Next-generation analysis is driven by the wealth of data curated and published by the experts in genomics space. At Golden Helix, we strive not only to provide seamless integration of input data into customized workflows, but to ensure that our customers can rely on high-quality annotations through our curation efforts. Golden Helix is a market leader in terms of the depth and breadth of annotations available within our software, and we’re proud to add LitVar2, a powerful tool for imbuing literature availability into variant analysis, to our host of available annotations.
Augmenting actionable variants
Each annotation contributes something unique to a tertiary analysis workflow, with the net effect being a comprehensive and nuanced picture of the clinical actionability or research relevance of variants and other genomic markers. LitVar2, an expert-curated database matching variants to literature in which they are referenced, is a titan when it comes to filling in the gaps left by similar tools, pointing users both to relevant information for already-pertinent variants, as well as providing an additional datapoint, i.e., presence in published papers, that can help tip the scales in favor of investigating edge-case variants.
Included in our shipped copy of LitVar2 are around 12 million variants across 41,000 genes, nearly 30 million references to literature — this is the novelty that LitVar2 offers, potentially casting light on otherwise-ignored variants. Conversely, LitVar2 carries literature references for about half of the variants present in ClinGen VCEP and CIViC, and about a quarter of those in ClinVar: additional actionable signal and a concrete path to bringing in trenchant information for variants that are already probably making it through filter chains.
Direct integration into VSClinical
The data itself is, of course, only part of the picture. VarSeq users are familiar not only with the abundance of high quality data available directly within the software, but the mechanisms by which we bring concise information to the forefront. LitVar2 is no different. In our upcoming release, VarSeq 3.1.0, users can look forward to seeing LitVar2 integrated directly into the VSClinical interface, with links to and summaries of referenced papers visible at a single click (Fig. 1 & Fig. 2).
LitVar2’s addition to our fleet of curated annotations and integrated tools is just one of many updates we’re excited to share as we get closer to our next major VarSeq release, and yet another example of our continued commitment to both quality and breadth. Interested in seeing how LitVar2 and other tools available within the VarSeq suite can speed up and improve your clinical analysis pipeline? Click the link below!
