Addressing challenges in the production and analysis of illumina sequencing data

Advances in DNA sequencing technologies have made it possible to generate large amounts of sequence data very rapidly and at substantially lower cost than capillary sequencing. These new technologies have specific characteristics and limitations that require either consideration during project design, or which must be addressed during data analysis. Specialist skills, both at the laboratory and the computational stages of project design and analysis, are crucial to the generation of high quality data from these new platforms. The Illumina sequencers (including the Genome Analyzers I/II/IIe/IIx and the new HiScan and HiSeq) represent a widely used platform providing parallel readout of several hundred million immobilized sequences using fluorescent-dye reversible-terminator chemistry. Sequencing library quality, sample handling, instrument settings and sequencing chemistry have a strong impact on sequencing run quality. The presence of adapter chimeras and adapter sequences at the end of short-insert molecules, as well as increased error rates and short read lengths complicate many computational analyses. We discuss here some of the factors that influence the frequency and severity of these problems and provide solutions for circumventing these. Further, we present a set of general principles for good analysis practice that enable problems with sequencing runs to be identified and dealt with

Failure to Recognize Nontuberculous Mycobacteria Leads to Misdiagnosis of Chronic Pulmonary Tuberculosis

BACKGROUND: Nontuberculous mycobacterial (NTM) infections cause morbidity worldwide. They are difficult to diagnose in resource-limited regions, and most patients receive empiric treatment for tuberculosis (TB). Our objective here is to evaluate the potential impact of NTM diseases among patients treated presumptively for tuberculosis in Mali. METHODS: We re-evaluated sputum specimens among patients newly diagnosed with TB (naïve) and those previously treated for TB disease (chronic cases). Sputum microscopy, culture and Mycobacterium tuberculosis drug susceptibility testing were performed. Identification of strains was performed using molecular probes or sequencing of secA1 and/or 16S rRNA genes. RESULTS: Of 142 patients enrolled, 61 (43%) were clinically classified as chronic cases and 17 (12%) were infected with NTM. Eleven of the 142 (8%) patients had NTM disease alone (8 M. avium, 2 M. simiae and 1 M. palustre). All these 11 were from the chronic TB group, comprising 11/61 (18%) of that group and all were identified as candidates for second line treatment. The remaining 6/17 (35.30%) NTM infected patients had coinfection with M. tuberculosis and all 6 were from the TB treatment naïve group. These 6 were candidates for the standard first line treatment regimen of TB. M. avium was identified in 11 of the 142 (8%) patients, only 3/11 (27.27%) of whom were HIV positive. CONCLUSIONS: NTM infections should be considered a cause of morbidity in TB endemic environments especially when managing chronic TB cases to limit morbidity and provide appropriate treatment

Games of Incomplete Information and Myopic Equilibria

A new concept of an equilibrium in games is introduced that solves an open question posed by A. Neyman

Association of parents' nutritional status, and sociodemographic and dietary factors with overweight/obesity in schoolchildren 7 to 14 years old Associação entre estado nutricional dos pais, variáveis sociodemográficas e dietéticas e o sobrepeso/obesidade em escolares de 7 a 14 anos

To assess the association of parents' nutritional status, and dietary and sociodemographic factors with overweight/obesity in schoolchildren in Florianópolis Island, Santa Catarina State, Brazil, this cross-sectional epidemiological study examined 2,826 schoolchildren 7 to 14 years old, classified according to body mass index curves for age and sex recommended by the International Obesity Task Force. Data were analyzed using Poisson regression. The final model showed overweight/obesity in boys associated directly with father's educational level, mother's age, and parents' nutritional status, and inversely with mother's educational level, and number of daily meals. Among girls, it associated directly with parents' nutritional status and the schoolchildren's age, and inversely with consumption of risk foods. The variables that associated with overweight/obesity differed between the sexes, except parents' nutritional status. Boys and girls with both parents overweight or obese were, respectively, 80% and 150% more likely to exhibit the same diagnosis, indicating the need for interventions that include the family environment.<br>O objetivo deste estudo foi analisar a associação entre estado nutricional dos pais, variáveis sociodemográficas, dietéticas e o sobrepeso/obesidade em escolares de 7-14 anos de Florianópolis, Santa Catarina, Brasil. Estudo transversal com 2.826 escolares, classificados com base nas curvas de índice de massa corporal para idade e sexo segundo a International Obesity Task Force. Para as análises utilizou-se a Regressão de Poisson. No modelo final, mostraram associação direta ao sobrepeso/obesidade em meninos: escolaridade do pai, idade da mãe e estado nutricional dos pais; e inversa: escolaridade da mãe e número de refeições diárias. Entre as meninas houve associação direta com estado nutricional dos pais, e inversa com idade do escolar e consumo de alimentos de risco. As variáveis associadas ao sobrepeso/obesidade diferiram entre os sexos, com exceção do estado nutricional dos pais. Filhos e filhas de ambos os pais com sobrepeso/obesidade têm risco cerca de, respectivamente, 80% e 150% maior de apresentar o mesmo diagnóstico, indicando a necessidade de intervenções também no ambiente familiar

The Unique Challenges Facing HIV-Positive Patients Who Smoke Cigarettes: HIV Viremia, Art Adherence, Engagement in HIV care, and Concurrent Substance Use

Evidence suggests that smoking may have negative associations with HIV health outcomes. The smoking rate in our sample of people living with HIV (N = 333) was triple that of the general population (57% v. 19%). Regression analyses revealed that smokers (v. non-smokers) reported lower medication adherence (unstandardized beta = 9.01) and were more likely to have a detectable viral load (OR = 2.85, 95%CI [1.53–5.30]). Smokers attended fewer routine medical visits (β = −0.16) and were more likely to report recent hospitalization (OR = 1.89, 95%CI [0.99, 3.57]). Smokers ranked “health” as less important to their quality of life (β = −0.13) and were more likely to report problematic alcohol (OR = 2.40, 95%CI [1.35, 4.30]), cocaine (OR = 2.87, 95%CI [1.48–5.58]), heroin (OR = 4.75, 95%CI [1.01, 22.30]), or marijuana use (OR = 3.08, 95%CI [1.76–5.38]). Findings underscore the need for integrated behavioral smoking cessation interventions and routine tobacco screenings in HIV primary care