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1.
Clin Microbiol Rev ; 37(1): e0010122, 2024 03 14.
Artículo en Inglés | MEDLINE | ID: mdl-38235979

RESUMEN

Pneumocystis jirovecii is a ubiquitous opportunistic fungus that can cause life-threatening pneumonia. People with HIV (PWH) who have low CD4 counts are one of the populations at the greatest risk of Pneumocystis jirovecii pneumonia (PCP). While guidelines have approached the diagnosis, prophylaxis, and management of PCP, the numerous studies of PCP in PWH are dominated by the 1980s and 1990s. As such, most studies have included younger male populations, despite PCP affecting both sexes and a broad age range. Many studies have been small and observational in nature, with an overall lack of randomized controlled trials. In many jurisdictions, and especially in low- and middle-income countries, the diagnosis can be challenging due to lack of access to advanced and/or invasive diagnostics. Worldwide, most patients will be treated with 21 days of high-dose trimethoprim sulfamethoxazole, although both the dose and the duration are primarily based on historical practice. Whether treatment with a lower dose is as effective and less toxic is gaining interest based on observational studies. Similarly, a 21-day tapering regimen of prednisone is used for patients with more severe disease, yet other doses, other steroids, or shorter durations of treatment with corticosteroids have not been evaluated. Now with the widespread availability of antiretroviral therapy, improved and less invasive PCP diagnostic techniques, and interest in novel treatment strategies, this review consolidates the scientific body of literature on the diagnosis and management of PCP in PWH, as well as identifies areas in need of more study and thoughtfully designed clinical trials.


Asunto(s)
Infecciones por VIH , Pneumocystis carinii , Neumonía por Pneumocystis , Femenino , Humanos , Masculino , Neumonía por Pneumocystis/diagnóstico , Neumonía por Pneumocystis/tratamiento farmacológico , Neumonía por Pneumocystis/prevención & control , Infecciones por VIH/complicaciones , Infecciones por VIH/tratamiento farmacológico , Combinación Trimetoprim y Sulfametoxazol/uso terapéutico , Combinación Trimetoprim y Sulfametoxazol/farmacología
2.
J Am Heart Assoc ; 12(14): e028865, 2023 07 18.
Artículo en Inglés | MEDLINE | ID: mdl-37421275

RESUMEN

Background PARAGON-HF (Efficacy and Safety of LCZ696 Compared to Valsartan, on Morbidity and Mortality in Heart Failure Patients With Preserved Ejection Fraction) suggested a potential benefit of sacubitril-valsartan in women with preserved ejection fraction. Among patients with heart failure previously treated with angiotensin-converting enzyme inhibitors (ACEIs) or angiotensin II receptor blockers (ARBs), we studied whether effectiveness of treatment with sacubitril-valsartan compared with ACEI/ARB monotherapy differed between men and women for both preserved and reduced ejection fraction. Methods and Results Data were derived from the Truven Health MarketScan Databases between January 1, 2011, and December 31, 2018. We included patients with a primary diagnosis of heart failure on treatment with ACEIs, ARBs, or sacubitril-valsartan on the basis of the first prescription after diagnosis. A total of 7181 patients treated with sacubitril-valsartan, 25 408 patients using an ACEI, and 16 177 patients treated with ARBs were included. A total of 790 readmissions or deaths occurred among 7181 patients in the sacubitril-valsartan group and 11 901 events in 41 585 patients treated with an ACEI/ARB. Adjusted for covariates, the hazard ratio (HR) for treatment with sacubitril-valsartan compared with an ACEI or ARB was 0.74 (95% CI, 0.68-0.80). The protective effect of sacubitril-valsartan was evident for men and women (women: HR, 0.75 [95% CI, 0.66-0.86]; P<0.01; men: HR, 0.71 [95% CI, 0.64-0.79]; P<0.01; P interaction 0.03). A protective effect for both sexes was seen only among those with systolic dysfunction. Conclusions Treatment with sacubitril-valsartan is more effective at reducing death and admission to the hospital for heart failure compared with ACEIs/ARBs similarly among men and women with systolic dysfunction; sex differences in the effectiveness of sacubitril-valsartan in diastolic dysfunction requires further investigation.


Asunto(s)
Antagonistas de Receptores de Angiotensina , Insuficiencia Cardíaca , Femenino , Humanos , Masculino , Inhibidores de la Enzima Convertidora de Angiotensina/efectos adversos , Caracteres Sexuales , Tetrazoles/efectos adversos , Volumen Sistólico/fisiología , Valsartán , Insuficiencia Cardíaca/diagnóstico , Insuficiencia Cardíaca/tratamiento farmacológico , Compuestos de Bifenilo/farmacología , Combinación de Medicamentos , Resultado del Tratamiento
3.
BMJ Open ; 12(7): e053039, 2022 07 21.
Artículo en Inglés | MEDLINE | ID: mdl-35863836

RESUMEN

INTRODUCTION: Pneumocystis jirovecii pneumonia (PJP) is an opportunistic infection of immunocompromised hosts with significant morbidity and mortality. The current standard of care, trimethoprim-sulfamethoxazole (TMP-SMX) at a dose of 15-20 mg/kg/day, is associated with serious adverse drug events (ADE) in 20%-60% of patients. ADEs include hypersensitivity reactions, drug-induced liver injury, cytopenias and renal failure, all of which can be treatment limiting. In a recent meta-analysis of observational studies, reduced dose TMP-SMX for the treatment of PJP was associated with fewer ADEs, without increased mortality. METHODS AND ANALYSIS: A phase III randomised, placebo-controlled, trial to directly compare the efficacy and safety of low-dose TMP-SMX (10 mg/kg/day of TMP) with the standard of care (15 mg/kg/day of TMP) among patients with PJP, for a composite primary outcome of change of treatment, new mechanical ventilation, or death. The trial will be undertaken at 16 Canadian hospitals. Data will be analysed as intention to treat. Primary and secondary outcomes will be compared using logistic regression adjusting for stratification and presented with 95% CI. ETHICS AND DISSEMINATION: This study has been conditionally approved by the McGill University Health Centre; Ethics approval will be obtained from all participating centres. Results will be submitted for publication in a peer-reviewed journal. TRIAL REGISTRATION NUMBER: NCT04851015.


Asunto(s)
Pneumocystis carinii , Neumonía por Pneumocystis , Canadá , Ensayos Clínicos Fase III como Asunto , Humanos , Neumonía por Pneumocystis/inducido químicamente , Neumonía por Pneumocystis/tratamiento farmacológico , Ensayos Clínicos Controlados Aleatorios como Asunto , Estudios Retrospectivos , Combinación Trimetoprim y Sulfametoxazol/efectos adversos
4.
Clin Microbiol Infect ; 28(9): 1203-1210, 2022 Sep.
Artículo en Inglés | MEDLINE | ID: mdl-35598856

RESUMEN

BACKGROUND: The benefits of remdesivir in the treatment of hospitalized patients with COVID-19 remain debated with the National Institutes of Health and the World Health Organization providing contradictory recommendations for and against use. OBJECTIVES: To evaluate the role of remdesivir for hospitalized inpatients as a function of oxygen requirements. DATA SOURCES: Beginning with our prior systematic review, we searched MEDLINE using PubMed from 15 January 2021 through 5 May 2022. STUDY ELIGIBILITY CRITERIA: Randomised controlled trials; all languages. PARTICIPANTS: All hospitalized adults with COVID-19. INTERVENTIONS: Remdesivir, in comparison to either placebo, or standard of care. ASSESSMENT OF RISK OF BIAS: We used the ROB-2 criteria. METHODS OF DATA SYNTHESIS: The primary outcome was mortality, stratified by oxygen use (none, supplemental oxygen without mechanical ventilation, and mechanical ventilation). We conducted a frequentist random effects meta-analysis on the risk ratio scale and, to contextualize the probabilistic benefits, we also performed a Bayesian random effects meta-analysis on the risk difference scale. A ≥1% absolute risk reduction was considered clinically important. RESULTS: We identified eight randomized trials, totaling 10 751 participants. The risk ratio for mortality comparing remdesivir vs. control was 0.77 (95% CI, 0.5-1.19) in the patients who did not require supplemental oxygen; 0.89 (95% CI, 0.79-0.99) for nonventilated patients requiring oxygen; and 1.08 (95% CI, 0.88-1.31) in the setting of mechanical ventilation. Using neutral priors, the probabilities that remdesivir reduces mortality were 76.8%, 93.8%, and 14.7%, respectively. The probability that remdesivir reduced mortality by ≥ 1% was 77.4% for nonventilated patients requiring oxygen. CONCLUSIONS: Based on this meta-analysis, there is a high probability that remdesivir reduces mortality for nonventilated patients with COVID-19 requiring supplemental oxygen therapy. Treatment guidelines should be re-evaluated.


Asunto(s)
Tratamiento Farmacológico de COVID-19 , Adenosina Monofosfato/análogos & derivados , Adulto , Alanina/análogos & derivados , Teorema de Bayes , Humanos , Oxígeno , SARS-CoV-2 , Estados Unidos
6.
CMAJ Open ; 9(1): E189-E200, 2021.
Artículo en Inglés | MEDLINE | ID: mdl-33688027

RESUMEN

BACKGROUND: Burnout among postgraduate medical trainees (PMTs) is increasingly being recognized as a crisis in the medical profession. We aimed to establish the prevalence of burnout among PMTs, identify risk and protective factors, and assess whether burnout varied by country of training, year of study and specialty of practice. METHODS: We systematically searched MEDLINE, Embase, PsycINFO, the Cochrane Database of Systematic Reviews, Web of Science and Education Resources Information Center from their inception to Aug. 21, 2018, for studies of burnout among PMTs. The primary objective was to identify the global prevalence of burnout among PMTs. Our secondary objective was to evaluate the association between burnout and country of training, year of study, specialty of training and other sociodemographic factors commonly thought to be related to burnout. We employed random-effects meta-analysis and meta-regression techniques to estimate a pooled prevalence and conduct secondary analyses. RESULTS: In total, 8505 published studies were screened, 196 met eligibility and 114 were included in the meta-analysis. The pooled prevalence of burnout was 47.3% (95% confidence interval 43.1% to 51.5%), based on studies published over 20 years involving 31 210 PMTs from 47 countries. The prevalence of burnout remained unchanged over the past 2 decades. Burnout varied by region, with PMTs of European countries experiencing the lowest level. Burnout rates among medical and surgical PMTs were similar. INTERPRETATION: Current wellness efforts and policies have not changed the prevalence of burnout worldwide. Future research should focus on understanding systemic factors and leveraging these findings to design interventions to combat burnout. STUDY REGISTRATION: PROSPERO no. CRD42018108774.


Asunto(s)
Agotamiento Profesional/epidemiología , Internado y Residencia , África/epidemiología , Asia/epidemiología , Australia/epidemiología , Europa (Continente)/epidemiología , Humanos , Satisfacción en el Trabajo , Medio Oriente/epidemiología , América del Norte/epidemiología , Admisión y Programación de Personal , Prevalencia , Factores Protectores , Factores de Riesgo , América del Sur/epidemiología
7.
Open Forum Infect Dis ; 8(12): ofab545, 2021 Dec.
Artículo en Inglés | MEDLINE | ID: mdl-34988242

RESUMEN

Pneumocystis jirovecii pneumonia (PCP) is a common opportunistic infection causing more than 400000 cases annually worldwide. Although antiretroviral therapy has reduced the burden of PCP in persons with human immunodeficiency virus (HIV), an increasing proportion of cases occur in other immunocompromised populations. In this review, we synthesize the available randomized controlled trial (RCT) evidence base for PCP treatment. We identified 14 RCTs that were conducted 25-35 years ago, principally in 40-year-old men with HIV. Trimethoprim-sulfamethoxazole, at a dose of 15-20 mg/kg per day, is the treatment of choice based on historical practice rather than on quality comparative, dose-finding studies. Treatment duration is similarly based on historical practice and is not evidence based. Corticosteroids have a demonstrated role in hypoxemic patients with HIV but have yet to be studied in RCTs as an adjunctive therapy in non-HIV populations. The echinocandins are potential synergistic treatments in need of further investigation.

8.
J Clin Epidemiol ; 79: 130-139, 2016 11.
Artículo en Inglés | MEDLINE | ID: mdl-27387965

RESUMEN

OBJECTIVE: To assess the frequency and features of secondary publications of randomized controlled trials (RCTs). STUDY DESIGN AND SETTING: For 191 RCTs published in high-impact journals in 2009, we searched for secondary publications coauthored by at least one same author of the primary trial publication. We evaluated the probability of having secondary publications, characteristics of the primary trial publication that predict having secondary publications, types of secondary analyses conducted, and statistical significance of those analyses. RESULTS: Of 191 primary trials, 88 (46%) had a total of 475 secondary publications by 2/2014. Eight trials had >10 (up to 51) secondary publications each. In multivariable modeling, the risk of having subsequent secondary publications increased 1.32-fold (95% CI 1.05-1.68) per 10-fold increase in sample size, and 1.71-fold (95% CI 1.19-2.45) in the presence of a design article. In a sample of 197 secondary publications examined in depth, 193 tested different hypotheses than the primary publication. Of the 193, 43 tested differences between subgroups, 85 assessed predictive factors associated with an outcome of interest, 118 evaluated different outcomes than the original article, 71 had differences in eligibility criteria, and 21 assessed different durations of follow-up; 176 (91%) presented at least one analysis with statistically significant results. CONCLUSIONS: Approximately half of randomized trials in high-impact journals have secondary publications published with a few trials followed by numerous secondary publications. Almost all of these publications report some statistically significant results.


Asunto(s)
Publicaciones Periódicas como Asunto/estadística & datos numéricos , Ensayos Clínicos Controlados Aleatorios como Asunto/estadística & datos numéricos , Humanos
9.
Diabetes Res Clin Pract ; 117: 28-31, 2016 Jul.
Artículo en Inglés | MEDLINE | ID: mdl-27329019

RESUMEN

Incretin-based therapies are normally prescribed to individuals with type 2 diabetes but has recently come under scrutiny due to the possibility of associated pancreatitis. A 2014 systematic review published in the BMJ found no increase risk of acute pancreatitis in adults with type 2 diabetes, as partly evident from the meta-analysis of RCTs (OR=1.11, 95% CI 0.57-2.17). By contrast, a second meta-analysis added 3 large outcome trials in patients with previous cardiovascular disease to the previous 55 RCTs from Li et al. and showed an increased risk in acute pancreatitis. While the discrepancy in result may be due to better quality large trials, as the authors suggest, it is likely that since the large outcome trials investigated patients with cardiovascular disease, the increased risk is present only in this group.


Asunto(s)
Enfermedades Cardiovasculares/complicaciones , Diabetes Mellitus Tipo 2/tratamiento farmacológico , Hipoglucemiantes/efectos adversos , Incretinas/efectos adversos , Pancreatitis/etiología , Adulto , Enfermedades Cardiovasculares/fisiopatología , Ensayos Clínicos como Asunto , Humanos , Metaanálisis como Asunto , Pancreatitis/patología , Factores de Riesgo
10.
BMC Cardiovasc Disord ; 16: 91, 2016 May 11.
Artículo en Inglés | MEDLINE | ID: mdl-27169565

RESUMEN

BACKGROUND: The effect of glucagon-like peptide-1(GLP-1) receptor agonists on heart failure remains uncertain. We therefore conducted a systematic review to assess the possible impact of GLP-1 agonists on heart failure or hospitalization for heart failure in patients with type 2 diabetes. METHODS: We searched MEDLINE, EMBASE, the Cochrane Central Register of Controlled Trials (CENTRAL) and ClinicalTrials.gov to identify randomized controlled trials (RCTs) and observational studies that addressed the effect of GLP-1 receptor agonists in adults with type 2 diabetes, and explicitly reported heart failure or hospitalization for heart failure. Two paired reviewers screened reports, collected data, and assessed the risk of bias. We pooled data from RCTs and observational studies separately, and used the GRADE approach to rate the quality of evidence. RESULTS: We identified 25 studies that were eligible for our review; 21 RCTs (n = 18,270) and 4 observational studies (n = 111,029). Low quality evidence from 20 RCTs suggested, if anything, a lower incidence of heart failure between GLP-1 agonists versus control (17/7,441 vs. 19/4,317; odds ratio (OR) 0.62, 95 % confidence interval (CI) 0.31 to 1.22; risk difference (RD) 19 fewer, 95 % CI 34 fewer to 11 more per 1000 over 5 years). Three cohort studies comparing GLP-1 agonists to alternative agents provided very low quality evidence that GLP-1 agonists do not increase the incidence of heart failure. One RCT provided moderate quality evidence that GLP-1 agonists were not associated with hospitalization for heart failure (lixisenatide vs placebo: 122/3,034 vs. 127/3,034; adjusted hazard ratio 0.96, 95 % CI 0.75 to 1.23; RD 4 fewer, 95 % CI 25 fewer to 23 more per 1000 over 5 years) and a case-control study provided very low quality evidence also suggesting no association (GLP-1 agonists vs. other anti-hyperglycemic drugs: 1118 cases and 17,626 controls, adjusted OR 0.67, 95 % CI 0.32 to 1.42). CONCLUSIONS: The current evidence suggests that GLP-1 agonists do not increase the risk of heart failure or hospitalization for heart failure among patients with type 2 diabetes.


Asunto(s)
Diabetes Mellitus Tipo 2/tratamiento farmacológico , Receptor del Péptido 1 Similar al Glucagón/agonistas , Insuficiencia Cardíaca/etiología , Hipoglucemiantes/uso terapéutico , Animales , Distribución de Chi-Cuadrado , Diabetes Mellitus Tipo 2/complicaciones , Diabetes Mellitus Tipo 2/diagnóstico , Diabetes Mellitus Tipo 2/mortalidad , Receptor del Péptido 1 Similar al Glucagón/metabolismo , Insuficiencia Cardíaca/diagnóstico , Insuficiencia Cardíaca/mortalidad , Hospitalización , Humanos , Hipoglucemiantes/efectos adversos , Estudios Observacionales como Asunto , Oportunidad Relativa , Ensayos Clínicos Controlados Aleatorios como Asunto , Medición de Riesgo , Factores de Riesgo , Factores de Tiempo , Resultado del Tratamiento
11.
PLoS One ; 11(4): e0152107, 2016.
Artículo en Inglés | MEDLINE | ID: mdl-27049325

RESUMEN

BACKGROUND: Metabolic abnormalities that lead to type 2 diabetes mellitus begin in early childhood. OBJECTIVES: We investigate whether common genetic variants identified in adults have an effect on glucose in early life. METHODS: 610 newborns, 463 mothers, and 366 fathers were included in the present study. Plasma glucose and anthropometric characteristics were collected at birth, 3, and 5 years. After quality assessment, 37 SNPs, which have demonstrated an association with fasting plasma glucose at the genome-wide threshold in adults, were studied. Quantitative trait disequilibrium tests and mixed-effects regressions were conducted to estimate an effect of the SNPs on glucose. RESULTS: Risk alleles for 6 loci increased glucose levels from birth to 5 years of age (ADCY5, ADRA2A, CDKAL1, CDKN2A/B, GRB10, and TCF7L2, 4.85x10-3 ≤ P ≤ 4.60x10-2). Together, these 6 SNPs increase glucose by 0.05 mmol/L for each risk allele in a genotype score (P = 6.33x10-5). None of the associations described in the present study have been reported previously in early childhood. CONCLUSION: Our data support the notion that a subset of loci contributing to plasma glucose variation in adults has an effect at birth and in early life.


Asunto(s)
Alelos , Glucemia/análisis , Predisposición Genética a la Enfermedad , Adenilil Ciclasas/genética , Adulto , Preescolar , Quinasa 5 Dependiente de la Ciclina/genética , Inhibidor p15 de las Quinasas Dependientes de la Ciclina/genética , Diabetes Mellitus Tipo 2/genética , Femenino , Proteína Adaptadora GRB10/genética , Genes p16 , Humanos , Lactante , Recién Nacido , Masculino , Polimorfismo de Nucleótido Simple , Sitios de Carácter Cuantitativo , Receptores Adrenérgicos alfa 2/genética , ARNt Metiltransferasas
12.
BMJ ; 352: i610, 2016 Feb 17.
Artículo en Inglés | MEDLINE | ID: mdl-26888822

RESUMEN

OBJECTIVES: To examine the association between dipeptidyl peptidase-4 (DPP-4) inhibitors and the risk of heart failure or hospital admission for heart failure in patients with type 2 diabetes. DESIGN: Systematic review and meta-analysis of randomised and observational studies. DATA SOURCES: Medline, Embase, Cochrane Central Register of Controlled Trials, and ClinicalTrials.gov searched up to 25 June 2015, and communication with experts. ELIGIBILITY CRITERIA: Randomised controlled trials, non-randomised controlled trials, cohort studies, and case-control studies that compared DPP-4 inhibitors against placebo, lifestyle modification, or active antidiabetic drugs in adults with type 2 diabetes, and explicitly reported the outcome of heart failure or hospital admission for heart failure. DATA COLLECTION AND ANALYSIS: Teams of paired reviewers independently screened for eligible studies, assessed risk of bias, and extracted data using standardised, pilot tested forms. Data from trials and observational studies were pooled separately; quality of evidence was assessed by the GRADE approach. RESULTS: Eligible studies included 43 trials (n=68,775) and 12 observational studies (nine cohort studies, three nested case-control studies; n=1,777,358). Pooling of 38 trials reporting heart failure provided low quality evidence for a possible similar risk of heart failure between DPP-4 inhibitor use versus control (42/15,701 v 33/12,591; odds ratio 0.97 (95% confidence interval 0.61 to 1.56); risk difference 2 fewer (19 fewer to 28 more) events per 1000 patients with type 2 diabetes over five years). The observational studies provided effect estimates generally consistent with trial findings, but with very low quality evidence. Pooling of the five trials reporting admission for heart failure provided moderate quality evidence for an increased risk in patients treated with DPP-4 inhibitors versus control (622/18,554 v 552/18,474; 1.13 (1.00 to 1.26); 8 more (0 more to 16 more)). The pooling of adjusted estimates from observational studies similarly suggested (with very low quality evidence) a possible increased risk of admission for heart failure (adjusted odds ratio 1.41, 95% confidence interval 0.95 to 2.09) in patients treated with DPP-4 inhibitors (exclusively sitagliptin) versus no use. CONCLUSIONS: The relative effect of DPP-4 inhibitors on the risk of heart failure in patients with type 2 diabetes is uncertain, given the relatively short follow-up and low quality of evidence. Both randomised controlled trials and observational studies, however, suggest that these drugs may increase the risk of hospital admission for heart failure in those patients with existing cardiovascular diseases or multiple risk factors for vascular diseases, compared with no use.


Asunto(s)
Diabetes Mellitus Tipo 2/tratamiento farmacológico , Inhibidores de la Dipeptidil-Peptidasa IV/efectos adversos , Insuficiencia Cardíaca/inducido químicamente , Hipoglucemiantes/efectos adversos , Enfermedades Cardiovasculares/complicaciones , Inhibidores de la Dipeptidil-Peptidasa IV/uso terapéutico , Hospitalización/estadística & datos numéricos , Humanos , Hipoglucemiantes/uso terapéutico , Estudios Observacionales como Asunto , Oportunidad Relativa , Ensayos Clínicos Controlados Aleatorios como Asunto , Factores de Riesgo
13.
BMC Genet ; 16: 50, 2015 May 15.
Artículo en Inglés | MEDLINE | ID: mdl-25975208

RESUMEN

BACKGROUND: Advances in genomics technology have led to a dramatic increase in the number of published genetic association studies. Systematic reviews and meta-analyses are a common method of synthesizing findings and providing reliable estimates of the effect of a genetic variant on a trait of interest. However, summary estimates are subject to bias due to the varying methodological quality of individual studies. We embarked on an effort to develop and evaluate a tool that assesses the quality of published genetic association studies. Performance characteristics (i.e. validity, reliability, and item discrimination) were evaluated using a sample of thirty studies randomly selected from a previously conducted systematic review. RESULTS: The tool demonstrates excellent psychometric properties and generates a quality score for each study with corresponding ratings of 'low', 'moderate', or 'high' quality. We applied our tool to a published systematic review to exclude studies of low quality, and found a decrease in heterogeneity and an increase in precision of summary estimates. CONCLUSION: This tool can be used in systematic reviews to inform the selection of studies for inclusion, to conduct sensitivity analyses, and to perform meta-regressions.


Asunto(s)
Estudios de Asociación Genética/normas , Metaanálisis como Asunto , Publicaciones Periódicas como Asunto , Investigación/normas , Programas Informáticos , Humanos , Reproducibilidad de los Resultados , Navegador Web
14.
PLoS One ; 10(3): e0118925, 2015.
Artículo en Inglés | MEDLINE | ID: mdl-25742008

RESUMEN

Bioinformatics tools have gained popularity in biology but little is known about their validity. We aimed to assess the early contribution of 415 single nucleotide polymorphisms (SNPs) associated with eight cardio-metabolic traits at the genome-wide significance level in adults in the Family Atherosclerosis Monitoring In earLY Life (FAMILY) birth cohort. We used the popular web-based tool SNAP to assess the availability of the 415 SNPs in the Illumina Cardio-Metabochip genotyped in the FAMILY study participants. We then compared the SNAP output with the Cardio-Metabochip file provided by Illumina using chromosome and chromosomal positions of SNPs from NCBI Human Genome Browser (Genome Reference Consortium Human Build 37). With the HapMap 3 release 2 reference, 201 out of 415 SNPs were reported as missing in the Cardio-Metabochip by the SNAP output. However, the Cardio-Metabochip file revealed that 152 of these 201 SNPs were in fact present in the Cardio-Metabochip array (false negative rate of 36.6%). With the more recent 1000 Genomes Project release, we found a false-negative rate of 17.6% by comparing the outputs of SNAP and the Illumina product file. We did not find any 'false positive' SNPs (SNPs specified as available in the Cardio-Metabochip by SNAP, but not by the Cardio-Metabochip Illumina file). The Cohen's Kappa coefficient, which calculates the percentage of agreement between both methods, indicated that the validity of SNAP was fair to moderate depending on the reference used (the HapMap 3 or 1000 Genomes). In conclusion, we demonstrate that the SNAP outputs for the Cardio-Metabochip are invalid. This study illustrates the importance of systematically assessing the validity of bioinformatics tools in an independent manner. We propose a series of guidelines to improve practices in the fast-moving field of bioinformatics software implementation.


Asunto(s)
Biología Computacional , Genoma Humano , Programas Informáticos , Genotipo , Humanos , Polimorfismo de Nucleótido Simple
15.
JAMA ; 312(10): 1024-32, 2014 Sep 10.
Artículo en Inglés | MEDLINE | ID: mdl-25203082

RESUMEN

IMPORTANCE: Reanalyses of randomized clinical trial (RCT) data may help the scientific community assess the validity of reported trial results. OBJECTIVES: To identify published reanalyses of RCT data, to characterize methodological and other differences between the original trial and reanalysis, to evaluate the independence of authors performing the reanalyses, and to assess whether the reanalysis changed interpretations from the original article about the types or numbers of patients who should be treated. DESIGN: We completed an electronic search of MEDLINE from inception to March 9, 2014, to identify all published studies that completed a reanalysis of individual patient data from previously published RCTs addressing the same hypothesis as the original RCT. Four data extractors independently screened articles and extracted data. MAIN OUTCOMES AND MEASURES: Changes in direction and magnitude of treatment effect, statistical significance, and interpretation about the types or numbers of patients who should be treated. RESULTS: We identified 37 eligible reanalyses in 36 published articles, 5 of which were performed by entirely independent authors (2 based on publicly available data and 2 on data that were provided on request; data availability was unclear for 1). Reanalyses differed most commonly in statistical or analytical approaches (n = 18) and in definitions or measurements of the outcome of interest (n = 12). Four reanalyses changed the direction and 2 changed the magnitude of treatment effect, whereas 4 led to changes in statistical significance of findings. Thirteen reanalyses (35%) led to interpretations different from that of the original article, 3 (8%) showing that different patients should be treated; 1 (3%), that fewer patients should be treated; and 9 (24%), that more patients should be treated. CONCLUSIONS AND RELEVANCE: A small number of reanalyses of RCTs have been published to date. Only a few were conducted by entirely independent authors. Thirty-five percent of published reanalyses led to changes in findings that implied conclusions different from those of the original article about the types and number of patients who should be treated.


Asunto(s)
Interpretación Estadística de Datos , Ensayos Clínicos Controlados Aleatorios como Asunto , Humanos
16.
Diabetologia ; 57(11): 2270-81, 2014 Nov.
Artículo en Inglés | MEDLINE | ID: mdl-25145545

RESUMEN

AIMS/HYPOTHESIS: South Asians are up to four times more likely to develop type 2 diabetes than white Europeans. It is postulated that the higher prevalence results from greater genetic risk. To evaluate this hypothesis, we: (1) systematically reviewed the literature for single nucleotide polymorphisms (SNPs) predisposing to type 2 diabetes in South Asians; (2) compared risk estimates, risk alleles and risk allele frequencies of predisposing SNPs between South Asians and white Europeans; and (3) tested the association of novel SNPs discovered from South Asians in white Europeans. METHODS: MEDLINE, Embase, the Cumulative Index to Nursing and Allied Health Literature (CINAHL) and the Cochrane registry were searched for studies of genetic variants associated with type 2 diabetes in South Asians. Meta-analysis estimates for common and novel bi-allelic SNPs in South Asians were compared with white Europeans from the DIAbetes Genetics Replication And Meta-analysis (DIAGRAM) consortium. The population burden from predisposing SNPs was assessed using a genotype score. RESULTS: Twenty-four SNPs from 21 loci were associated with type 2 diabetes in South Asians after meta-analysis. The majority of SNPs increase odds of the disorder by 15-35% per risk allele. No substantial differences appear to exist in risk estimates between South Asians and white Europeans from SNPs common to both groups, and the population burden also does not differ. Eight of the 24 are novel SNPs discovered from South Asian genome-wide association studies, some of which show nominal associations with type 2 diabetes in white Europeans. CONCLUSIONS/INTERPRETATION: Based on current literature there is no strong evidence to indicate that South Asians possess a greater genetic risk of type 2 diabetes than white Europeans.


Asunto(s)
Diabetes Mellitus Tipo 2/epidemiología , Diabetes Mellitus Tipo 2/genética , Heterogeneidad Genética , Pueblo Asiatico , Europa (Continente) , Predisposición Genética a la Enfermedad/genética , Estudio de Asociación del Genoma Completo , Humanos , Polimorfismo de Nucleótido Simple/genética , Población Blanca/genética
17.
J Asthma ; 48(9): 952-6, 2011 Nov.
Artículo en Inglés | MEDLINE | ID: mdl-22014007

RESUMEN

OBJECTIVE: Induced sputum is used to assess markers of inflammation in asthmatic individuals, and sputum cell differential counts provide an outcome to evaluate the presence, type, and degree of inflammation in the airways. Contamination of sputum slides with squamous epithelial cells (SECs) has been reported to adversely affect the reproducibility of sputum cell differential counts; however, this has not been studied in a controlled manner. Excluding sputum slides because of excessive squamous cell contamination can be problematic resulting in under-powering of studies. The aim of this study is to evaluate the effect of SEC contamination and cell dispersion on the reproducibility of differential counts of sputum cells prepared on glass slides. STUDY DESIGN: A total of 33 sputum samples were induced from 11 subjects with mild asthma under baseline conditions and following an allergen inhalation challenge. Mucoid and salivary portions of each sample were divided and processed in parallel. To evaluate the effect of increasing the proportion of SEC and to evaluate the effect of increasing the number of leukocytes per high power field (HPF), four slides with varying leukocyte numbers and SEC percentages were prepared from each sample by combining and adjusting the volume of cell suspensions derived from mucous and saliva. The four slides were prepared to fall in the following categories: (A) 50 cells/HPF and <20% SEC; (B) 50 cells/HPF and >20% SEC; (C) 100 cells/HPF and <20% SEC; and (D) 100 cells/HPF and >20% SEC. All slides were blinded and counted twice by an experienced observer, and twice by an inexperienced observer. RESULTS: The differential cell counts for eosinophils, macrophages, and neutrophils were highly reproducible under all conditions when enumerated by an experienced observer (ICC > 0.9), and furthermore, SEC contamination did not affect ICC when differential counts were enumerated by an inexperienced observer (ICC > 0.8). CONCLUSION: Our results demonstrate that slides containing SECs, up to 40% in this study, have reproducible differential cell counts.


Asunto(s)
Asma/patología , Células Epiteliales , Esputo/citología , Adulto , Recuento de Células , Femenino , Humanos , Masculino , Persona de Mediana Edad , Reproducibilidad de los Resultados , Adulto Joven
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