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This Week in Nature: Oct 25, 2013

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.

The Scan

US Supports Patent Waivers

NPR reports that the Biden Administration has announced its support for waiving intellectual property protections for SARS-CoV-2 vaccines.

Vaccines Versus Variants

Two studies find the Pfizer-BioNTech SARS-CoV-2 vaccine to be effective against viral variants, and Moderna reports on booster shots to combat variants.

CRISPR for What Ails You

The Wall Street Journal writes that CRISPR-based therapies could someday be used to treat common conditions like heart attacks.

Nature Papers Review Integration of Single-Cell Assay Data, Present Approach to Detect Rare Variants

In Nature this week: review of ways to integrate data from single-cell assays, and more.