Objectives
Genome‐wide association studies (GWAS) have become increasingly popular to identify associations between single nucleotide polymorphisms (SNPs) and phenotypic traits. The GWAS method is ...commonly applied within the social sciences. However, statistical analyses will need to be carefully conducted and the use of dedicated genetics software will be required. This tutorial aims to provide a guideline for conducting genetic analyses.
Methods
We discuss and explain key concepts and illustrate how to conduct GWAS using example scripts provided through GitHub (https://github.com/MareesAT/GWA_tutorial/).
In addition to the illustration of standard GWAS, we will also show how to apply polygenic risk score (PRS) analysis. PRS does not aim to identify individual SNPs but aggregates information from SNPs across the genome in order to provide individual‐level scores of genetic risk.
Results
The simulated data and scripts that will be illustrated in the current tutorial provide hands‐on practice with genetic analyses. The scripts are based on PLINK, PRSice, and R, which are commonly used, freely available software tools that are accessible for novice users.
Conclusions
By providing theoretical background and hands‐on experience, we aim to make GWAS more accessible to researchers without formal training in the field.
Multiple imputation by chained equations (MICE) requires specifying a suitable conditional imputation model for each incomplete variable and then iteratively imputes the missing values. In the ...presence of missing not at random (MNAR) outcomes, valid statistical inference often requires joint models for missing observations and their indicators of missingness. In this study, we derived an imputation model for missing binary data with MNAR mechanism from Heckman's model using a one-step maximum likelihood estimator. We applied this approach to improve a previously developed approach for MNAR continuous outcomes using Heckman's model and a two-step estimator. These models allow us to use a MICE process and can thus also handle missing at random (MAR) predictors in the same MICE process.
We simulated 1000 datasets of 500 cases. We generated the following missing data mechanisms on 30% of the outcomes: MAR mechanism, weak MNAR mechanism, and strong MNAR mechanism. We then resimulated the first three cases and added an additional 30% of MAR data on a predictor, resulting in 50% of complete cases. We evaluated and compared the performance of the developed approach to that of a complete case approach and classical Heckman's model estimates.
With MNAR outcomes, only methods using Heckman's model were unbiased, and with a MAR predictor, the developed imputation approach outperformed all the other approaches.
In the presence of MAR predictors, we proposed a simple approach to address MNAR binary or continuous outcomes under a Heckman assumption in a MICE procedure.
Despite improvement in clinical management, allogeneic hematopoietic stem cell transplantation (HSCT) is still hampered by high morbidity and mortality rates, mainly due to graft versus host disease ...(GvHD). Recently, it has been demonstrated that the allogeneic immune response might be influenced by external factors such as tissues microenvironment or host microbiota. Here we used high throughput metabolomics to analyze two cohorts of genotypically HLA-identical related recipient and donor pairs. Metabolomic profiles markedly differ between recipients and donors. At the onset of acute GvHD, in addition to host-derived metabolites, we identify significant variation in microbiota-derived metabolites, especially in aryl hydrocarbon receptor (AhR) ligands, bile acids and plasmalogens. Altogether, our findings support that the allogeneic immune response during acute GvHD might be influenced by bile acids and by the decreased production of AhR ligands by microbiota that could limit indoleamine 2,3-dioxygenase induction and influence allogeneic T cell reactivity.
Ornithine δ-aminotransferase (OAT, E.C. 2.6.1.13) catalyzes the transfer of the δ-amino group from ornithine (Orn) to α-ketoglutarate (aKG), yielding glutamate-5-semialdehyde and glutamate (Glu), and ...vice versa. In mammals, OAT is a mitochondrial enzyme, mainly located in the liver, intestine, brain, and kidney. In general, OAT serves to form glutamate from ornithine, with the notable exception of the intestine, where citrulline (Cit) or arginine (Arg) are end products. Its main function is to control the production of signaling molecules and mediators, such as Glu itself, Cit, GABA, and aliphatic polyamines. It is also involved in proline (Pro) synthesis. Deficiency in OAT causes gyrate atrophy, a rare but serious inherited disease, a further measure of the importance of this enzyme.
Citrulline: From metabolism to therapeutic use Bahri, Senda, Ph.D; Zerrouk, Naima, Pharm.D., Ph.D; Aussel, Christian, Pharm.D., Ph.D ...
Nutrition,
03/2013, Letnik:
29, Številka:
3
Journal Article
Recenzirano
Odprti dostop
Abstract Citrulline possesses a highly specific metabolism that bypasses splanchnic extraction because it is not used by the intestine or taken up by the liver. The administration of citrulline may ...be used to deliver available nitrogen for protein homeostasis in peripheral tissues and as an arginine precursor synthesized de novo in the kidneys and endothelial and immune cells. Fresh research has shown that citrulline is efficiently transported across the intestinal luminal membrane by a set of transporters belonging to the B0,+ , L, and b0,+ systems. Several pharmacokinetic studies have confirmed that citrulline is efficiently absorbed when administered orally. Oral citrulline could be used to deliver arginine to the systemic circulation or as a protein anabolic agent in specific clinical situations, because recent data have suggested that citrulline, although not a component of proteins, stimulates protein synthesis in skeletal muscle through the mammalian target of rapamycin signaling pathway. Hence, citrulline could play a pivotal role in maintaining protein homeostasis and is a promising pharmaconutrient in nutritional support strategies for malnourished patients, especially in aging and sarcopenia.
Summary Background & aims Aging is associated with a blunted anabolic response to dietary intake, possibly related to a decrease in systemically available amino acids (AAs), which in turn may stem ...from increased splanchnic AA metabolism. This splanchnic sequestration can be saturated by pulse feeding (80% of daily protein intake in a single meal), enabling increased protein synthesis. This study aimed to evaluate the efficacy of a new nutritional strategy, termed protein pulse feeding. Methods This prospective randomized study ( ClinicalTrials.gov registration number NCT00135590) enrolled 66 elderly malnourished or at-risk patients in an inpatient rehabilitation unit. All were given a controlled diet for 6 weeks. In a spread diet (SD) group ( n = 36), dietary protein was spread over the four daily meals. In a pulse diet (PD) group ( n = 30), 72% of dietary protein (1.31 g/kg weight/d on average) was consumed in one meal at noon. The patients were evaluated at admission and at 6 weeks for body composition lean mass (LM), appendicular skeletal muscle mass (ASMM), and body cell mass (BCM) indices, measured by X-ray absorptiometry combined with bioelectrical impedance analysis (primary outcome), hand grip strength, and activities of daily living (ADL) score. Results Protein pulse feeding was significantly more efficacious than protein spread feeding in improving LM index (mean changes from baseline for PD group: +0.38 kg/m2 ; 95% confidence interval (CI), 0; 0.60; for SD group: −0.21 kg/m2 ; 95% CI, −0.61; 0.20; p = 0.005 between the two groups), ASMM index (+0.21 kg/m2 ; 95% CI, 0; 0.34 and −0.11 kg/m2 ; 95% CI, −0.20; 0.09; p = 0.022), BCM index (+0.44 kg/m2 ; 95% CI, 0.08; 0.52 and −0.04 kg/m2 ; 95% CI, −0.09; 0.10; p = 0.004). There was no significant effect for hand-grip strength or ADL score. Conclusions This study demonstrates for the first time that protein pulse feeding has a positive, clinically relevant effect on lean mass in malnourished and at-risk hospitalized elderly patients.
Observations of a large Dent disease cohort Blanchard, Anne; Curis, Emmanuel; Guyon-Roger, Tiphaine ...
Kidney international,
August 2016, 2016-08-00, 20160801, Letnik:
90, Številka:
2
Journal Article
Recenzirano
Odprti dostop
Dent disease classically combines low-molecular-weight proteinuria, hypercalciuria with nephrocalcinosis, and renal failure. Nephrotic range proteinuria, normal calciuria, and hypokalemia have been ...rarely reported. It is unknown whether the changes in phenotype observed over time are explained by a decrease in glomerular filtration rate (GFR) or whether there is any phenotype-genotype relationship. To answer this we retrospectively analyzed data from 109 male patients with CLCN5 mutations (Dent-1) and 9 patients with mutation of the OCRL gene (Dent-2). In Dent-1 disease, the estimated GFR decreased with age, by 1.0 to 1.6 ml/min per 1.73 m2/yr in the absence and presence of nephrocalcinosis, respectively, with no significant difference. Median values of low-molecular-weight proteinuria were in the nephrotic range and remained at the same level even in late renal disease. End-stage renal disease occurred in 12 patients, at a median age of 40 years. Hypercalciuria decreased with glomerular filtration and was absent in 40% of the patients under 30 and 85% of those over the age of 30. Hypophosphatemia did not resolve with age and calcitriol concentrations were in the upper normal range. Kalemia decreased with age, with half of the patients over the age of 18 presenting with hypokalemia. Thus, no phenotype/genotype correlation was observed in this cohort of patients with Dent disease.
Background:
Substance use disorder emerges in a small proportion of drug users and has the characteristics of a chronic relapsing pathology.
Aims:
Our study aimed to demonstrate and characterize the ...variability in the expression of the rewarding effects of cocaine in the conditioned place preference (CPP) paradigm.
Methods:
A cocaine-CPP paradigm in male Sprague–Dawley rats with an extinction period of 12 days and reinstatement was conducted. A statistical model was developed to distinguish rats expressing or not a cocaine-induced place preference.
Results:
Two groups of rats were identified: rats that did express rewarding effects (CPP expression (CPPE), score >102 s) and rats that did not (no CPP expression (nCPPE), score between −85 and 59 s). These two groups did not show significant differences in a battery of behavioral tests. To identify differentially expressed genes in the CPPE and nCPPE groups, a whole-transcriptome ribonucleic acid-sequencing analysis was performed in the nucleus accumbens (NAc) 24 h after the CPP test. Four immediate early genes (Fos, Egr2, Nr4a1, and Zbtb37) were differentially expressed in the NAc of CPPE rats after expression of CPP. Variability in cocaine-induced place preference persisted in the CPPE and nCPPE groups after the extinction and reinstatement phases. Transcriptomic differences observed after reinstatement were distinct from those observed immediately after expression of CPP.
Conclusion:
These new findings provide insights into the identification of mechanisms underlying interindividual variability in the response to cocaine’s rewarding effects.
Although bone marrow aspiration (BMA) is still considered a painful procedure, pain level remains poorly documented. We therefore conducted a prospective study intended to evaluate pain level in ...adult patients undergoing BMA at the sternal or iliac crest site to identify factors associated with pain. We enrolled a total of 448 patients who underwent 461 BMA and asked those patients to score their pain intensity after BMA using numerical pain rating scale (NPRS). The following factors: level of anxiety, quality of the information given to the patient, operator's experience, and bone texture were recorded using a standardized questionnaire. The median NPRS score was 3.5 (IQR 2.0; 5.0) the sternal site (n = 405) was associated with an increased median NPRS score (3.5 2.0; 5.0) compared to the iliac crest (n = 56, 2.5 1.0; 4.0; p<0.0001). For those patients who underwent sternal BMA, the median NPRS score was significantly lower when using lidocaine infiltration (p = 0.0159) as compared with no anesthetic use. Additionally there was no significant effect of anesthetic cream found. After multivariate analysis, the model of NPRS score at the sternal site included patient anxiety (p<0.0001) and the use of lidocaine infiltration (0.0378). This study underlines the usefulness of a comprehensive management including pain relief and efforts to reduce anxiety including appropriate information given to the patient during BMA.
In patients with acute ischemic stroke (AIS) using a direct oral factor-Xa anticoagulant (DOAC) during the last 48 hours, a fixed plasma heparin-calibrated anti-Xa activity (0.5 IU/mL) was proposed ...as a threshold below which patients could be eligible for thrombolysis and/or thrombectomy. Besides, specific DOAC-calibrated anti-Xa thresholds up to 50 ng/mL have been proposed. However, specific DOAC assays are not widely available contrarily to low-molecularweight heparin (LMWH) anti-Xa activity. We developed and validated a nomogram for predicting apixaban and rivaroxaban concentrations based on LMWH anti-Xa assay.
Our prospective study included apixaban (n=325) and rivaroxaban (n=276) patients. On the same sample, we systematically measured specific DOAC concentration and LMWH anti-Xa activity, using STA®-Liquid-Anti-Xa (Stago) and specific DOAC- or LMWH-calibrators, respectively. The nomogram was built using quantifiable values for both assays on the derivation cohorts with a log-linear regression model. Model performances including sensitivity, specificity, and true positive rate for different thresholds were checked on the validation cohorts.
The models built from the derivation cohorts predicted that values <30 ng/mL and <50 ng/ mL DOAC thresholds corresponded to LMWH-anti-Xa values <0.10 IU/mL and <0.64 IU/mL for apixaban; <0.10 IU/mL and <0.71 IU/mL for rivaroxaban. The model accurately predicted apixaban/ rivaroxaban concentrations in the validation cohort.
This easy-to-use nomogram, developed with our reagent, allowed accurately predicting DOAC concentrations based on LMWH-anti-Xa results in emergency situations such as AIS when drug-specific assessments are not rapidly available. Using DOAC <50 ng/mL equivalent threshold, instead of the fixed LMWH <0.5 IU/mL one, would allow proposing thrombolysis to more patients.
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