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Background
Sequencing datasets consist of a finite number of reads which map to specific regions of a reference genome. Most effort in modeling these datasets focuses on the detection of univariate differentially expressed genes. However, for classification, we must consider multiple genes and their interactions.Results
Thus, we introduce a hierarchical multivariate Poisson model (MP) and the associated optimal Bayesian classifier (OBC) for classifying samples using sequencing data. Lacking closed-form solutions, we employ a Monte Carlo Markov Chain (MCMC) approach to perform classification. We demonstrate superior or equivalent classification performance compared to typical classifiers for two synthetic datasets and over a range of classification problem difficulties. We also introduce the Bayesian minimum mean squared error (MMSE) conditional error estimator and demonstrate its computation over the feature space. In addition, we demonstrate superior or leading class performance over an RNA-Seq dataset containing two lung cancer tumor types from The Cancer Genome Atlas (TCGA).Conclusions
Through model-based, optimal Bayesian classification, we demonstrate superior classification performance for both synthetic and real RNA-Seq datasets. A tutorial video and Python source code is available under an open source license at http://bit.ly/1gimnss.Electronic supplementary material
The online version of this article (doi:10.1186/s12859-014-0401-3) contains supplementary material, which is available to authorized users. 相似文献4.
Kaushalya C Amarasinghe Jason Li Sally M Hunter Georgina L Ryland Prue A Cowin Ian G Campbell Saman K Halgamuge 《BMC genomics》2014,15(1)
Background
Using whole exome sequencing to predict aberrations in tumours is a cost effective alternative to whole genome sequencing, however is predominantly used for variant detection and infrequently utilised for detection of somatic copy number variation.Results
We propose a new method to infer copy number and genotypes using whole exome data from paired tumour/normal samples. Our algorithm uses two Hidden Markov Models to predict copy number and genotypes and computationally resolves polyploidy/aneuploidy, normal cell contamination and signal baseline shift. Our method makes explicit detection on chromosome arm level events, which are commonly found in tumour samples. The methods are combined into a package named ADTEx (Aberration Detection in Tumour Exome). We applied our algorithm to a cohort of 17 in-house generated and 18 TCGA paired ovarian cancer/normal exomes and evaluated the performance by comparing against the copy number variations and genotypes predicted using Affymetrix SNP 6.0 data of the same samples. Further, we carried out a comparison study to show that ADTEx outperformed its competitors in terms of precision and F-measure.Conclusions
Our proposed method, ADTEx, uses both depth of coverage ratios and B allele frequencies calculated from whole exome sequencing data, to predict copy number variations along with their genotypes. ADTEx is implemented as a user friendly software package using Python and R statistical language. Source code and sample data are freely available under GNU license (GPLv3) at http://adtex.sourceforge.net/.Electronic supplementary material
The online version of this article (doi:10.1186/1471-2164-15-732) contains supplementary material, which is available to authorized users. 相似文献5.
Sean R Landman Tae Hyun Hwang Kevin AT Silverstein Yingming Li Scott M Dehm Michael Steinbach Vipin Kumar 《BMC genomics》2014,15(1)
Background
Personal genome assembly is a critical process when studying tumor genomes and other highly divergent sequences. The accuracy of downstream analyses, such as RNA-seq and ChIP-seq, can be greatly enhanced by using personal genomic sequences rather than standard references. Unfortunately, reads sequenced from these types of samples often have a heterogeneous mix of various subpopulations with different variants, making assembly extremely difficult using existing assembly tools. To address these challenges, we developed SHEAR (Sample Heterogeneity Estimation and Assembly by Reference; http://vk.cs.umn.edu/SHEAR), a tool that predicts SVs, accounts for heterogeneous variants by estimating their representative percentages, and generates personal genomic sequences to be used for downstream analysis.Results
By making use of structural variant detection algorithms, SHEAR offers improved performance in the form of a stronger ability to handle difficult structural variant types and better computational efficiency. We compare against the lead competing approach using a variety of simulated scenarios as well as real tumor cell line data with known heterogeneous variants. SHEAR is shown to successfully estimate heterogeneity percentages in both cases, and demonstrates an improved efficiency and better ability to handle tandem duplications.Conclusion
SHEAR allows for accurate and efficient SV detection and personal genomic sequence generation. It is also able to account for heterogeneous sequencing samples, such as from tumor tissue, by estimating the subpopulation percentage for each heterogeneous variant.Electronic supplementary material
The online version of this article (doi:10.1186/1471-2164-15-84) contains supplementary material, which is available to authorized users. 相似文献6.
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Purpose
To determine whether oral doxycycline treatment reduces pterygium lesions.Design
Double blind, randomized, placebo controlled clinical trial.Participants
98 adult patients with primary pterygium.Methods
Patients were randomly assigned to receive 100 mg oral doxycycline twice a day (49 subjects), or placebo (49 subjects), for 30 days. Photographs of the lesion were taken at the time of recruitment and at the end of the treatment. Follow-up sessions were performed 6 and 12 months post-treatment. Statistical analyses for both continuous and categorical variables were applied. p values of less than 0.05 were considered to indicate statistical significance.Main Outcome Measures
The primary endpoint was the change in lesion size after 30 days of treatment.Results
The primary endpoint was not met for the whole population but subgroup analysis showed that doxycycline was effective in patients of Caucasian origin while other ethnicities, mostly Hispanic, did not respond to the treatment. Moreover, there was a correlation between age and better response (p = 0.003). Adverse events were uncommon, mild, and in agreement with previous reports on short doxycycline treatments.Conclusions
Oral doxycycline was superior to placebo for the treatment of primary pterygia in older Caucasian patients. These findings support the use of doxycycline for pterygium treatment in particular populations.Trial Registration
European Union Clinical Trials Register EudraCT 2008-007178-39 相似文献8.
Tomoyuki Hayashi Hisashi Doyama Yukihiro Shirota Hirokazu Tsuji Youhei Marukawa Hajime Ohta Kazuhiro Miwa Takaharu Masunaga Shuichi Terasaki Yutaka Matano Kunihiro Tsuji Yoshibumi Kaneko Toshihide Okada Hiroshi Kurumaya Shuichi Kaneko 《PloS one》2014,9(7)
Objectives
Magnifying narrow-band imaging (M-NBI) is more accurate than white-light imaging for diagnosing small gastric cancers. However, it is uncertain whether moving M-NBI images have additional effects in the diagnosis of gastric cancers compared with still images.Design
A prospective multicenter cohort study.Methods
To identify the additional benefits of moving M-NBI images by comparing the diagnostic accuracy of still images only with that of both still and moving images. Still and moving M-NBI images of 40 gastric lesions were obtained by an expert endoscopist prior to this prospective multicenter cohort study. Thirty-four endoscopists from ten different Japanese institutions participated in the prospective multicenter cohort study. Each study participant was first tested using only still M-NBI images (still image test), then tested 1 month later using both still and moving M-NBI images (moving image test). The main outcome was a difference in the diagnostic accuracy of cancerous versus noncancerous lesions between the still image test and the moving image test.Results
Thirty-four endoscopists were analysed. There were no significant difference of cancerous versus noncancerous lesions between still and moving image tests in the diagnostic accuracy (59.9% versus 61.5%), sensitivity (53.4% versus 55.9%), and specificity (67.0% versus 67.6%). And there were no significant difference in the diagnostic accuracy between still and moving image tests of demarcation line (65.4% versus 65.5%), microvascular pattern (56.7% versus 56.9%), and microsurface pattern (48.1% versus 50.9%). Diagnostic accuracy showed no significant difference between the still and moving image tests in the subgroups of endoscopic findings of the lesions.Conclusions
The addition of moving M-NBI images to still M-NBI images does not improve the diagnostic accuracy for gastric lesions. It is reasonable to concentrate on taking sharp still M-NBI images during endoscopic observation and use them for diagnosis.Trial registration
Umin.ac.jp UMIN-CTR000008048 相似文献9.
Kento Imajo Hideyuki Hyogo Masato Yoneda Yasushi Honda Takaomi Kessoku Wataru Tomeno Yuji Ogawa Masataka Taguri Hironori Mawatari Yuichi Nozaki Koji Fujita Hiroyuki Kirikoshi Satoru Saito Yoshio Sumida Masafumi Ono Koichiro Wada Atsushi Nakajima Yuichiro Eguchi 《PloS one》2014,9(12)
Background
Non-alcoholic fatty liver disease (NAFLD) is associated with increased risks of atherosclerotic diseases, including cardiovascular disease. However, the difference in risk between patients with non-alcoholic fatty liver (NAFL) and non-alcoholic steatohepatitis (NASH) has not yet been determined. Accumulating evidence has shown that high amounts of small dense low-density lipoprotein (sdLDL) are closely associated with atherosclerotic diseases. This study investigated differences in risk factors for atherosclerotic diseases, especially LDL-migration index (LDL-MI), an indicator of sdLDL, between patients with NAFL and NASH.Methods
LDL-MI was analyzed in a primary cohort of 156 patients with NAFLD, including 53 with NAFL and 103 with NASH, and a validation cohort of 69 patients with NAFLD, including 25 with NAFL and 44 with NASH.Results
In the primary cohort, NASH was associated with elevated LDL-MI (p = 0.039). Multiple regression analysis showed that NASH and the non-use of lipid lowering medications were independently correlated with higher LDL-MI in all patients with NAFLD. Among patients not on lipid lowering medications, those with NASH had significantly higher LDL-MI than those with NAFL (p = 0.001). These findings were confirmed in a validation cohort, in that LDL-MI was significantly higher in patients with NASH than with NAFL (p = 0.043).Conclusion
This study is the first to show that LDL-MI, an indicator of sdLDL, was higher in patients with NASH than with NAFL, suggesting that the risk of atherosclerotic diseases may be higher in NASH than NAFL. Patients with NASH should be followed closely, especially for the progression of liver pathology and atherosclerotic diseases.Trial Registration
UMIN000009614 相似文献10.
Meliha Crnkic Kapetanovic Tore Saxne G?ran J?nsson Lennart Truedsson Pierre Geborek 《Arthritis research & therapy》2013,15(5):R171
Introduction
The objective of the study was to investigate the impact of newer biologic treatments including rituximab, abatacept and tocilizumab on antibody response following pneumococcal vaccination using a 7-valent conjugate vaccine in patients with established rheumatoid arthritis (RA).Methods
Patients with RA receiving rituximab, abatacept or tocilizumab as monotherapy or combined with methotrexate (MTX) participated in the study. Specific IgG antibodies against 23F and 6B serotypes were measured at vaccination and 4 to 6 weeks after vaccination using standardised ELISA. Geometric mean antibody levels (GML) were calculated. Antibody response (AR) was defined as the ratio between post- and pre-vaccination antibody levels and a positive antibody response (posAR) was AR ≥2.Results
In total, 88 patients were enrolled in the study. Of 55 patients treated with rituximab, 26 (46%) were on concomitant MTX. Of patients receiving abatacept (n = 17) and tocilizumab (n = 16) biologic treatment was given in combination with MTX in 13 (76%) and 9 (56%) patients, respectively. Patients treated with rituximab had significantly lower AR compared to those on tocilizumab, as well as compared to previously reported RA patients on MTX and controls (spondylarthropathy patients treated with NSAIDs and/or analgesics). In total, 10.3% of patients on rituximab monotherapy and no patient on rituximab + MTX had posAR for both serotypes. For abatacept and tocilizumab the corresponding figures were 17.6% and 50%.Conclusion
In this cohort of patients with established RA, treatment with rituximab and abatacept was associated with diminished antibody response but this was most pronounced for rituximab. Pneumococcal conjugate vaccine administrated during ongoing tocilizumab treatment seems to be associated with sufficient antibody response. Pneumococcal vaccination should preferably be encouraged before initiation of rituximab or abatacept treatment.Trial registration
NCT00828997 and EudraCT EU 2007-006539-29. 相似文献11.
Nickolai Titov Blake F. Dear Luke Johnston Carolyn Lorian Judy Zou Bethany Wootton Jay Spence Peter M. McEvoy Ronald M. Rapee 《PloS one》2013,8(7)
Background
Depression and anxiety are common, disabling and chronic. Self-guided internet-delivered treatments are popular, but few people complete them. New strategies are required to realise their potential.Aims
To evaluate the effect of automated emails on the effectiveness, safety, and acceptability of a new automated transdiagnostic self-guided internet-delivered treatment, the Wellbeing Course, for people with depression and anxiety.Method
A randomised controlled trial was conducted through the website: www.ecentreclinic.org. Two hundred and fifty seven people with elevated symptoms were randomly allocated to the 8 week course either with or without automated emails, or to a waitlist control group. Primary outcome measures were the Patient Health Questionnaire 9-Item (PHQ-9) and the Generalized Anxiety Disorder 7-Item (GAD-7).Results
Participants in the treatment groups had lower PHQ-9 and GAD-7 scores at post-treatment than controls. Automated emails increased rates of course completion (58% vs. 35%), and improved outcomes in a subsample with elevated symptoms.Conclusions
The new self-guided course was beneficial, and automated emails facilitated outcomes. Further attention to strategies that facilitate adherence, learning, and safety will help realise the potential of self-guided interventions.Trial Registration
Australian and New Zealand Clinical Trials Registry ACTRN12610001058066 相似文献12.
Stefano Balducci Silvano Zanuso Patrizia Cardelli Laura Salvi Alessandra Bazuro Luca Pugliese Carla Maccora Carla Iacobini Francesco G. Conti Antonio Nicolucci Giuseppe Pugliese for the Italian Diabetes Exercise Study Investigators 《PloS one》2012,7(11)
Background
While current recommendations on exercise type and volume have strong experimental bases, there is no clear evidence from large-sized studies indicating whether increasing training intensity provides additional benefits to subjects with type 2 diabetes.Objective
To compare the effects of moderate-to-high intensity (HI) versus low-to-moderate intensity (LI) training of equal energy cost, i.e. exercise volume, on modifiable cardiovascular risk factors.Design
Pre-specified sub-analysis of the Italian Diabetes and Exercise Study (IDES), a randomized multicenter prospective trial comparing a supervised exercise intervention with standard care for 12 months (2005–2006).Setting
Twenty-two outpatient diabetes clinics across Italy.Patients
Sedentary patients with type 2 diabetes assigned to twice-a-week supervised progressive aerobic and resistance training plus exercise counseling (n = 303).Interventions
Subjects were randomized by center to LI (n = 142, 136 completed) or HI (n = 161, 152 completed) progressive aerobic and resistance training, i.e. at 55% or 70% of predicted maximal oxygen consumption and at 60% or 80% of predicted 1-Repetition Maximum, respectively, of equal volume.Main Outcome Measure(s)
Hemoglobin (Hb) A1c and other cardiovascular risk factors; 10-year coronary heart disease (CHD) risk scores.Results
Volume of physical activity, both supervised and non-supervised, was similar in LI and HI participants. Compared with LI training, HI training produced only clinically marginal, though statistically significant, improvements in HbA1c (mean difference −0.17% [95% confidence interval −0.44,0.10], P = 0.03), triglycerides (−0.12 mmol/l [−0.34,0.10], P = 0.02) and total cholesterol (−0.24 mmol/l [−0.46, −0.01], P = 0.04), but not in other risk factors and CHD risk scores. However, intensity was not an independent predictor of reduction of any of these parameters. Adverse event rate was similar in HI and LI subjects.Conclusions
Data from the large IDES cohort indicate that, in low-fitness individuals such as sedentary subjects with type 2 diabetes, increasing exercise intensity is not harmful, but does not provide additional benefits on cardiovascular risk factors.Trial Registration
www.ISRCTN.org ISRCTN-04252749. 相似文献13.
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Paul W Jones James F Donohue Jerry Nedelman Steve Pascoe Gregory Pinault Cheryl Lassen 《Respiratory research》2011,12(1):161
Background
Relationships between improvements in lung function and other clinical outcomes in chronic obstructive pulmonary disease (COPD) are not documented extensively. We examined whether changes in trough forced expiratory volume in 1 second (FEV1) are correlated with changes in patient-reported outcomes.Methods
Pooled data from three indacaterol studies (n = 3313) were analysed. Means and responder rates for outcomes including change from baseline in Transition Dyspnoea Index (TDI), St. George''s Respiratory Questionnaire (SGRQ) scores (at 12, 26 and 52 weeks), and COPD exacerbation frequency (rate/year) were tabulated across categories of ΔFEV1. Also, generalised linear modelling was performed adjusting for covariates such as baseline severity and inhaled corticosteroid use.Results
With increasing positive ΔFEV1, TDI and ΔSGRQ improved at all timepoints, exacerbation rate over the study duration declined (P < 0.001). Individual-level correlations were 0.03-0.18, but cohort-level correlations were 0.79-0.95. At 26 weeks, a 100 ml increase in FEV1 was associated with improved TDI (0.46 units), ΔSGRQ (1.3-1.9 points) and exacerbation rate (12% decrease). Overall, adjustments for baseline covariates had little impact on the relationship between ΔFEV1 and outcomes.Conclusions
These results suggest that larger improvements in FEV1 are likely to be associated with larger patient-reported benefits across a range of clinical outcomes.Trial Registration
ClinicalTrials.gov , NCT00393458, and NCT00463567 NCT00624286相似文献15.
Background
DAVID is the most popular tool for interpreting large lists of gene/proteins classically produced in high-throughput experiments. However, the use of DAVID website becomes difficult when analyzing multiple gene lists, for it does not provide an adequate visualization tool to show/compare multiple enrichment results in a concise and informative manner.Result
We implemented a new R-based graphical tool, BACA (Bubble chArt to Compare Annotations), which uses the DAVID web service for cross-comparing enrichment analysis results derived from multiple large gene lists. BACA is implemented in R and is freely available at the CRAN repository (http://cran.r-project.org/web/packages/BACA/).Conclusion
The package BACA allows R users to combine multiple annotation charts into one output graph by passing DAVID website.Electronic supplementary material
The online version of this article (doi:10.1186/s12859-015-0477-4) contains supplementary material, which is available to authorized users. 相似文献16.
Background
Identification of DNA/Protein motifs is a crucial problem for biologists. Computational techniques could be of great help in this identification. In this direction, many computational models for motifs have been proposed in the literature.Methods
One such important model is the motif model. In this paper we describe a motif search web tool that predominantly employs this motif model. This web tool exploits the state-of-the art algorithms for solving the motif search problem.Results
The online tool has been helping scientists identify many unknown motifs. Many of our predictions have been successfully verified as well. We hope that this paper will expose this crucial tool to many more scientists.Availability and requirements
Project name: PMS - Panoptic Motif Search Tool. Project home page: http://pms.engr.uconn.edu or http://motifsearch.com. Licence: PMS tools will be readily available to any scientist wishing to use it for non-commercial purposes, without restrictions. The online tool is freely available without login. 相似文献17.
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Kathleen M. Griffiths Andrew J. Mackinnon Dimity A. Crisp Helen Christensen Kylie Bennett Louise Farrer 《PloS one》2012,7(12)
Background
Internet support groups (ISGs) are popular, particularly among people with depression, but there is little high quality evidence concerning their effectiveness.Aim
The study aimed to evaluate the efficacy of an ISG for reducing depressive symptoms among community members when used alone and in combination with an automated Internet-based psychotherapy training program.Method
Volunteers with elevated psychological distress were identified using a community-based screening postal survey. Participants were randomised to one of four 12-week conditions: depression Internet Support Group (ISG), automated depression Internet Training Program (ITP), combination of the two (ITP+ISG), or a control website with delayed access to e-couch at 6 months. Assessments were conducted at baseline, post-intervention, 6 and 12 months.Results
There was no change in depressive symptoms relative to control after 3 months of exposure to the ISG. However, both the ISG alone and the combined ISG+ITP group showed significantly greater reduction in depressive symptoms at 6 and 12 months follow-up than the control group. The ITP program was effective relative to control at post-intervention but not at 6 months.Conclusions
ISGs for depression are promising and warrant further empirical investigation.Trial Registration
Controlled-Trials.com ISRCTN65657330 相似文献19.
Claus Niederau Stefan Mauss Andreas Schober Albrecht Stoehr Tim Zimmermann Michael Waizmann Gero Moog Stefan Pape Bernd Weber Konrad Isernhagen Petra Sandow Bernd Bokemeyer Ulrich Alshuth Hermann Steffens Dietrich Hüppe 《PloS one》2014,9(9)
Background
Previous trials have often defined genotype 2 and 3 patients as an “easy to treat” group and guidelines recommend similar management.Aims
The present study looks for differences between the two genotypes and analyzes predictive factors for SVR.Methods
Prospective, community-based cohort study involving 421 physicians throughout Germany. The analysis includes 2,347 patients with untreated chronic HCV genotype 2 (n = 391) and 3 (n = 1,956) infection treated with PEG-IFN α-2a plus ribavirin between August 2007 and July 2012.Results
When compared with genotype 2 patients, those with genotype 3 were younger, had a shorter duration of infection, lower values of total cholesterol, LDL cholesterol and BMI, a higher frequency of drug use as infection mode and male gender (p<0.0001, respectively), and a higher APRI score (p<0.005). SVR was higher in genotype 2 when compared with genotype 3 (64.7% vs. 56.9%, p = 0.004). By multivariate analysis of genotype 2 patients, low baseline γ -GT and RVR predicted SVR. In genotype 3 age ≤45 years, cholesterol>130 mg/dl, a low APRI score, and a γ-GT ≥3-times ULN, RVR, and RBV starting dose were associated with SVR by multivariate analysis.Conclusions
The present study corroborates that liver fibrosis is more pronounced in genotype 3 vs. 2. SVR is higher in genotype 2 versus genotype 3 partly because of follow-up problems in genotype 3 patients, in particular in those infected by drug use. Thus, subgroups of genotype 3 patients have adherence problems and need special attention also because they often have significant liver fibrosis.Trial Registration
Verband Forschender Arzneimittelhersteller e.V., Berlin, Germany ML21645 ClinicalTrials.gov NCT02106156相似文献20.
Jennifer A Dickens Bruce E Miller Lisa D Edwards Edwin K Silverman David A Lomas Ruth Tal-Singer 《Respiratory research》2011,12(1):146