Genotypic summaries to assist variant interpretation
DECIPHER provides a suite of tools to assist in assessing the pathogenicity of variants, including genome and protein browsers.
Protein browser: A protein browser is available for protein-coding genes, showing a genotypic summary which helps users to determine if a variant is located in a mutational hot spot or established functional domain (Fig. 5A). The protein browser is fully interactive and is customisable via a settings menu. In the centre of the protein browser, Pfam domains (Mistry et al ., 2021) are displayed allowing users to identify distinct functional/structural elements of the protein. Clinically relevant variants from DECIPHER and ClinVar are plotted above and below the Pfam domains, with annotated pathogenicity and predicted molecular consequence (e.g. missense, likely loss-of-function (LOF)) indicated through colouring. In addition to the location of the variants being shown, for likely LOF variants, the location of the protein truncating codon is indicated, since this information is essential in determining if a transcript will escape nonsense mediated decay (NMD). A predicted (NMD) track is also displayed. The location of variation in the general population is shown through display of gnomAD missense and LOF tracks. Regional missense constraint data is also available (regional missense constraint improves variant deleteriousness prediction, Samocha et al ., https://www.biorxiv.org/content/10.1101/148353v1), in addition to exon structure. Protein secondary structures (e.g. locations of helices and turns) and the locations of 3D structures (where available from the Protein Data Bank in Europe (PDBe)) are displayed at the bottom of the protein browser. Clicking on these 3D structures will display an interactive 3D protein viewer (Marco Biasini, 2015, pv v1.8.1. Zenodo. https://doi.org/10.5281/zenodo.20980) which provides zooming, panning and rotation, and hovering over an amino acid with a pointing device identifies the visualised amino acid and position (similar behaviour exists for ligands). DECIPHER variants are shown in this 3D view, allowing users to determine, for example if the variants are all within a DNA binding pocket or enzyme active site.
When looking at the protein browser from a patient record with a sequence variant, the location of the patient’s variant is displayed by a vertical line, allowing easy orientation. In the case of a patient with a CNV, the protein browser is accessible from the CNV’s genes tab, which displays a table of genes that overlap the CNV, along with other relevant information such as gene/disease association information and predictive scores. Clicking on a row displays further information about that gene, including the protein browser. An additional track is shown on the protein browser, indicating which part of the protein overlaps the CNV.
Genome browser: The Genoverse genome browser (http://genoverse.org), developed by the DECIPHER team, is a portable, interactive, customizable genome browser which allows the user to explore data. It displays a number of tracks containing information relevant to variant pathogenicity assessment such as genes associated with disease phenotypes (as curated and maintained by Online Mendelian Inheritance in Man (OMIM,https://omim.org, Amberger etal., 2019), protein ortholog sequences from Ensembl indicating conversation, transcripts (as maintained by Ensembl), and regional missense constraint. Information from population resources such as gnomAD and Database of Genomic Variants (DGV) Gold (Church et al ., 2010) are displayed to enable users to determine if their patient’s variant has been observed in healthy individuals. Disease relevant variant tracks are also available, which include DECIPHER sequence variants and CNVs, ClinVar sequence and structural variants, and variants from Human Gene Mutation Database (HGMD) public (Stensonet al ., 2020). The tracks which are displayed by default are tailored according to the type of variant being assessed.