In Nature Biotechnology this week, a group led by Foundation Medicine researchers report on a clinical cancer genomic profiling test that uses massively parallel DNA sequencing to help improve patient diagnosis. Using the sequencing technology, they characterized base substitutions, short insertions and deletions, copy number alterations, and selected fusions across 287 cancer-related genes from routine formalin-fixed and paraffin-embedded clinical specimens. With a validation strategy of reference samples of pooled cell lines that model key determinants of accuracy, the scientists were able to achieve 95 to 99 percent sensitivity across alteration types, with high specificity. Accuracy was confirmed in samples using established assays.
Meanwhile, in Nature Methods, Cornell University and Scripps Florida researchers describe a new tool for imaging targeted RNAs in living human cells. The tool is based on a designer RNA sequence dubbed Spinach that can be attached to any normally occurring cellular RNA in order to label it with fluorescence and track its location in the cell. However, weak fluorescence has limited its utility. To address this, the team developed Spinach2, which improved the original sequence’s folding and stability, allowing a broader range of RNAs to be imaged. The investigators were able to use their creation to label GCC RNA sequence repeats associated with Fragile X-associated tremor/ataxia syndrome.