This track shows the genomic positions of variants in the AVADA database. AVADA is a database of variants built by a machine learning software that analyzes full text research articles to find the gene mentions in the text that look like they are most relevant for monogenic (non-cancer) genetic diagnosis, finds variant descriptions and uses the genes to map the variants to the genome. For details see the AVADA paper.
As the data is automatically extracted from full-text publications, it includes some false positives. In the original study, out of 200 randomly selected articles, -only 99 were considered relevant after manual curation. Ideally, the track is used +only 99 were considered relevant after manual curation. However, this share is very high +compared to the Genomenom track. Ideally, the track is used in combination with variants found in human patients, to find relevant literature, or with Genome Browser tracks of variant databases that curated a single study for each variant, like our tracks for HGMD or LOVD.
Genomic locations of a variants are labeled with the variant description in the original next. This is not a normalized HGVS string, but the original text as the authors of the study described it. The Pubmed ID, gene and transcript for each variant are shown on the variant's details page, as well as the PubMed title, authors and abstract. Mouse over the variants to show the gene, variant, first author, year and title.
+The data has been lifted from hg19 to hg38.
The raw data can be explored interactively with the Table Browser, for download, intersection or correlations with other tracks. To join this track with others based on the chromosome positions, use the Data Integrator.
For automated download and analysis, the genome annotation is stored in a bigBed file that can be downloaded from our download server. The file for this track is called avada.bb. Individual regions or the whole genome annotation can be obtained using our tool bigBedToBed which can be compiled from the source code or downloaded as a precompiled binary for your system. Instructions for downloading source code and binaries can be found