High precision diagnostics how to#
High precision diagnostics software#

He also pointed out that the tools were run by the developers, who would know how to tweak parameters to maximize results. Two-thirds of all predicted circRNAs were novel compared to a set of previously reported circRNAs drawn from 13 databases.īoutros said that he wished the authors had been clearer on how they blinded themselves to certain data to eliminate bias. Based on the validation results, precision and sensitivity metrics were determined for each tool. Of the 315,000 circRNA candidates identified by the tools, 1,560 were validated using three different orthogonal methods: RT-qPCR, resistance to RNase R treatment to confirm circularity, and amplicon sequencing. 'After two years of workflow optimizations (interrupted by the COVID-19 pandemic), the most exciting time came in July 2021 when we were able to execute more than 6,000 RT–qPCR reactions and get a real view of the empirical validation rate of a large set of predicted circRNAs,' first author Marieke Vromman said in a statement.

The benchmarking project was born in 2019 out of a search for a tool to use in work being conducted at Ghent University, which ballooned into an international collaboration. Earlier this week, GenomeWeb reported that the firm is planning to launch a diagnostic test for response to depression treatment Zoloft (sertraline) based on a circRNA biomarker. Several startups have been launched to commercialized circRNA research, including Circular Genomics, which raised $4.5 million in seed funding in 2021. Their study also used CIRCexplorer, a program developed in 2014 by researchers at the Chinese Academy of Sciences. Previous studies based on ever-growing RNA-seq databases have found tens, even hundreds of thousands of circRNAs, and their ubiquity in different tumor types suggests that they could be used in diagnostics.įor example, in a 2019 study published in Cell, researchers at the University of Michigan profiled circRNAs in more than 800 tumor and other samples, yielding nearly 129,000 circRNAs in 40 cancer types. They play various biological functions, such as acting as molecular sponges for RNA-binding proteins and microRNAs that might otherwise bind to linear RNAs.

' Circular RNA quantification and detection methods haven't been well benchmarked at all,' he said.Ĭircular RNAs are an abundant class of molecules found throughout all domains of life and are the predominant transcript isoform for hundreds of human genes. 'This work might represent a gold standard dataset for publishing novel circRNA identification methods, and it will also be a valuable guide for experimental validation of circRNAs for research groups working on complex disorders such as neurodegenerative diseases or cancer,' Eduardo Andrés-Léon, a bioinformatician at Spain's Institute of Parasitology and Biomedicine López-Neyra, said in a statement.īoutros agreed that the study filled a 'critical gap' in the field. 'Unambiguously, I think the study suggests everybody should.' 'We'll move to using an ensemble almost immediately,' he said. Previously, he used CIRCexplorer, one of the tools benchmarked in the study, as his main workhorse. The results have already convinced Paul Boutros, a circRNA researcher at the University of California, Los Angeles who was not involved with the study, to expand the number of tools he uses at a time. They published their results earlier this month in Nature Methods. Half of all circRNAs were reported by just one tool, circseq_cup, developed by researchers at China's Zhejiang University.Īnd a combination of two high-precision tools increased the number of detected circRNAs substantially while keeping the number of false discoveries low, the authors said. 'The range of detected circRNAs varied between 1,372 and 58,032 circRNAs per tool in a given cell type,' the authors said.

High precision diagnostics software#

Overall, the software programs were precise, but there was a wide range of sensitivity. Led by researchers from Belgium's Ghent University, an international coalition applied 16 different software-based circRNA identification tools to the same RNA-seq dataset generated from three cancer cell lines.

NEW YORK – Researchers looking for circular RNA (circRNA) biomarkers in RNA-seq datasets should consider using an ensemble of bioinformatics tools, according to a recent benchmarking study. Advances in Clinical Genomics Profiling.