Readying the release of GRCm39

GRCm38, the current mouse reference assembly, whose chromosomes represent the C57BL/6J strain, supports a broad range of research activities. Despite being one of the highest quality mammalian genome assemblies ever produced, it still has more than 600 gaps and includes sub-optimal representations for some genes. To address these issues and provide the murine research community with an improved substrate for their work, the GRC has been applying new technologies, such as optical/genome mapping, and using new sequence resources to curate an update to the reference genome assembly. The public release of the updated assembly, GRCm39, is planned for the end of 2019/early 2020.Since the 2012 release ofGRCm38, the last coordinate-changing update to the mouse reference, the GRC has provided 6 publicly accessible minor assembly updates, the last of which (GRCm38.p6) was released in September, 2017. These non-coordinate changing assembly versions, known as patch releases, cumulatively include 65 fix patches (chromosome path changes) and 9 novel patches (alternate representations of chromosome sequences, derived from other strains). In GRCm39, these fix patches will be incorporated into the chromosomes, and the novel patches will persist as alternate loci.In preparation for the release of GRCm39, the GRC also analyzed a non-public updated version of the reference assembly. In the production of this updated assembly, 322 reported genome issues were resolved, 70% of which addressed ...

Source: GenomeRef - May 23, 2019 Category: Genetics & Stem Cells Source Type: blogs