BPG: Seamless, automated and interactive visualization of scientific data.

BACKGROUND: We introduce BPG, a framework for generating publication-quality, highly-customizable plots in the R statistical environment. RESULTS: This open-source package includes multiple methods of displaying high-dimensional datasets and facilitates generation of complex multi-panel figures, making it suitable for complex datasets. A web-based interactive tool allows online figure customization, from which R code can be downloaded for integration with computational pipelines. CONCLUSION: BPG provides a new approach for linking interactive and scripted data visualization and is available at http://labs.oicr.on.ca/boutros-lab/software/bpg or via CRAN at https://cran.r-project.org/web/packages/BoutrosLab.plotting.general.

Enhancing knowledge discovery from cancer genomics data with Galaxy.

The field of cancer genomics has demonstrated the power of massively parallel sequencing techniques to inform on the genes and specific alterations that drive tumor onset and progression. Although large comprehensive sequence data sets continue to be made increasingly available, data analysis remains an ongoing challenge, particularly for laboratories lacking dedicated resources and bioinformatics expertise. To address this, we have produced a collection of Galaxy tools that represent many popular algorithms for detecting somatic genetic alterations from cancer genome and exome data. We developed new methods for parallelization of these tools within Galaxy to accelerate runtime and have demonstrated their usability and summarized their runtimes on multiple cloud service providers. Some tools represent extensions or refinement of existing toolkits to yield visualizations suited to cohort-wide cancer genomic analysis. For example, we present Oncocircos and Oncoprintplus, which generate data-rich summaries of exome-derived somatic mutation. Workflows that integrate these to achieve data integration and visualizations are demonstrated on a cohort of 96 diffuse large B-cell lymphomas and enabled the discovery of multiple candidate lymphoma-related genes. Our toolkit is available from our GitHub repository as Galaxy tool and dependency definitions and has been deployed using virtualization on multiple platforms including Docker.

Clinical aspects of patients with sarcoglycanopathies under steroids therapy.

UNLABELLED: Patients with sarcoglycanopathies, which comprise four subtypes of autosomal recessive limb-girdle muscular dystrophies, usually present with progressive weakness leading to early loss of ambulation and premature death, and no effective treatment is currently available. OBJECTIVE: To present clinical aspects and outcomes of six children with sarcoglycanopathies treated with steroids for at least one year. METHOD: Patient files were retrospectively analyzed for steroid use. RESULTS: Stabilization of muscle strength was noted in one patient, a slight improvement in two, and a slight worsening in three. In addition, variable responses of forced vital capacity and cardiac function were observed. CONCLUSIONS: No overt clinical improvement was observed in patients with sarcoglycanopathies under steroid therapy. Prospective controlled studies including a larger number of patients are necessary to determine the effects of steroids for sarcoglycanopathies.

Clinical aspects of patients with sarcoglycanopathies under steroids therapy / Aspectos clínicos de pacientes com sarcoglicanopatias sob efeito de corticoterapia

Patients with sarcoglycanopathies, which comprise four subtypes of autosomal recessive limb-girdle muscular dystrophies, usually present with progressive weakness leading to early loss of ambulation and premature death, and no effective treatment is currently available. Objective To present clinical aspects and outcomes of six children with sarcoglycanopathies treated with steroids for at least one year. Method Patient files were retrospectively analyzed for steroid use. Results Stabilization of muscle strength was noted in one patient, a slight improvement in two, and a slight worsening in three. In addition, variable responses of forced vital capacity and cardiac function were observed. Conclusions No overt clinical improvement was observed in patients with sarcoglycanopathies under steroid therapy. Prospective controlled studies including a larger number of patients are necessary to determine the effects of steroids for sarcoglycanopathies. .

Pacientes com sarcoglicanopatias, que compreendem quatro subtipos de distrofias musculares de cinturas autossômicas recessivas, geralmente apresentam fraqueza progressiva, levando à perda precoce da deambulação e morte prematura, e não há tratamento eficaz disponível até o momento. Objetivo Descrever os aspectos clínicos e a evolução de seis crianças com sarcoglicanopatias tratados com corticosteróides por pelo menos um ano. Método Prontuários dos pacientes foram analisados retrospectivamente. Resultados Estabilização da força muscular foi observada em um paciente, uma ligeira melhora em dois, e um ligeiro agravamento em três. Além disso, foram observadas respostas variáveis de capacidade vital forçada e da função cardíaca. Conclusões Não houve melhora clínica evidente em pacientes com sarcoglicanopatias sob terapia com corticosteróides. Estudos prospectivos controlados incluindo maior número de pacientes são necessários para determinar os efeitos dos corticosteróides para sarcoglicanopatias. .

SeqControl: process control for DNA sequencing.

As high-throughput sequencing continues to increase in speed and throughput, routine clinical and industrial application draws closer. These 'production' settings will require enhanced quality monitoring and quality control to optimize output and reduce costs. We developed SeqControl, a framework for predicting sequencing quality and coverage using a set of 15 metrics describing overall coverage, coverage distribution, basewise coverage and basewise quality. Using whole-genome sequences of 27 prostate cancers and 26 normal references, we derived multivariate models that predict sequencing quality and depth. SeqControl robustly predicted how much sequencing was required to reach a given coverage depth (area under the curve (AUC) = 0.993), accurately classified clinically relevant formalin-fixed, paraffin-embedded samples, and made predictions from as little as one-eighth of a sequencing lane (AUC = 0.967). These techniques can be immediately incorporated into existing sequencing pipelines to monitor data quality in real time. SeqControl is available at http://labs.oicr.on.ca/Boutros-lab/software/SeqControl/.

Congenital muscular dystrophy with dropped head linked to the LMNA gene in a Brazilian cohort.

BACKGROUND: Congenital muscular dystrophy is a clinically and genetically heterogeneous group of myopathies. Congenital muscular dystrophy related to lamin A/C is rare and characterized by early-onset hypotonia with axial muscle weakness typically presenting with a loss in motor acquisitions within the first year of life and a dropped-head phenotype. METHODS: Here we report the clinical and histological characteristics of four unrelated Brazilian patients with dropped-head syndrome and mutations in the LMNA gene. RESULTS: All patients had previously described mutations (p.E358K, p.R249W, and p.N39S) and showed pronounced cervical muscle weakness, elevation of serum creatine kinase, dystrophic pattern on muscle biopsy, and respiratory insufficiency requiring ventilatory support. Three of the patients manifested cardiac arrhythmias, and one demonstrated a neuropathic pattern on nerve conduction study. CONCLUSION: Although lamin A/C--related congenital muscular dystrophy is a clinically distinct and recognizable phenotype, genotype/phenotype correlation, ability to anticipate onset of respiratory and cardiac involvement, and need for nutritional support remain difficult.