared to those carrying the GG genotype in African populations (OR=1.83, 95% CI 1.26–2.67, P=0.002), but not in Caucasian populations (OR=1.00, 95% CI 0.92–1.08, P=0.938). The present meta-analysis provides the first evidence of the ethnic-specific association of the IL6 -174G/C polymorphism with cancer risk. Further investigations with a large number of cases and controls are required to confirm the associations between this polymorphism and cancer in Africans.
interleukin-6; polymorphism; cancer risk; meta-analysis