Mastermind quickly sorts and prioritizes CNV results with automated, semantic search – but how can this be visualized? This blog will introduce our new “Stacked Pancake” Plot for CNVs, and will explore how it adds even more flexibility to your experience.
With Mastermind’s automated, semantic search for Copy Number Variants (CNVs), sorting and prioritization of CNV results help navigate the evidence for relevant CNV citations quickly and easily.
Mastermind’s initial CNV release included a visualization called the “Gene Hotspot” plot, which helps reveal which causative areas may exist within the relevant evidence for a given CNV by highlighting which protein-coding genes are most commonly included in those overlapping CNVs.
This plot is especially useful when further filtering the CNV literature search by specific phenotypes of interest.
However, many times it’s easier and more practical to visually browse through the relevant, overlapping CNVs by position plotted on the chromosome. We’re excited to announce what we affectionately refer to internally as the “Stacked Pancake” Plot for CNVs.
This new CNV chart plots the listed, overlapping CNVs from the results list on the chromosome by their genomic start and end coordinates. At the bottom of the plot, there are two additional sections aligned to the chromosomal positions. So, the three total sections of the plot are:
- Overlapping CNVs – The overlapping CNVs referenced by the literature from the start to the end position of your searched CNV.
- Evidence Hotspots – The number of articles citing CNVs which overlap each position in the chromosome.
- Genes – Plotted on the chromosome by start and end positions for each gene.
Depending on the size of the searched CNV and the number of overlapping CNV citations in the literature, this can be a lot of data to traverse, so we’ve made the chart fully interactive, allowing you to zoom and pan through the data, hovering over each CNV to show its details.
While this will now be the new default visualization for all CNV-based searches in Mastermind, you can still toggle to the Gene Hotspots in the upper right corner of the chart, which is helpful when filtering by additional genomic evidence-based associations such as phenotype(s).
These new data visualization solutions for CNVs represent an ongoing mission to ensure that you can trust Mastermind as the first resource for variant interpretation. Our next steps are driven by you – we welcome your thoughts at email@example.com.
See the latest updates for yourself. Sign up for Mastermind here.