Suchergebnisse

The Association of Bimolecular Resource Facilities (ABRF) annual meeting was held in Palm Springs, California, USA on February 29-March 2, 2020. With 860 in attendance, the conference program featured five satellite workshops, one eminent scientist talk, four keynote talks, 24 sessions, 2 poster sessions, and fourteen technology showcases. The theme of the meeting "Empowering Team Science" encompassed bench to bedside, including extraterrestrial microbes, single cell 'omics, multi 'omics, quantitative imaging, multidisciplinary research, shared resource management and precision medicine. Presentations on technology and applications for genomics, proteomics, metabolomics, bioinformatics, imaging and cytometry based multidisciplinary research from shared resource core laboratories continues to be the focus of the conference. Highlighted this year were the ABRF Research Groups and studies designed and analyzed to inform scientific rigor in research performed across multi institutional academic, government and industry laboratories.

Standardized benchmarking methods and tools are essential to robust accuracy assessment of NGS variant calling. Benchmarking variant calls requires careful attention to definitions of performance metrics, sophisticated comparison approaches, and stratification by variant type and genome context. To address these needs, the Global Alliance for Genomics and Health (GA4GH) Benchmarking Team convened representatives from sequencing technology developers, government agencies, academic bioinformatics researchers, clinical laboratories, and commercial technology and bioinformatics developers for whom benchmarking variant calls is essential to their work. This team addressed challenges in (1) matching variant calls with different representations, (2) defining standard performance metrics, (3) enabling stratification of performance by variant type and genome context, and (4) developing and describing limitations of high-confidence calls and regions that can be used as "truth". Our methods are publicly available on GitHub (https://github.com/ga4gh/benchmarking-tools) and in a web-based app on precisionFDA, which allow users to compare their variant calls against truth sets and to obtain a standardized report on their variant calling performance. Our methods have been piloted in the precisionFDA variant calling challenges to identify the best-in-class variant calling methods within high-confidence regions. Finally, we recommend a set of best practices for using our tools and critically evaluating the results.

During the COVID-19 pandemic, genomics and bioinformatics have emerged as essential public health tools. The genomic data acquired using these methods have supported the global health response, facilitated the development of testing methods and allowed the timely tracking of novel SARS-CoV-2 variants. Yet the virtually unlimited potential for rapid generation and analysis of genomic data is also coupled with unique technical, scientific and organizational challenges. Here, we discuss the application of genomic and computational methods for efficient data-driven COVID-19 response, the advantages of the democratization of viral sequencing around the world and the challenges associated with viral genome data collection and processing.