Try this out by downloading our tiny demo (choose trio or beyond trio version), containing:
- Phenotype: An anonymized patient summary PDF file
- Genotype: a tiny simulated variant file for a trio (proband, mother, father).
Load the patient summary into the software by starting the software and then using the menu at the right of the top black bar to choose “Load or save patient”. Load the Summary file, and then you will be offered the opportunity to load the variant file. After the file loads, you get a technical report about the variants read.
The Genotype tab
Explore:
Click Diagnose on the black bar, and you will see that VLDLR-related cerebellar hypoplasia is the #1 diagnosis.
Click the Phenotype tab to see what clinical findings were used.
Click the Genotype tab to see the plausible gene zygosities that were found based on the variants, the affected status of the individuals, and the severity assessments of the zygosities.
Mini-variant table
Click on the gene zygosity you want to explore, in this case, VLDLR (biallelic). Then click on the “Show the VLDLR variant” green button in the top right of the Genotype tab.
Here, VLDLR gene variants (biallelic) is #1, with severity 5. Clicking that, a button “Show the 1 VLDLR variant” appears, and clicking it shows a mini variant table.
- Color: In the mini variant table, affected individuals are named in red.
- Visible information: Each line has a variant with sequence annotation (with ClinVar link), chromosomal position (with UCSC Genome Browser graph link and with genome assembly specified), effect, and zygosity in each individual (with names derived from the variant table).
- Hover: Hover over a zygosity to get depth and quality scores for that individual. The basis for the severity is explained; such explanations can include functional and conservation scores, homoshares information, and other relevant details, such as high-frequency or excessive de novo variants in the variant table.
Variants with frequency above disease incidence (e.g., ALMS1)
Explore variants for other genes and you will see some with blue shading, indicating a variant that seems too frequent given the incidence of the disease. The type of frequency data has descriptors derived from the variant table.
