Showing papers by "Lukas Forer published in 2015"
TL;DR: Patients with moderate CKD under specialist care have a high disease burden and improved diagnostic accuracy, rigorous management of risk factors and unravelling of the genetic predisposition may represent strategies for improving prognosis.
Abstract: Background A main challenge for targeting chronic kidney disease (CKD) is the heterogeneity of its causes, co-morbidities and outcomes. Patients under nephrological care represent an important reference population, but knowledge about their characteristics is limited.
Methods
We enrolled 5217 carefully phenotyped patients with moderate CKD [estimated glomerular filtration rate (eGFR) 30–60 mL/min per 1.73 m2 or overt proteinuria at higher eGFR] under routine care of nephrologists into the German Chronic Kidney Disease (GCKD) study, thereby establishing the currently worldwide largest CKD cohort.
Results
The cohort has 60% men, a mean age (±SD) of 60 ± 12 years, a mean eGFR of 47 ± 17 mL/min per 1.73 m2 and a median (IQR) urinary albumin/creatinine ratio of 51 (9–392) mg/g. Assessment of causes of CKD revealed a high degree of uncertainty, with the leading cause unknown in 20% and frequent suspicion of multifactorial pathogenesis. Thirty-five per cent of patients had diabetes, but only 15% were considered to have diabetic nephropathy. Cardiovascular disease prevalence was high (32%, excluding hypertension); prevalent risk factors included smoking (59% current or former smokers) and obesity (43% with BMI >30). Despite widespread use of anti-hypertensive medication, only 52% of the cohort had an office blood pressure <140/90 mmHg. Family histories for cardiovascular events (39%) and renal disease (28%) suggest familial aggregation.
Conclusions
Patients with moderate CKD under specialist care have a high disease burden. Improved diagnostic accuracy, rigorous management of risk factors and unravelling of the genetic predisposition may represent strategies for improving prognosis.
118 citations
TL;DR: This paper presents the experiences with workflows and workflow systems within the bioinformatics community participating in a series of hackathons and workshops of the EU COST action SeqAhead, and defines a set of recommendations for future systems to enable efficient yet simple bioInformatics workflow construction and execution.
Abstract: High-throughput technologies, such as next-generation sequencing, have turned molecular biology into a data-intensive discipline, requiring bioinformaticians to use high-performance computing resources and carry out data management and analysis tasks on large scale. Workflow systems can be useful to simplify construction of analysis pipelines that automate tasks, support reproducibility and provide measures for fault-tolerance. However, workflow systems can incur significant development and administration overhead so bioinformatics pipelines are often still built without them. We present the experiences with workflows and workflow systems within the bioinformatics community participating in a series of hackathons and workshops of the EU COST action SeqAhead. The organizations are working on similar problems, but we have addressed them with different strategies and solutions. This fragmentation of efforts is inefficient and leads to redundant and incompatible solutions. Based on our experiences we define a set of recommendations for future systems to enable efficient yet simple bioinformatics workflow construction and execution.
69 citations
TL;DR: The finding of shared mutations between primary tumors, recurrences and metastasis indicates a clonal origin of malignant cells in oral cancer and that NGS is capable of reliably detecting and quantifying heteroplasmies down to the 1%-level.
Abstract: Background
Oral squamous cell carcinoma (OSCC) is mainly caused by smoking and alcohol abuse and shows a five-year survival rate of ~50%. We aimed to explore the variation of somatic mitochondrial DNA (mtDNA) mutations in primary oral tumors, recurrences and metastases.
39 citations
TL;DR: In the presence of CKD there is a significant association between shorter RTL and CVD manifestations, and RTL appears to be a marker reflecting changes in homeostasis associated with CKD that may contribute to the excess CVD risk.
29 citations
TL;DR: The data are in support of a higher plasticity of shortening and elongations of RTL as until recently anticipated, and whether the longer RTL in patients with long-lasting disease is caused by an activation of telomerase to counteract the shortening ofRTL due to oxidative stress and inflammation needs to be investigated in longitudinal studies.
20 citations
25 May 2015
TL;DR: Cloudflow is presented, a high-level framework to hide the implementation details of Hadoop and to provide a set of building blocks to create biomedical pipelines in a more intuitive way and it will be shown how the framework can be combined with theHadoop workflow system Cloudgene and the cloud orchestration platform CloudMan to provide Hadoops pipelines as a service to everyone.
Abstract: The data-driven parallelization framework Hadoop MapReduce allows analysing large data sets in a scalable way. Since the development of MapReduce programs can be a time-intensive and challenging task, the application and usage of Hadoop in Biomedical Research is still limited. Here we present Cloudflow, a high-level framework to hide the implementation details of Hadoop and to provide a set of building blocks to create biomedical pipelines in a more intuitive way. We demonstrate the benefit of Cloudflow on three different genetic use cases. It will be shown how the framework can be combined with the Hadoop workflow system Cloudgene and the cloud orchestration platform CloudMan to provide Hadoop pipelines as a service to everyone. The framework is open source and free available at https://github.com/genepi/cloudflow.
4 citations