As a parent, sometimes the most powerful answer you can give your children is “no”.
Once they know where the boundaries are, they just might stop trying to navigate the gray area to find loopholes. The same can be said for genomic variant curation.
Genomic variant interpreters can spend a lot of time in the gray area known as “VUS” or variant of uncertain significance – searching for evidence that a genomic variant is pathogenic or benign. Sometimes the most powerful answer you can get on a literature search on a variant is “zero”. Knowing that there are no literature citations associated with a patient’s variant provides the confidence to stop searching, declare the variant as a VUS, and move on to research the next variant.
This week, we announced the new Mastermind Cited Variant Reference (CVR), available for download from our website here. Over the last 3 months, we’ve shared and tested the CVR with a number of our partners, allowing them to quickly search for and filter variants at the *nucleotide level, based on the number of citations or articles that the variant has been found in.
The Mastermind Cited Variants Reference is an essential resource that we’ve made freely available for download. The CVR file simply and clearly displays the number of articles that Mastermind has found for each variant in the medical literature. This file can be used first to determine if the variant can be found in the literature, and then to quickly view the articles in Mastermind, where you can get deep insight into each article.
A common use-case for the CVR is to integrate this information into a genomic analysis pipeline for NGS (next-generation sequencing) data. Variant citation counts can be used to annotate a patient VCF file to prioritize those variants with clinical evidence and speed up the variant curation process.
One of the most interesting pieces of feedback we’ve received on the CVR is the “power of zero”. That is to say – the CVR is very helpful in pointing out when a variant hasn’t been found in the literature for any disease, and cuts short the time that variant scientists need to spend researching the literature.
Sometimes the most powerful answer is “zero”. When you are confident that a search will yield no clinically relevant literature citations on a VUS, your ability to confidently move on to the next variant can save a lot of time in the variant interpretation process.
*While the CVR file does contain over 3.7 million variants seen in the medical literature, it doesn’t include everything in Mastermind’s ever-expanding database. Read more about the CVR.