PopViz webserver provides a user-friendly gene-centric approach to rapidly extract and visualize the population genetics and the mutation damaging scores of variants in the specific gene of interest.
The variants data were collected from gnomAD r2.0.2 WES data for 123,136 individuals from 7 populations, and applied with several inclustion/exclusion creteria: (1) the variant must have PASS in its FILTER field in VCF file, (2) the variant must be based on canonical transcript, (3) the variant must have gene symbol annotated, and the gene must be supported in Ensembl database, (4) the variant should be annotated as one of the 14 selected consequences, (5) the variant has MAF=0 for all populations were be excluded, (6) the indels that have more than 10 nucleotide changes were excluded. The variants were then integrated with various mutation damaging scores (incl. CADD, EIGEN, LINSIGHT, SIFT, PolyPhen2), as well as a number of gene/protein information.
PopViz offers the flexibility of choosing different parameters as X/Y-axis for visualization. The optons for X-axis are: general MAF, maximum MAF, or amino acid position; and the options for Y-axis are: CADD, EIGEN, LINSIGHT, general MAF, or maximum MAF.PopViz also presents a variety of search options (including reference genome, parameters for visulization, MAF range, MAF cutoff by (mode of inheritance and disease revalence), population, mutation consequence, gene-level MSC cutoff, and several other functional filters) for user to customize their search. It also allows users to input up-to 1000 user-defined mutations.
PopViz returns an interavtive plot for the varitants, and an informative table for the gene/protein. The interactive plot allows to expand the details of each variant, show/hide the variants of certain consequence, zoom in/out any region of interest, export/print the plot. The informative table provides the cross-reference links to various databases (incl. Ensembl, GeneCard, Uniprot, Human Protein Atlas, and OMIM), and gives gene description, protein length, GO terms, OMIM phenotyes. Additionally, PopViz warns the user if any mistakes in the input mutations (e.g. incorrect chromosome, incorrect positioin).