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Locus Reference Genomic (LRG) Sequences Mapped to Feb. 2009 (GRCh37/hg19) Assembly   (All Mapping and Sequencing tracks)

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View table schema Data last updated: 2014-07-07 16:39:08

Description

Locus Reference Genomic (LRG) sequences are manually curated, stable DNA sequences that surround a locus (typically a gene) and provide an unchanging coordinate system for reporting sequence variants. They are not necessarily identical to the corresponding sequence in a particular reference genome assembly (such as Feb. 2009 (GRCh37/hg19)), but can be mapped to each version of a reference genome assembly in order to convert between the stable LRG variant coordinates and the various assembly coordinates.

Each LRG record also includes at least one stable transcript on which variants may be reported. These transcripts appear in the LRG Transcripts track in the Gene Predictions track section.

Methods

LRG sequences are suggested by the community studying a locus (for example, Locus-Specific Database curators, research laboratories, mutation consortia). LRG curators then examine the submitted transcript as well as other known transcripts at the locus, in the context of alignment and public expression data. For more information on the selection and annotation process, see the LRG FAQ, (Dalgleish, et al.) and (MacArthur, et al.).

References

Dalgleish R, Flicek P, Cunningham F, Astashyn A, Tully RE, Proctor G, Chen Y, McLaren WM, Larsson P, Vaughan BW et al. Locus Reference Genomic sequences: an improved basis for describing human DNA variants. Genome Med. 2010 Apr 15;2(4):24. PMID: 20398331; PMC: PMC2873802

MacArthur JAL, Morales J, Tully RE, Astashyn A, Gil L, Bruford EA, Larsson P, Flicek P, Dalgleish R, Maglott DR, Cunningham F. Locus Reference Genomic: reference sequences for the reporting of clinically relevant sequence variants. NAR. 2014 Jan 1;42(D1):D873-D878. PMID: 24285302; PMC: PMC3965024

Credits

This track was produced at UCSC using LRG XML files. Thanks to LRG collaborators for making these data available.