MVAR: A Mouse Variation Registry

• Published in: Journal of molecular biology Vol. 436; no. 17; p. 168518
• Main Authors: El Kassaby, Bahá, Castellanos, Francisco, Gerring, Matthew, Kunde-Ramamoorthy, Govindarajan, Bult, Carol J.
• Format: Journal Article
• Language: English
• Published: Netherlands Elsevier Ltd 01.09.2024
• Subjects: canonicalization; Mouse genome variation; relational database; short genetic variants; variant annotation; variant annotation; Mouse genome variation; canonicalization; relational database; short genetic variants
• ISSN: 0022-2836; 1089-8638; 1089-8638
• DOI: 10.1016/j.jmb.2024.168518

[Display omitted] •MVAR aggregates and annotates genome variation from large-scale sequencing of different mouse strains and expertly curated variants for phenotypic alleles.•Variant annotation in MVAR includes variant type, molecular consequence, impact, and region.•Data in MVAR are accessible in both human- and machine- readable formats.•MVAR serves as both a stand-alone database of mouse genome variation and as a variant annotation service.•MVAR is a platform for facilitating genotype-phenotype associations in the laboratory mouse.•MVAR resource was implemented using a micro-services architecture, providing both interoperability and ease of software maintenance. The Mouse Variation Registry (MVAR) resource is a scalable registry of mouse single nucleotide variants and small indels and variant annotation. The resource accepts data in standard Variant Call Format (VCF) and assesses the uniqueness of the submitted variants via a canonicalization process. Novel variants are assigned a unique, persistent MVAR identifier; variants that are equivalent to an existing variant in the resource are associated with the existing identifier. Annotations for variant type, molecular consequence, impact, and genomic region in the context of specific transcripts and protein sequences are generated using Ensembl’s Variant Effect Predictor (VEP) and Jannovar. Access to the data and annotations in MVAR are supported via an Application Programming Interface (API) and web application. Researchers can search the resource by gene symbol, genomic region, variant (expressed in Human Genome Variation Society syntax), refSNP identifiers, or MVAR identifiers. Tabular search results can be filtered by variant annotations (variant type, molecular consequence, impact, variant region) and viewed according to variant distribution across mouse strains. The registry currently comprises more than 99 million canonical single nucleotide variants for 581 strains of mice. MVAR is accessible from https://mvar.jax.org.