MGI (Mouse Genome Informatics)

MGI has a new weekly report of Mouse Protein Coding Genes having one-to-one Orthology with Human Genes, the HOM_ProteinCoding.rpt: https://www.informatics.jax.org/downloads/reports/index.html

This report uses homology class data from the Alliance of Genome Resources. There are currently 16,472 genes in this report.

MGI SNP data increased 4-fold.

MGI increased its SNP records 4-fold to over 66 million. These data include the Sanger MGP (v5) SNP set. Use our preeminent SNP Query (https://www.informatics.jax.org/snp) to search for SNPs by gene symbols or chromosomal regions across 101 mouse strains. Search results are limited to 100,000 SNPs (displayed or downloaded), and filters are available to refine search results that exceed the return limit.

To query this large data set efficiently, we implemented the search with Elasticsearch, which allows large data sets to be queried in parallel and improves search speeds. We plan on using this search for other large data sets in MGI/GXD.

In order to update the SNP coordinates to GRCm39 we temporarily lost the dbSNP function classes, such as whether the SNP is in an intron or coding region, and therefore, the Function Class filter in a SNP summary report is limited to "within coordinates of." A future release will provide more function classes. The function classes for individual SNPs can be found by searching the Alliance of Genome Resources (https://www.alliancegenome.org) with the RefSNP ID, one ID at a time. For queries that specify one or more Reference strains, MGI's Allele Agreement filters restrict results to SNPs with strain allele calls that agree or differ from reference strain alleles.

Please send questions and comments to [email protected]

Improving laboratory animal genetic reporting: LAG-R guidelines

The LAG-R framework (Laboratory Animal Genetic Reporting) has just been published in Nature Communications (https://doi.org/10.1038/s41467-024-49439-y). The LAG-R framework is a set of guidelines to support more complete documentation of the genetic make-up of animals that are used in research, with the aim of bolstering reproducibility, reliability, and overall scientific rigor.

A New York Times article on an ongoing study to examine how city mice compare to rural mice:

Got a Mouse in Your Apartment? These Scientists Will Take It. A research study is examining how mice that live in cities, close to humans, may have evolved differently from their country cousins.