Search

The increase in speed, reliability, and cost-effectiveness of high-throughput sequencing has led to the widespread clinical application of genome (WGS), exome (WXS), and transcriptome analysis. WXS and RNA sequencing is now being implemented as the standard of care for patients and for patients included in clinical studies. To keep track of sample relationships and analyses, a platform is needed that can unify metadata for diverse sequencing strategies with sample metadata whilst supporting automated and reproducible analyses, in essence ensuring that analyses are conducted consistently and data are Findable, Accessible, Interoperable, and Reusable (FAIR).We present "Trecode", a framework that records both clinical and research sample (meta) data and manages computational genome analysis workflows executed for both settings, thereby achieving tight integration between analysis results and sample metadata. With complete, consistent, and FAIR (meta) data management in a single platform, stacked bioinformatic analyses are performed automatically and tracked by the database, ensuring data provenance, reproducibility, and reusability, which is key in worldwide collaborative translational research. The Trecode data model, codebooks, NGS workflows, and client programs are publicly available. In addition, the complete software stack is coded in an Ansible playbook to facilitate automated deployment and adoption of Trecode by other users. [ABSTRACT FROM AUTHOR]

Purpose: DNA methylation profiling has previously uncovered biologically and clinically meaningful subgroups within many tumor types, but was not yet performed in angiosarcoma. Angiosarcoma is a rare sarcoma with very heterogeneous clinical presentations, which may be based on differences in biological background. In this exploratory study, DNA methylation profiling of 36 primary angiosarcoma samples from visceral, deep soft tissue, radiation-induced, and UV-induced localizations was performed., Experimental Design: Primary angiosarcoma formalin-fixed paraffin-embedded samples from visceral, soft tissue, radiation-induced, and UV-induced origin were collected from a nationwide search for angiosarcoma in the Netherlands. DNA was extracted for methylation profiling with the Illumina Infinium MethylationEPIC array. Quality control assessment and unsupervised hierarchical clustering were performed. Copy-number profiles were generated and analyzed for chromosomal stability. Clinical data were obtained from the Netherlands Cancer Registry., Results: DNA methylation profiling by unsupervised hierarchical clustering of 36 angiosarcoma samples (6 visceral, 5 soft tissue, 14 radiation-induced, 11 UV-induced) revealed two main clusters (A and B), which were divided into four subclusters. The clusters largely corresponded with clinical subtypes, showing enrichment of UV-induced cases in cluster A1 and radiation-induced cases in cluster A2. Visceral and soft tissue cases almost exclusively fell into cluster B. Cluster A showed significantly increased chromosomal instability and better overall survival (22 vs. 6 months, P = 0.046) compared with cluster B., Conclusions: In this novel methylation profiling study, we demonstrated for the first time four different angiosarcoma clusters. These clusters correlated with clinical subtype, overall survival, and chromosomal stability., (©2019 American Association for Cancer Research.)