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New Products: Knome's KnomeBase, Sanger Institute's COSMIC v56


Knome has launched KnomeBase, an informatics service that "transforms raw sequence data from human genomes into a format optimized for comparison and interpretation," according to the company (see article this week).

The service costs $750 per whole genome or exome, and the firm provides academic and volume discounts.

The service, which accepts whole-genome data from several platforms, including Illumina and Complete Genomics, converts raw sequence data into a standard genome format and summarizes the distribution of variants among the genomes studied.

It also annotates variants in the genome and creates a database that contains SNPs and short indels at known and novel variable sites in the genome; call confidence; variant frequencies in appropriate populations; gene IDs and associated phenotypes; variant-specific effects on protein sequence and function; and gene-to-gene interactions.

Users of KnomeBase also receive KnomeGDK, a suite of software tools, scripts, and libraries, including Variants, a query interface to find suspect variants in many genomes, and KnomePathways, a gene interaction visualization tool to find sets of genes that are enriched for suspect variants in one set of genomes versus another.

The Wellcome Trust Sanger Institute has released version 56 of COSMIC, the Catalog of Somatic Mutations in Cancer. The new version includes three new cancer genes (IL7R, MED12, and SF3B1), 13 new fusion gene pairs, and data from seven recent genome-wide screens.

In addition, the COSMIC team has added four new cancer genes (IL7R, VTI1A, TCF7L2, and NDRG1) to the catalog's cancer gene census, bringing the total number of cancer-related genes in the resource to 468.

The Scan

Not as High as Hoped

The Associated Press says initial results from a trial of CureVac's SARS-CoV-2 vaccine suggests low effectiveness in preventing COVID-19.

Finding Freshwater DNA

A new research project plans to use eDNA sampling to analyze freshwater rivers across the world, the Guardian reports.

Rise in Payments

Kaiser Health News investigates the rise of payments made by medical device companies to surgeons that could be in violation of anti-kickback laws.

Nature Papers Present Ginkgo Biloba Genome Assembly, Collection of Polygenic Indexes, More

In Nature this week: a nearly complete Ginkgo biloba genome assembly, polygenic indexes for dozens of phenotypes, and more.