In Nature Biotechnology this week, a team from Cornell University provided details of a new clinical cancer genomic profiling test. The researchers used massively parallel DNA sequencing to characterize 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. They used a "practical validation strategy" with reference samples of pooled cell lines that model key determinants of accuracy including mutant allele frequency, indel length, and amplitude of copy change. They achieved a sensitivity of 95 to 99 percent across alteration types and high specificity with the test, and confirmed accuracy using 249 cancer specimens characterized by established assays.
In Nature Methods, investigators from the European Molecular Biology Laboratory published a method to identify and quantify microbes according to their sequence data. The method establishes metagenomic operational taxonomic units based on single-copy phylogenetic marker genes, and when applied to 252 human fecal samples, showed that about 43 percent of the species abundance and 58 percent of the richness cannot be captured by current reference genome-based methods.