Discovering joint associations between disease and gene pairs with a novel similarity test

Genes in a functional pathway can have complex interactions. A gene might activate or suppress another gene, so it is of interest to test joint associations of gene pairs. To simultaneously detect the joint association between disease and two genes (or two chromosomal regions), we propose a new test with the use of genomic similarities. Our test is designed to detect epistasis in the absence of main effects, main effects in the absence of epistasis, or the presence of both main effects and epistasis. Results: The simulation results show that our similarity test with the matching measure is more powerful than the Pearson's chi(2) test when the disease mutants were introduced at common haplotypes, but is less powerful when the disease mutants were introduced at rare haplotypes. Our similarity tests with the counting measures are more sensitive to marker informativity and linkage disequilibrium patterns, and thus are often inferior to the similarity test with the matching measure and the Pearson 's chi(2) test. Conclusions: In detecting joint associations between disease and gene pairs, our similarity test is a complementary method to the Pearson's chi(2) test

AntEpiSeeker: detecting epistatic interactions for case-control studies using a two-stage ant colony optimization algorithm

<p>Abstract</p> <p>Background</p> <p>Epistatic interactions of multiple single nucleotide polymorphisms (SNPs) are now believed to affect individual susceptibility to common diseases. The detection of such interactions, however, is a challenging task in large scale association studies. Ant colony optimization (ACO) algorithms have been shown to be useful in detecting epistatic interactions.</p> <p>Findings</p> <p>AntEpiSeeker, a new two-stage ant colony optimization algorithm, has been developed for detecting epistasis in a case-control design. Based on some practical epistatic models, AntEpiSeeker has performed very well.</p> <p>Conclusions</p> <p>AntEpiSeeker is a powerful and efficient tool for large-scale association studies and can be downloaded from <url>http://nce.ads.uga.edu/~romdhane/AntEpiSeeker/index.html</url>.</p

Cre/lox Studies Identify Resident Macrophages as the Major Source of Circulating Coagulation Factor XIII-A

Objective— To establish the cellular source of plasma factor (F)XIII-A. Approach and Results— A novel mouse floxed for the F13a1 gene, FXIII-Aflox/flox (Flox), was crossed with myeloid- and platelet-cre–expressing mice, and cellular FXIII-A mRNA expression and plasma and platelet FXIII-A levels were measured. The platelet factor 4-cre.Flox cross abolished platelet FXIII-A and reduced plasma FXIII-A to 23±3% (P<0.001). However, the effect of platelet factor 4-cre on plasma FXIII-A was exerted outside of the megakaryocyte lineage because plasma FXIII-A was not reduced in the Mpl−/− mouse, despite marked thrombocytopenia. In support of this, platelet factor 4-cre depleted FXIII-A mRNA in brain, aorta, and heart of floxed mice, where FXIII-Apos cells were identified as macrophages as they costained with CD163. In the integrin αM-cre.Flox and the double copy lysozyme 2-cre.cre.Flox crosses, plasma FXIII-A was reduced to, respectively, 75±5% (P=0.003) and 30±7% (P<0.001), with no change in FXIII-A content per platelet, further consistent with a macrophage origin of plasma FXIII-A. The change in plasma FXIII-A levels across the various mouse genotypes mirrored the change in FXIII-A mRNA expression in aorta. Bone marrow transplantation of FXIII-A+/+ bone marrow into FXIII-A−/− mice both restored plasma FXIII-A to normal levels and replaced aortic and cardiac FXIII-A mRNA, while its transplantation into FXIII-A+/+ mice did not increase plasma FXIII-A levels, suggesting that a limited population of niches exists that support FXIII-A-releasing cells. Conclusions— This work suggests that resident macrophages maintain plasma FXIII-A and exclude the platelet lineage as a major contributor

Epistatic Module Detection for Case-Control Studies: A Bayesian Model with a Gibbs Sampling Strategy

The detection of epistatic interactive effects of multiple genetic variants on the susceptibility of human complex diseases is a great challenge in genome-wide association studies (GWAS). Although methods have been proposed to identify such interactions, the lack of an explicit definition of epistatic effects, together with computational difficulties, makes the development of new methods indispensable. In this paper, we introduce epistatic modules to describe epistatic interactive effects of multiple loci on diseases. On the basis of this notion, we put forward a Bayesian marker partition model to explain observed case-control data, and we develop a Gibbs sampling strategy to facilitate the detection of epistatic modules. Comparisons of the proposed approach with three existing methods on seven simulated disease models demonstrate the superior performance of our approach. When applied to a genome-wide case-control data set for Age-related Macular Degeneration (AMD), the proposed approach successfully identifies two known susceptible loci and suggests that a combination of two other loci—one in the gene SGCD and the other in SCAPER—is associated with the disease. Further functional analysis supports the speculation that the interaction of these two genetic variants may be responsible for the susceptibility of AMD. When applied to a genome-wide case-control data set for Parkinson's disease, the proposed method identifies seven suspicious loci that may contribute independently to the disease

Is it reliable to assess visual attention of drivers affected by Parkinson's disease from the backseat?—a simulator study

BACKGROUND: Current methods of determining licence retainment or cancellation is through on-road driving tests. Previous research has shown that occupational therapists frequently assess drivers' visual attention while sitting in the back seat on the opposite side of the driver. Since the eyes of the driver are not always visible, assessment by eye contact becomes problematic. Such procedural drawbacks may challenge validity and reliability of the visual attention assessments. In terms of correctly classified attention, the aim of the study was to establish the accuracy and the inter-rater reliability of driving assessments of visual attention from the back seat. Furthermore, by establishing eye contact between the assessor and the driver through an additional mirror on the wind screen, the present study aimed to establish how much such an intervention would enhance the accuracy of the visual attention assessment. METHODS: Two drivers with Parkinson's disease (PD) and six control drivers drove a fixed route in a driving simulator while wearing a head mounted eye tracker. The eye tracker data showed where the foveal visual attention actually was directed. These data were time stamped and compared with the simultaneous manual scoring of the visual attention of the drivers. In four of the drivers, one with Parkinson's disease, a mirror on the windscreen was set up to arrange for eye contact between the driver and the assessor. Inter-rater reliability was performed with one of the Parkinson drivers driving, but without the mirror. RESULTS: Without mirror, the overall accuracy was 56% when assessing the three control drivers and with mirror 83%. However, for the PD driver without mirror the accuracy was 94%, whereas for the PD driver with a mirror the accuracy was 90%. With respect to the inter-rater reliability, a 73% agreement was found. CONCLUSION: If the final outcome of a driving assessment is dependent on the subcategory of a protocol assessing visual attention, we suggest the use of an additional mirror to establish eye contact between the assessor and the driver. The clinicians' observations on-road should not be a standalone assessment in driving assessments. Instead, eye trackers should be employed for further analyses and correlation in cases where there is doubt about a driver's attention

Riverbed sediments buffer phosphorus concentrations downstream of sewage treatment works across the River Wensum catchment, UK

Purpose: Wastewater effluent discharged into rivers from sewage treatment works (STWs) represents one of the most important point sources of soluble reactive phosphorus (SRP) pollution and is a major driver of freshwater eutrophication. In this study, we assess the ability of riverbed sediments to act as a self-regulating buffering system to reduce SRP dissolved in the water column downstream of STW outflows. Materials and methods: River water and riverbed sediment samples were collected from 10 tributary outlets across the River Wensum catchment, Norfolk, UK, at monthly intervals between July and October 2016, such that 40 sediment and 40 water samples were collected in total. Of these locations, five were located downstream of STWs and five were on tributaries without STWs. Dissolved SRP concentrations were analysed and the Equilibrium Phosphorus Concentration (EPC0) of each sediment sample was measured to determine whether riverbed sediments were acting as net sources or sinks of SRP. Results and discussion: The mean SRP concentration downstream of STWs (382 µg P L-1) was double that of sites without a STW (185 µg P L-1), whilst the mean EPC0 for effluent impacted sites (105 µg P L-1) was 70% higher than that recorded at unaffected sites (62 µg P L-1). Regardless of STW influence, riverbed sediments across all 10 sites almost always acted as net sinks for SRP from the overlying water column. This was particularly true at sites downstream of STWs which displayed enhanced potential to buffer the river against increases in SRP released in sewage effluent. Conclusions: Despite EPC0 values revealing riverbed sediments were consistently acting as sinks for SRP, elevated SRP concentrations downstream of STWs clearly demonstrate the sediments have insufficient SRP sorption capacity to completely buffer the river against effluent discharge. Consequently, SRP concentrations across the catchment continue to exceed recommended standards for good chemical status, thus emphasising the need for enhanced mitigation efforts at STWs to minimise riverine phosphorus loading

A Markov blanket-based method for detecting causal SNPs in GWAS

<p>Abstract</p> <p>Background</p> <p>Detecting epistatic interactions associated with complex and common diseases can help to improve prevention, diagnosis and treatment of these diseases. With the development of genome-wide association studies (GWAS), designing powerful and robust computational method for identifying epistatic interactions associated with common diseases becomes a great challenge to bioinformatics society, because the study of epistatic interactions often deals with the large size of the genotyped data and the huge amount of combinations of all the possible genetic factors. Most existing computational detection methods are based on the classification capacity of SNP sets, which may fail to identify SNP sets that are strongly associated with the diseases and introduce a lot of false positives. In addition, most methods are not suitable for genome-wide scale studies due to their computational complexity.</p> <p>Results</p> <p>We propose a new Markov Blanket-based method, DASSO-MB (Detection of ASSOciations using Markov Blanket) to detect epistatic interactions in case-control GWAS. Markov blanket of a target variable T can completely shield T from all other variables. Thus, we can guarantee that the SNP set detected by DASSO-MB has a strong association with diseases and contains fewest false positives. Furthermore, DASSO-MB uses a heuristic search strategy by calculating the association between variables to avoid the time-consuming training process as in other machine-learning methods. We apply our algorithm to simulated datasets and a real case-control dataset. We compare DASSO-MB to other commonly-used methods and show that our method significantly outperforms other methods and is capable of finding SNPs strongly associated with diseases.</p> <p>Conclusions</p> <p>Our study shows that DASSO-MB can identify a minimal set of causal SNPs associated with diseases, which contains less false positives compared to other existing methods. Given the huge size of genomic dataset produced by GWAS, this is critical in saving the potential costs of biological experiments and being an efficient guideline for pathogenesis research.</p

Evaluation of the safety of C-spine clearance by paramedics: design and methodology

<p>Abstract</p> <p>Background</p> <p>Canadian Emergency Medical Services annually transport 1.3 million patients with potential neck injuries to local emergency departments. Less than 1% of those patients have a c-spine fracture and even less (0.5%) have a spinal cord injury. Most injuries occur before the arrival of paramedics, not during transport to the hospital, yet most patients are transported in ambulances immobilized. They stay fully immobilized until a bed is available, or until physician assessment and/or X-rays are complete. The prolonged immobilization is often unnecessary and adds to the burden of already overtaxed emergency medical services systems and crowded emergency departments.</p> <p>Methods/Design</p> <p>The goal of this study is to evaluate the safety and potential impact of an active strategy that allows paramedics to assess very low-risk trauma patients using a validated clinical decision rule, the Canadian C-Spine Rule, in order to determine the need for immobilization during transport to the emergency department.</p> <p>This cohort study will be conducted in Ottawa, Canada with one emergency medical service. Paramedics with this service participated in an earlier validation study of the Canadian C-Spine Rule. Three thousand consecutive, alert, stable adult trauma patients with a potential c-spine injury will be enrolled in the study and evaluated using the Canadian C-Spine Rule to determine the need for immobilization. The outcomes that will be assessed include measures of safety (numbers of missed fractures and serious adverse outcomes), measures of clinical impact (proportion of patients transported without immobilization, key time intervals) and performance of the Rule.</p> <p>Discussion</p> <p>Approximately 40% of all very low-risk trauma patients could be transported safely, without c-spine immobilization, if paramedics were empowered to make clinical decisions using the Canadian C-Spine Rule. This safety study is an essential step before allowing all paramedics across Canada to selectively immobilize trauma victims before transport. Once safety and potential impact are established, we intend to implement a multi-centre study to study actual impact.</p> <p>Trial Registration</p> <p>ClinicalTrials.gov <a href="http://www.clinicaltrials.gov/ct2/show/NCT01188447">NCT01188447</a></p