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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

Tens of Millions Saved

The Associated Press writes that vaccines against COVID-19 saved an estimated 20 million lives in their first year.

Supersized Bacterium

NPR reports that researchers have found and characterized a bacterium that is visible to the naked eye.

Also Subvariants

Moderna says its bivalent SARS-CoV-2 vaccine leads to a strong immune response against Omicron subvariants, the Wall Street Journal reports.

Science Papers Present Gene-Edited Mouse Models of Liver Cancer, Hürthle Cell Carcinoma Analysis

In Science this week: a collection of mouse models of primary liver cancer, and more.