Estimation of Odds Ratios from Matched Case-Control Studies with Incomplete Data

Matched case-control studies often include pairs with incomplete exposure information. This work presents and compares two estimators for the odds ratio that can be used when the exposures of some of the cases and controls are missing. A simulation study shows that the estimator that uses the marginal exposure frequencies is usually more efficient than the estimator based on discordant pairs.     

Association of Genetic Markers with CSF Oligoclonal Bands in Multiple Sclerosis Patients

Objective

to explore the association between genetic markers and Oligoclonal Bands (OCB) in the Cerebro Spinal Fluid (CSF) of Italian Multiple Sclerosis patients.

Methods

We genotyped 1115 Italian patients for HLA-DRB1*15 and HLA-A*02. In a subset of 925 patients we tested association with 52 non-HLA SNPs associated with MS susceptibility and we calculated a weighted Genetic Risk Score. Finally, we performed a Genome Wide Association Study (GWAS) with OCB status on a subset of 562 patients. The best associated SNPs of the Italian GWAS were replicated in silico in Scandinavian and Belgian populations, and meta-analyzed.

Results

HLA-DRB1*15 is associated with OCB+: p = 0.03, Odds Ratio (OR) = 1.6, 95% Confidence Limits (CL) = 1.1–2.4. None of the 52 non-HLA MS susceptibility loci was associated with OCB, except one SNP (rs2546890) near IL12B gene (OR: 1.45; 1.09–1.92). The weighted Genetic Risk Score mean was significantly (p = 0.0008) higher in OCB+ (7.668) than in OCB− (7.412) patients. After meta-analysis on the three datasets (Italian, Scandinavian and Belgian) for the best associated signals resulted from the Italian GWAS, the strongest signal was a SNP (rs9320598) on chromosome 6q (p = 9.4×10⁻⁷) outside the HLA region (65 Mb).

Discussion

genetic factors predispose to the development of OCB.     

AFLP技术运用于小麦种子超干燥保存遗传完整性的初探

小麦种子被干燥和超干燥至9．0％,8．0％,7．0％,6．0％,5．0％,4．0％后,密封包装于江西南昌常温保存。保存五年后,发芽结果表明,小麦种子于亚热带地区常温保存,必须先经过干燥密封包装。种子最适含水量介于7．0％～9．0％之间。不同品种阃有差异。种子经发芽生长至三叶一心期,取幼苗(茎与叶),用AFLP分子技术对其单株及20株的混合样品进行遗传稳定性鉴定。结果表明,每对引物的AFLP图谱谱带丰富,不同引物的清晰带有26至52条,不同品种间差异带在3至6条。同一品种不同的含水量之间AFLP图谱谱带整齐划一,未见明显差异。同一含水量不同混合样品或单株样品间也未见差异,表明小麦种子经干燥、超干燥后于亚热带地区(江西南昌)常温保存五年后。在AFLP分子水平上未见遗传变异。同时本研究也为贮藏种子的遗传完整性研究提供了一个新的思路。     

May the Force Be with You: Metabolism of Arginine and Pyrimidines

<正>"Why do arginine and pyrimidines have to be considered together?"This was the question I asked when I was invited by Barbara Zimmermann to attend the 23rd International Conference on Arginine and Pyrimidines(ICAP)three years ago.The meeting was held in the summer of 2012 at Bogota,Columbia,known as the"the Athens of South America".I am not alone in wanting to know more about the relationship between arginine and pyrimidines.Last summer,when I was organising the next ICAP meeting at Oxford(Aughey et al.,2014),one of my colleagues asked me,"Why such a weird name for a conference?"I am not sure if I had given her a satisfying answer and I was enthused to find out what the reasons may be.     

名贵易混淆植物性药材的DNA分子遗传标记鉴定研究进展

名贵易混淆药材的伪品和掺假品较为常见,采用常规的方法较难鉴别.DNA分子遗传标记鉴定具有取样量小、减少贵重样品损消耗、鉴定结果准确、灵敏性高等特点.本文以人参、西红花、天麻、当归等药材为代表,对近年来DNA分子遗传标记技术在名贵易混淆植物性药材鉴定中的研究情况予以综述.     

Why Even More Clinical Research Studies May Be False: Effect of Asymmetrical Handling of Clinically Unexpected Values

Background

In medical practice, clinically unexpected measurements might be quite properly handled by the remeasurement, removal, or reclassification of patients. If these habits are not prevented during clinical research, how much of each is needed to sway an entire study?

Methods and Results

Believing there is a difference between groups, a well-intentioned clinician researcher addresses unexpected values. We tested how much removal, remeasurement, or reclassification of patients would be needed in most cases to turn an otherwise-neutral study positive. Remeasurement of 19 patients out of 200 per group was required to make most studies positive. Removal was more powerful: just 9 out of 200 was enough. Reclassification was most powerful, with 5 out of 200 enough. The larger the study, the smaller the proportion of patients needing to be manipulated to make the study positive: the percentages needed to be remeasured, removed, or reclassified fell from 45%, 20%, and 10% respectively for a 20 patient-per-group study, to 4%, 2%, and 1% for an 800 patient-per-group study. Dot-plots, but not bar-charts, make the perhaps-inadvertent manipulations visible. Detection is possible using statistical methods such as the Tadpole test.

Conclusions

Behaviours necessary for clinical practice are destructive to clinical research. Even small amounts of selective remeasurement, removal, or reclassification can produce false positive results. Size matters: larger studies are proportionately more vulnerable. If observational studies permit selective unblinded enrolment, malleable classification, or selective remeasurement, then results are not credible. Clinical research is very vulnerable to “remeasurement, removal, and reclassification”, the 3 evil R''s.     

Association of Hemostatic Markers with Atrial Fibrillation: A Meta-Analysis and Meta-Regression

Background

There is growing evidence that indicates the presence of a prothrombotic state in atrial fibrillation (AF). However, the role of hemostatic markers in AF remains inconclusive.

Methods

We conducted a meta-analysis of observational studies to evaluate the association between hemostatic markers and AF. A meta-regression was performed to explore potential sources of heterogeneity.

Results

A total of 59 studies met our inclusion criteria for the meta-analysis. For platelet activation, increased circulating platelet factor-4, β-thromboglobulin (BTG) and P-selectin were significantly higher in AF cases compared with controls (standardized mean difference [SMD][95% confidence interval (CI)]: 1.72[0.96–2.49], 1.61[1.03–2.19] and 0.50[0.23–0.77], respectively). For coagulation activation, increased levels of plasma D-dimer, fibrinogen, thrombin-antithrombin, prothrombin fragment 1+2, and antithrombin-III were significantly associated with AF (SMD[95% CI]: 1.82[1.38–2.26], 0.72[0.55–0.89], 0.42[0.13–0.72], 1.00 [0.00–1.99] and 1.38[0.16–2.60], respectively). For fibrinolytic function, tissue-type plasminogen activator and plasminogen activator inhibitor-1 were significantly increased in AF cases compared with controls (SMD[95% CI]: 0.86[0.04–1.67] and 0.87[0.28–1.47], respectively) but the associations became nonsignificant after performing subgroup analysis by anticoagulants treatment status. For endothelial function, increased von Willebrand factor was significantly associated with AF (SMD, 0.79; 95% CI, 0.60–0.99); however, no association was observed for soluble thrombomodulin (SMD, 0.60; 95% CI, -0.13–1.33).

Conclusions

Increased circulating hemostatic factors (PF-4, BTG, P-selectin, D-dimer, fibrinogen, TAT, F1+2, AT- III, and vWf) are significantly associated with AF. Future research is necessary to elucidate the precise mechanism of the prothrombotic state and how hemostatic markers promote thromboembolism in AF.     

Genetic Polymorphisms of the CASP8 Gene Promoter May Not Be Associated with Colorectal Cancer in Han Chinese from Southwest China

Purpose

Caspase 8 (CASP8) plays a critical role in the apoptotic pathway and aberrant regulation of this pathway causes many diseases including cancers. Genetic variants rs3834129 (CTTACT/−) and rs3769821 (T/C) in the promoter region of the CASP8 gene were documented to be associated with multiple solid cancers and non-Hodgkin’s lymphoma (NHL), respectively, despite of some controversies. We aimed to discern potential association of these two variants and rs113686495 (CTGTCATT/−), as well as CASP8 mRNA and protein expression levels with colorectal cancer (CRC) in Han Chinese.

Methods

We genotyped CASP8 genetic variants in 305 CRC patients and 342 healthy individuals from Kunming, Southwest China. Expression levels of CASP8 mRNA and protein were quantified in paired cancerous and paracancerous normal tissues by using real-time quantitative PCR and western blot, respectively. We compared the frequencies of alleles, genotypes, and haplotypes between the cases and controls. Correlation of CASP8 mRNA and protein expression levels in paired cancerous and paracancerous normal tissues from patients with different genotypes and clinical expression were also evaluated.

Results

There was no association of the CASP8 genetic variants with CRC in our case-control study. The CASP8 gene mRNA expression levels in cancerous and paracancerous normal tissues were similar and there was no significant difference between subjects with different genotypes and clinical features. However, we found that CASP8 protein level was significantly lower in cancerous tissues than in paired paracancerous normal tissues.

Conclusions

Our results suggest that the three CASP8 genetic variants may not be associated with CRC risk in Han Chinese from southwest China. Aberrant CASP8 protein expression may play a role in the pathogenesis of CRC.     

A Genetic Association Study of Serum Acute-Phase C-Reactive Protein Levels in Rheumatoid Arthritis: Implications for Clinical Interpretation

Background

The acute-phase increase in serum C-reactive protein (CRP) is used to diagnose and monitor infectious and inflammatory diseases. Little is known about the influence of genetics on acute-phase CRP, particularly in patients with chronic inflammation.

Methods and Findings

We studied two independent sets of patients with chronic inflammation due to rheumatoid arthritis (total 695 patients). A tagSNP approach captured common variation at the CRP locus and the relationship between genotype and serum CRP was explored by linear modelling. Erythrocyte sedimentation rate (ESR) was incorporated as an independent marker of inflammation to adjust for the varying levels of inflammatory disease activity between patients. Common genetic variants at the CRP locus were associated with acute-phase serum CRP (for the most associated haplotype: p = 0.002, p<0.0005, p<0.0005 in patient sets 1, 2, and the combined sets, respectively), translating into an approximately 3.5-fold change in expected serum CRP concentrations between carriers of two common CRP haplotypes. For example, when ESR = 50 mm/h the expected geometric mean CRP (95% confidence interval) concentration was 43.1 mg/l (32.1–50.0) for haplotype 1 and 14.2 mg/l (9.5–23.2) for haplotype 4.

Conclusions

Our findings raise questions about the interpretation of acute-phase serum CRP. In particular, failure to take into account the potential for genetic effects may result in the inappropriate reassurance or suboptimal treatment of patients simply because they carry low-CRP–associated genetic variants. CRP is increasingly being incorporated into clinical algorithms to compare disease activity between patients and to predict future clinical events: our findings impact on the use of these algorithms. For example, where access to effective, but expensive, biological therapies in rheumatoid arthritis is rationed on the basis of a DAS28-CRP clinical activity score, then two patients with identical underlying disease severity could be given, or denied, treatment on the basis of CRP genotype alone. The accuracy and utility of these algorithms might be improved by using a genetically adjusted CRP measurement. Please see later in the article for the Editors'' Summary     

Association of Genetic Markers in the BCL-2 Family of Apoptosis-Related Genes with Endometrial Cancer Risk in a Chinese Population

BackgroundIn vitro studies have demonstrated the role of the BCL-2 family of genes in endometrial carcinogenesis. The role of genetic variants in BCL-2 genes and their interactions with non-genetic factors in the development of endometrial cancer has not been investigated in epidemiological studies.ResultsSignificant associations with endometrial cancer risk were found for 9 SNPs in the BCL2 gene (P trend<0.05 for all). For SNPs rs17759659 and rs7243091 (minor allele for both: G), the associations were independent. The odds ratio was 1.27 (95% CI: 1.04–1.53) for women with AG genotype for the SNP rs17759659 and 1.82 (95% CI: 1.21–2.73) for women with the GG genotype for the SNP rs7243091. No interaction between these two SNPs and established non-genetic risk factors of endometrial cancer was noticed.ConclusionGenetic polymorphisms in the BCL2 gene may be associated with the risk of endometrial cancer in Chinese women.     

Common Genetic Variation Near the Phospholamban Gene Is Associated with Cardiac Repolarisation: Meta-Analysis of Three Genome-Wide Association Studies

To identify loci affecting the electrocardiographic QT interval, a measure of cardiac repolarisation associated with risk of ventricular arrhythmias and sudden cardiac death, we conducted a meta-analysis of three genome-wide association studies (GWAS) including 3,558 subjects from the TwinsUK and BRIGHT cohorts in the UK and the DCCT/EDIC cohort from North America. Five loci were significantly associated with QT interval at P<1×10⁻⁶. To validate these findings we performed an in silico comparison with data from two QT consortia: QTSCD (n = 15,842) and QTGEN (n = 13,685). Analysis confirmed the association between common variants near NOS1AP (P = 1.4×10⁻⁸³) and the phospholamban (PLN) gene (P = 1.9×10⁻²⁹). The most associated SNP near NOS1AP (rs12143842) explains 0.82% variance; the SNP near PLN (rs11153730) explains 0.74% variance of QT interval duration. We found no evidence for interaction between these two SNPs (P = 0.99). PLN is a key regulator of cardiac diastolic function and is involved in regulating intracellular calcium cycling, it has only recently been identified as a susceptibility locus for QT interval. These data offer further mechanistic insights into genetic influence on the QT interval which may predispose to life threatening arrhythmias and sudden cardiac death.     

Novel Genetic Analysis for Case-Control Genome-Wide Association Studies: Quantification of Power and Genomic Prediction Accuracy

Genome-wide association studies (GWAS) are routinely conducted for both quantitative and binary (disease) traits. We present two analytical tools for use in the experimental design of GWAS. Firstly, we present power calculations quantifying power in a unified framework for a range of scenarios. In this context we consider the utility of quantitative scores (e.g. endophenotypes) that may be available on cases only or both cases and controls. Secondly, we consider, the accuracy of prediction of genetic risk from genome-wide SNPs and derive an expression for genomic prediction accuracy using a liability threshold model for disease traits in a case-control design. The expected values based on our derived equations for both power and prediction accuracy agree well with observed estimates from simulations.     

Field Synopsis and Re-analysis of Systematic Meta-analyses of Genetic Association Studies in Multiple Sclerosis: a Bayesian Approach

To provide an up-to-date summary of multiple sclerosis-susceptible gene variants and assess the noteworthiness in hopes of finding true associations, we investigated the results of 44 meta-analyses on gene variants and multiple sclerosis published through December 2016. Out of 70 statistically significant genotype associations, roughly a fifth (21%) of the comparisons showed noteworthy false-positive rate probability (FPRP) at a statistical power to detect an OR of 1.5 and at a prior probability of 10^?6 assumed for a random single nucleotide polymorphism. These associations (IRF8/rs17445836, STAT3/rs744166, HLA/rs4959093, HLA/rs2647046, HLA/rs7382297, HLA/rs17421624, HLA/rs2517646, HLA/rs9261491, HLA/rs2857439, HLA/rs16896944, HLA/rs3132671, HLA/rs2857435, HLA/rs9261471, HLA/rs2523393, HLA-DRB1/rs3135388, RGS1/rs2760524, PTGER4/rs9292777) also showed a noteworthy Bayesian false discovery probability (BFDP) and one additional association (CD24 rs8734/rs52812045) was also noteworthy via BFDP computation. Herein, we have identified several noteworthy biomarkers of multiple sclerosis susceptibility. We hope these data are used to study multiple sclerosis genetics and inform future screening programs.     

The Enemy of My Enemy Hypothesis: Why Coexisting with Grasses May Be an Adaptive Strategy for Savanna Trees

Savannas are characterized by the coexistence of trees and flammable grasses. Yet, tree–grass coexistence has been labeled as paradoxical—how do these two functional groups coexist over such an extensive area, despite being generally predisposed to excluding each other? For instance, many trees develop dense canopies that limit grass growth, and many grasses facilitate frequent/intense fires, increasing tree mortality. This study revisits tree–grass coexistence with a model of hierarchical competition between pyrogenic grasses, “forest trees” adapted to closed-canopy competition, and “savanna trees” that are inferior competitors in closed-canopy communities, but more resistant to fire. The assumptions of this model are supported by empirical observations, including a systematic review of savanna and forest tree community composition reported here. In general, the model simulations show that when savanna trees exert weaker competitive effects on grasses, a self-reinforcing grass community is maintained, which limits forest tree expansion while still allowing savanna trees to persist (albeit as a subdominant to grasses). When savanna trees exert strong competitive effects on grasses, savanna trees cover increases initially, but as grasses decline their inhibitory effect on forest trees weakens, allowing forest trees to expand and exclude grasses and savanna trees. Rather than paradoxical, these results suggest that having weaker competitive effects on grasses may be advantageous for savanna trees, leading to greater long-term abundance and stability. We label this the “enemy of my enemy hypothesis,” which might apply to species coexistence in communities defined by hierarchical competition or with species capable of generating strong ecological feedbacks.     

Integration Efficiency in DNA-Induced Transformation of PNEUMOCOCCUS. II. Genetic Studies of Mutant Integrating All the Markers with a High Efficiency

Transformation of the pneumococcus mutant 401 by DNA's bearing the standard reference marker and several other markers belonging to two unlinked loci has shown that differences in the integration efficiencies of these markers were considerably reduced in this strain compared to the wild-type strain Cl(3). The sensitivities of mutant 401 to ultraviolet light and to X-ray irradiation are the same as those of Cl(3). However, in 401 all the markers tested are more resistant to inactivation as shown by transformation of 401 and Cl(3) by ultraviolet-irradiated DNA. The increase in resistance is greater for low efficiency (LE) markers than for high efficiency (HE) markers.-The decreased discrimination between LE and HE markers in strain 401 is not due to a mechanism related to modification of markers in the transforming DNA by the recipient cells, nor are the proteins inducing competence of the cells responsible for the differences in the integration efficiencies of various markers.-Genetic studies of the fate of recombinants as well as the measure of the amount of DNA taken up have shown that all the markers are integrated in strain 401 by the same recombination process, that specific to high efficiency markers.