Intradetrusor onabotulinumtoxinA injections are significantly more efficacious than oral oxybutynin for treatment of neurogenic detrusor overactivity: results of a randomized, controlled, 24-week trial.

OBJECTIVE: To prospectively compare the results of intradetrusor onabotulinumtoxinA injections and oral oxybutynin for urinary continence, urodynamic parameters and quality of life in patients with neurogenic detrusor overactivity due to spinal cord injury. METHODS: Adult patients under intermittent catheterization were randomized 1:1 to receive one injection of onabotulinumtoxinA 300U or oxybutynin 5mg, per oris, three times/day. Primary study endpoint was change in urinary incontinence episodes/24 hours and secondary study endpoints were maximum cystometric capacity, maximum detrusor pressure, bladder compliance and quality of life before randomization and at week 24. RESULTS: Sixty-eight patients participated in the trial. Significant improvements in urinary incontinence per 24 hours, all investigated urodynamic parameters and quality of life were observed in both groups. Compared with oral oxybutynin, onabotulinumtoxinA was significantly more efficacious for all parameters investigated. Non-response to treatment was higher for oral oxybutynin (23.5%) than onabotulinumtoxinA (11.8%). Dry mouth was the most common adverse in patients with oral oxybutynin (72%) and transient macroscopic hematuria in patients with onabotulinumtoxinA (28%). Only one patient with oral oxybutynin dropped out the study because of adverse effects. CONCLUSION: The comparison of the two study drugs showed that onabotulinumtoxinA was significantly more efficacious than oral oxybutynin with regard to continence, urodynamic parameters and quality of life. Clinicaltrials.gov: NCT:01477736.

Characterizing reduced coverage regions through comparison of exome and genome sequencing data across 10 centers.

PURPOSE: As massively parallel sequencing is increasingly being used for clinical decision making, it has become critical to understand parameters that affect sequencing quality and to establish methods for measuring and reporting clinical sequencing standards. In this report, we propose a definition for reduced coverage regions and describe a set of standards for variant calling in clinical sequencing applications. METHODS: To enable sequencing centers to assess the regions of poor sequencing quality in their own data, we optimized and used a tool (ExCID) to identify reduced coverage loci within genes or regions of particular interest. We used this framework to examine sequencing data from 500 patients generated in 10 projects at sequencing centers in the National Human Genome Research Institute/National Cancer Institute Clinical Sequencing Exploratory Research Consortium. RESULTS: This approach identified reduced coverage regions in clinically relevant genes, including known clinically relevant loci that were uniquely missed at individual centers, in multiple centers, and in all centers. CONCLUSION: This report provides a process road map for clinical sequencing centers looking to perform similar analyses on their data.

Intradetrusor onabotulinumtoxinA injections are significantly more efficacious than oral oxybutynin for treatment of neurogenic detrusor overactivity: results of a randomized, controlled, 24-week trial / Injeções intradetrusoras de onabotulinumtoxinA são significativamente mais eficazes que oxibutinina oral para tratamento da hiperatividade detrusora neurogênica: resultados de estudo randomizado e controlado de 24 semanas

ABSTRACT Objective To prospectively compare the results of intradetrusor onabotulinumtoxinA injections and oral oxybutynin for urinary continence, urodynamic parameters and quality of life in patients with neurogenic detrusor overactivity due to spinal cord injury. Methods Adult patients under intermittent catheterization were randomized 1:1 to receive one injection of onabotulinumtoxinA 300U or oxybutynin 5mg, per oris, three times/day. Primary study endpoint was change in urinary incontinence episodes/24 hours and secondary study endpoints were maximum cystometric capacity, maximum detrusor pressure, bladder compliance and quality of life before randomization and at week 24. Results Sixty-eight patients participated in the trial. Significant improvements in urinary incontinence per 24 hours, all investigated urodynamic parameters and quality of life were observed in both groups. Compared with oral oxybutynin, onabotulinumtoxinA was significantly more efficacious for all parameters investigated. Non-response to treatment was higher for oral oxybutynin (23.5%) than onabotulinumtoxinA (11.8%). Dry mouth was the most common adverse in patients with oral oxybutynin (72%) and transient macroscopic hematuria in patients with onabotulinumtoxinA (28%). Only one patient with oral oxybutynin dropped out the study because of adverse effects. Conclusion The comparison of the two study drugs showed that onabotulinumtoxinA was significantly more efficacious than oral oxybutynin with regard to continence, urodynamic parameters and quality of life. Clinicaltrials.gov: NCT:01477736.

RESUMO Objetivo Comparar prospectivamente os resultados de injeções intradetrusoras de onabotulinumtoxinA e oxibutinina oral em pacientes com hiperatividade neurogênica do detrusor devido à lesão da medula espinhal, para avaliar a continência urinária, os parâmetros urodinâmicos e a qualidade de vida. Métodos Pacientes adultos em cateterismo intermitente foram randomizados 1:1 para tratamento com uma injeção de onabotulinumtoxinA 300U ou oxibutinina 5mg via oral, três vezes por dia. O desfecho primário foi alteração nos episódios de incontinência urinária em 24 horas, e os secundários foram capacidade cistométrica máxima, pressão máxima do detrusor, complacência vesical e qualidade de vida antes da randomização e na 24ª semana. Resultados Participaram do estudo 68 pacientes. Observou-se melhora significativa na incontinência urinária por 24 horas em todos os parâmetros urodinâmicos investigados e na qualidade de vida em ambos os grupos. Em comparação com a oxibutinina oral, a onabotulinumtoxinA foi significativamente mais eficaz para todos os parâmetros investigados. A falha no tratamento foi maior para oxibutinina oral (23,5%) em comparação com onabotulinumtoxinA (11,8%). A boca seca foi o evento adverso mais comum em pacientes tratados com oxibutinina oral (72%), e a hematúria macroscópica transitória naqueles tratados com onabotulinumtoxinA (28%). Apenas um paciente tratado com oxibutinina oral interrompeu o estudo por conta dos efeitos adversos. Conclusão A comparação dos dois fármacos do estudo mostrou que onabotulinumtoxinA foi significativamente mais eficaz que oxibutinina oral em relação a continência, parâmetros urodinâmicos e qualidade de vida. Clinicaltrials.gov: NCT:01477736.

Efeito da participação em aulas de educação física escolar sobre indicadores de crescimento, composição corporal e aptidão neuromotora em crianças / Effect of participation in classes of school physical education on indicators of growth, body composition and neuromotor fitness in children / Efecto de la participación en clases de educación física escolar sobre indicadores de crecimiento, composición corporal y aptitud neuromotora en niños

O objetivo deste estudo foi examinar os efeitos de 12 semanas de aulas de Educação Física sobre os indicadores de crescimento, composição corporal e testes neuromotores em crianças. Foram avaliados 23 indivíduos, de ambos os sexos (6 a 10 anos), quanto às variáveis antro-pométricas (massa corporal total, estatura, altura sentada, IMC e RCQ), composição corporal e testes neuromotores (força, flexibilidade e RML abdominal). Para comparação das variá-veis, a ANOVA two-way para medidas repetidas, seguida de Bonferroni, como post-hoc, e o teste t pareado foram utilizados. Foram observadas alterações significativas positivas na mas-sa corporal total, IMC, massa corporal magra e RML abdominal e uma redução significativa na RCQ (p<0,05). O envolvimento em aulas de Educação Física por um período de 12 sema-nas foi suficiente para promover alterações positivas em variáveis antropométricas, da com-posição corporal e neuromotoras em crianças de 6 a 10 anos de idade.

The aim of this study was to examine the effects of 12 weeks of physical education classes on somatic growth, body composition and neuromotor tests in children. Twenty-three (23) sub-jects of both sexes (6-10 years old) were evaluated for the anthropometric variables (weight, height, sitting height, BMI and WHR), body composition and neuromotor tests (muscle strength, flexibility and sit-up´s). For comparison of variables, two-way ANOVA for repeated measures, followed by Bonferroni, as post-hoc and paired t-test were used. Significant posi-tive results in total body mass, BMI, lean body mass and abdominal muscular endurance and a significant reduction in WHR (p<0,05) were observed.Participation in physical education classes for a period of 12 weeks was sufficient to promote positive changes in anthropometric variables, the body composition and neuromotor tests in children from 6 to 10 years.

El objetivo de este estudio fue examinar los efectos de 12 semanas de clases de Educación Física, tomando como base los indicadores de crecimiento, composición corporal y pruebas neuromotoras en niños. Se evaluaron 23 individuos, de ambos sexos (6 a 10 años), sobre las variables antropométricas (masa corporal total, estatura, altura sentada, IMC y RCQ), compo-sición corporal y pruebas neuromotoras (fuerza, flexibilidad y RML abdominal). Para la com-paración de las variables, la ANOVA two-way para medidas repetidas, seguido de Bonferroni, como post-hoc y la prueba t pareada fueron utilizados. Se observaron alteraciones significati-vas positivas en la masa corporal total, IMC, masa corporal magra y RML abdominal y una reducción significativa en la RCQ (p<0,05). La participación en clases de Educación Física durante un período de 12 semanas fue suficiente para suscitar modificaciones positivas en variables antropométricas, de la composición corporal y neuromotoras en niños de 6 a 10 años de edad.

Semiconductor-based DNA sequencing of histone modification states.

The recent development of a semiconductor-based, non-optical DNA sequencing technology promises scalable, low-cost and rapid sequence data production. The technology has previously been applied mainly to genomic sequencing and targeted re-sequencing. Here we demonstrate the utility of Ion Torrent semiconductor-based sequencing for sensitive, efficient and rapid chromatin immunoprecipitation followed by sequencing (ChIP-seq) through the application of sample preparation methods that are optimized for ChIP-seq on the Ion Torrent platform. We leverage this method for epigenetic profiling of tumour tissues.

The advantages of SMRT sequencing.

Of the current next-generation sequencing technologies, SMRT sequencing is sometimes overlooked. However, attributes such as long reads, modified base detection and high accuracy make SMRT a useful technology and an ideal approach to the complete sequencing of small genomes.

From FastQ data to high confidence variant calls: the Genome Analysis Toolkit best practices pipeline.

This unit describes how to use BWA and the Genome Analysis Toolkit (GATK) to map genome sequencing data to a reference and produce high-quality variant calls that can be used in downstream analyses. The complete workflow includes the core NGS data processing steps that are necessary to make the raw data suitable for analysis by the GATK, as well as the key methods involved in variant discovery using the GATK.

Pacific biosciences sequencing technology for genotyping and variation discovery in human data.

BACKGROUND: Pacific Biosciences technology provides a fundamentally new data type that provides the potential to overcome some limitations of current next generation sequencing platforms by providing significantly longer reads, single molecule sequencing, low composition bias and an error profile that is orthogonal to other platforms. With these potential advantages in mind, we here evaluate the utility of the Pacific Biosciences RS platform for human medical amplicon resequencing projects. RESULTS: We evaluated the Pacific Biosciences technology for SNP discovery in medical resequencing projects using the Genome Analysis Toolkit, observing high sensitivity and specificity for calling differences in amplicons containing known true or false SNPs. We assessed data quality: most errors were indels (~14%) with few apparent miscalls (~1%). In this work, we define a custom data processing pipeline for Pacific Biosciences data for human data analysis. CONCLUSION: Critically, the error properties were largely free of the context-specific effects that affect other sequencing technologies. These data show excellent utility for follow-up validation and extension studies in human data and medical genetics projects, but can be extended to other organisms with a reference genome.

Medulloblastoma exome sequencing uncovers subtype-specific somatic mutations.

Medulloblastomas are the most common malignant brain tumours in children. Identifying and understanding the genetic events that drive these tumours is critical for the development of more effective diagnostic, prognostic and therapeutic strategies. Recently, our group and others described distinct molecular subtypes of medulloblastoma on the basis of transcriptional and copy number profiles. Here we use whole-exome hybrid capture and deep sequencing to identify somatic mutations across the coding regions of 92 primary medulloblastoma/normal pairs. Overall, medulloblastomas have low mutation rates consistent with other paediatric tumours, with a median of 0.35 non-silent mutations per megabase. We identified twelve genes mutated at statistically significant frequencies, including previously known mutated genes in medulloblastoma such as CTNNB1, PTCH1, MLL2, SMARCA4 and TP53. Recurrent somatic mutations were newly identified in an RNA helicase gene, DDX3X, often concurrent with CTNNB1 mutations, and in the nuclear co-repressor (N-CoR) complex genes GPS2, BCOR and LDB1. We show that mutant DDX3X potentiates transactivation of a TCF promoter and enhances cell viability in combination with mutant, but not wild-type, ß-catenin. Together, our study reveals the alteration of WNT, hedgehog, histone methyltransferase and now N-CoR pathways across medulloblastomas and within specific subtypes of this disease, and nominates the RNA helicase DDX3X as a component of pathogenic ß-catenin signalling in medulloblastoma.

Model transcriptional networks with continuously varying expression levels.

BACKGROUND: At a time when genomes are being sequenced by the hundreds, much attention has shifted from identifying genes and phenotypes to understanding the networks of interactions among genes. We developed a gene network developmental model expanding on previous models of transcription regulatory networks. In our model, each network is described by a matrix representing the interactions between transcription factors, and a vector of continuous values representing the transcription factor expression in an individual. RESULTS: In this work we used the gene network model to look at the impact of mating as well as insertions and deletions of genes in the evolution of complexity of these networks. We found that the natural process of diploid mating increases the likelihood of maintaining complexity, especially in higher order networks (more than 10 genes). We also show that gene insertion is a very efficient way to add more genes to a network as it provides a much higher chance of developmental stability. CONCLUSIONS: The continuous model affords a more complete view of the evolution of interacting genes. The notion of a continuous output vector also incorporates the reality of gene networks and graded concentrations of gene products.

Colloquium papers: Adaptive landscapes and protein evolution.

The principles governing protein evolution under strong selection are important because of the recent history of evolved resistance to insecticides, antibiotics, and vaccines. One experimental approach focuses on studies of mutant proteins and all combinations of mutant sites that could possibly be intermediates in the evolutionary pathway to resistance. In organisms carrying each of the engineered proteins, a measure of protein function or a proxy for fitness is estimated. The correspondence between protein sequence and fitness is widely known as a fitness landscape or adaptive landscape. Here, we examine some empirical fitness landscapes and compare them with simulated landscapes in which the fitnesses are randomly assigned. We find that mutant sites in real proteins show significantly more additivity than those obtained from random simulations. The high degree of additivity is reflected in a summary statistic for adaptive landscapes known as the "roughness," which for the actual proteins so far examined lies in the smallest 0.5% tail of random landscapes.

Lesão medular no Centro de Reabilitação e Readaptação Dr. Henrique Santillo (CRER- GO) / Lesión medular en el Centro de Rehabilitación y Readaptación Dr. Henrique Santillo (CRER-GO) / Spinal cord injury in Dr. Henrique Santillo Rehabilitation and Readaptation Center (CRER-GO)

OBJETIVO: avaliação epidemiológica de pacientes com diagnóstico de lesão medular internados para reabilitação na enfermaria do Centro de Reabilitação e Readaptação Dr. Henrique Santillo (CRER) em Goiânia, Goiás. MÉTODOS: estudo epidemiológico retrospectivo baseado na coleta de dados dos prontuários médicos dos pacientes internados no período de Março de 2007 a Março de 2009. RESULTADOS: foram avaliados 208 pacientes, com predomínio do sexo masculino (78,85 por cento) e idade média de 35,3 anos. O déficit neurológico mais prevalente foi paraplegia (64,90 por cento), sendo 54,33 por cento dos pacientes classificados como ASIA A (lesão completa) de acordo com a classificação da American Spinal Injury Association (ASIA). O tempo médio de lesão até a admissão no CRER foi de 129,7 dias, e o tempo médio de internação para reabilitação destes pacientes foi de 44,9 dias. A principal etiologia da lesão medular foi traumática, sendo 44,70 por cento representadas por acidente de trânsito. A complicação mais comum na internação foi infecção do trato urinário. CONCLUSÃO: os dados epidemiológicos de pacientes com lesão medular, admitidos no CRER para reabilitação, se mostraram em conformidade com dados já descritos na literatura, demonstrando cada vez mais a importância da divulgação e realização de campanhas de prevenção do trauma raquimedular. Assim como a necessidade do encaminhamento precoce destes pacientes ao centro de reabilitação, uma vez que a grande maioria é jovem, com sequelas neurológicas graves e altamente incapacitantes.

OBJECTIVE: retrospective epidemiological analysis of spinal cord injury patients admitted to Centro de Reabilitação e Readaptação Dr. Henrique Santillo (CRER) in Goiânia, Goiás. METHODS: retrospective epidemiological study based on the analysis of medical records data of patients who were hospitalized in the period from March 2007 to March 2009. RESULTS: 208 patients were analyzed, predominantly male (78.85 percent) with a mean age of 35.3 years. The most neurological deficit was paraplegic (64.90 percent), and 54.33 percent of the patients were classified as ASIA A (complete lesion), according to the American Spinal Injury Association (ASIA). The average time from injury to admission was 129.7 days, and the mean time of hospitalization was 44.9 days. The main cause was traumatic spinal cord injury and of these, 44.70 percent were from traffic accidents. The main complication was urinary tract infection. CONCLUSION: the epidemiological data of spinal cord injury patients admitted to rehabilitation in CRER was in accordance with data already reported in literature, demonstrating the importance of dissemination and implementation campaigns for the prevention of spinal cord trauma. As well as the need for early referral of patients to a rehabilitation center, since most of them are young with severe neurological deficit and highly disabling.

OBJETIVO: evaluación epidemiológica de pacientes con diagnóstico de lesión medular internados para rehabilitación en urgencias del Centro de Rehabilitación y Readaptación Dr. Henrique Santillo (CRER) en Goiânia, Goiás. MÉTODOS: estudio epidemiológico retrospectivo con base en la recogida de datos de las historias médica de los pacientes internados en el periodo de Marzo de 2007 a Marzo de 2009. RESULTADOS: fueron evaluados 208 pacientes, con predominio de sexo masculino (78.85 por ciento), edad promedio de 35.3 años. El déficit neurológico más relevante fue paraplejia (64.90 por ciento), siendo 54.33 por ciento clasificados como ASIA A (lesión completa) de acuerdo con la clasificación de la American Spinal Injury Association (ASIA). El tiempo promedio de una lesión a la admisión en el CRER fue de 129.7 días y media estancia en el hospital para la rehabilitación de estos pacientes fue de 44.9 días. La principal etiología de la lesión medular fue traumática, siendo 44.70 por ciento representados por accidente de tráfico. La complicación más común en la internación fue infección del tracto urinario. CONCLUSIÓN: los datos epidemiológicos de pacientes con lesión medular admitidos en el CRER para rehabilitación se mostraron en conformidad con aquellos ya descritos en la literatura, demostrando cada vez mayor importancia de la divulgación y realización de campañas de prevención del trauma raquimedular. También hay necesidad de remitir de forma precoz a estos pacientes al centro de rehabilitación, una vez que la gran mayoría son pacientes jóvenes, con secuelas neurológicas graves y altamente discapacitantes.

Population genomic inferences from sparse high-throughput sequencing of two populations of Drosophila melanogaster.

Short-read sequencing techniques provide the opportunity to capture genome-wide sequence data in a single experiment. A current challenge is to identify questions that shallow-depth genomic data can address successfully and to develop corresponding analytical methods that are statistically sound. Here, we apply the Roche/454 platform to survey natural variation in strains of Drosophila melanogaster from an African (n = 3) and a North American (n = 6) population. Reads were aligned to the reference D. melanogaster genomic assembly, single nucleotide polymorphisms were identified, and nucleotide variation was quantified genome wide. Simulations and empirical results suggest that nucleotide diversity can be accurately estimated from sparse data with as little as 0.2x coverage per line. The unbiased genomic sampling provided by random short-read sequencing also allows insight into distributions of transposable elements and copy number polymorphisms found within populations and demonstrates that short-read sequencing methods provide an efficient means to quantify variation in genome organization and content. Continued development of methods for statistical inference of shallow-depth genome-wide sequencing data will allow such sparse, partial data sets to become the norm in the emerging field of population genomics.