TCGA Expedition: A Data Acquisition and Management System for TCGA Data

Background

The Cancer Genome Atlas Project (TCGA) is a National Cancer Institute effort to profile at least 500 cases of 20 different tumor types using genomic platforms and to make these data, both raw and processed, available to all researchers. TCGA data are currently over 1.2 Petabyte in size and include whole genome sequence (WGS), whole exome sequence, methylation, RNA expression, proteomic, and clinical datasets. Publicly accessible TCGA data are released through public portals, but many challenges exist in navigating and using data obtained from these sites. We developed TCGA Expedition to support the research community focused on computational methods for cancer research. Data obtained, versioned, and archived using TCGA Expedition supports command line access at high-performance computing facilities as well as some functionality with third party tools. For a subset of TCGA data collected at University of Pittsburgh, we also re-associate TCGA data with de-identified data from the electronic health records. Here we describe the software as well as the architecture of our repository, methods for loading of TCGA data to multiple platforms, and security and regulatory controls that conform to federal best practices.

Results

TCGA Expedition software consists of a set of scripts written in Bash, Python and Java that download, extract, harmonize, version and store all TCGA data and metadata. The software generates a versioned, participant- and sample-centered, local TCGA data directory with metadata structures that directly reference the local data files as well as the original data files. The software supports flexible searches of the data via a web portal, user-centric data tracking tools, and data provenance tools. Using this software, we created a collaborative repository, the Pittsburgh Genome Resource Repository (PGRR) that enabled investigators at our institution to work with all TCGA data formats, and to interrogate these data with analysis pipelines, and associated tools. WGS data are especially challenging for individual investigators to use, due to issues with downloading, storage, and processing; having locally accessible WGS BAM files has proven invaluable.

Conclusion

Our open-source, freely available TCGA Expedition software can be used to create a local collaborative infrastructure for acquiring, managing, and analyzing TCGA data and other large public datasets.

Plasma concentrations of N-terminal brain natriuretic peptide in healthy children, adolescents, and young adults: effect of age and gender

Children with congenital heart disease need adequate diagnostic classification regarding their cardiovascular status (CVS). N-terminal brain natriuretic peptide (N-BNP) plasma concentration indicates dysfunction of the cardiovascular system and guides decisions concerning treatment and prognosis. Reference values are established for adults, with age-dependent increasing values and higher values in women. To avoid misclassification concerning the CVS, a large group of healthy children and adolescents can be used show the relationship between gender, age, and N-BNP and these can serve as reference values. N-BNP was measured in 434 healthy subjects (240 female and 194 male) with ages ranging from 0 to 32 years without any cardiovascular disease or renal or hepatic impairment. Measurements were performed with an electrochemiluminescence immunoassay from Roche Diagnostics. Mean N-BNP decreased from 12.6 fmol/ml (0-9 years; n = 79) to 9.41 fmol/ml (10-14 years; n = 154) and in adolescents from 6.1 (15-19 years; n = 99) to 4.8 fmol/ml (> 19 years; n = 102) in adults (p < 0.05). Mean N-BNP concerning gender did not differ in any age group younger than 19 years. In contrast, the adult female group had 78% higher N-BNP compared to the male group (p < 0.05). There was a significant peak in N-BNP at the age of 12-14 years. This study shows that reference values for N-BNP differed profoundly in children compared to adults and were up to 260% higher in children without any gender difference. Therefore, these reference values will help to avoid CVS misclassification in children for the biomarker N-BNP.

Evaluation of the effect of dopamine and other catecholamines on the electrocardiogram and blood pressure of rats by means of on-line biosignal processing

We compared the effects of dopamine and other catecholamines under identical conditions on electrocardiograms (ECG), heart rate, and blood pressure of rats. The experiments were carried out on anesthetized male Wistar rats weighting 330-370 g. The ECG was taken by a bipolar ECG lead in the direction of the heart axis, mean arterial pressure was measured in the carotid artery. Dopamine, adrenaline, noradrenaline, isoproterenol, and isotonic saline (control) were administered by continuous intravenous infusion. The infusion rate was increased 10-fold every 10 min starting with therapeutic dosages. All data were evaluated by continuous on-line biosignal processing. The results confirmed the well-known cardiovascular effects of the catecholamines; heart rate and mean arterial pressure increased after all adrenergic drugs except for isoproterenol, which caused a fall in pressure. In the ECG the PRc interval was significantly increased only by the highest doses of adrenaline and noradrenaline. A widening of the QRS complex was not observed during dopamine infusion, whereas it was present during adrenaline, noradrenaline, and especially, isoproterenol infusions. Taking the widening of QRS as indicative of cardiotoxic drug effects, the tested catecholamines may be arranged in the following order of cardiotoxicity; dopamine > adrenaline congruent to noradrenaline < isoproterenol.