To introduce you to the major features of the Genomics Analysis Platform, this QuickStart will walk you through the process of a single annotation analysis.
All the resources used in the QuickStart, including the files and analyses, are available to you when you sign up for a free account: there is no need to take out a subscription — just use some of your free 5000NTD/150USD/1050RMB credits.
We'll start by uploading a VCF files. Then, we'll use one of Genomics Analysis Platform the single analysis workflows to carry out the analysis. Finally, we'll examine our results.
The first step to running an analysis on the Genomics Analysis Platform is to upload a VCF file. To do this, click UPLOAD NEW SAMPLE under the SAMPLES tab in the left navigation bar.
Once you choose a VCF file from your PC, you'll need to fill some information about this VCF, including its gender, genome build (hg19/38), sequence type (WGS/WES/PANEL), and add more information using tags.
The second step to running an analysis on the Genomics Analysis Platform is to do quality control (QC) If your format of VCF file is correct, you can click QC Summary in the sample lists. The QC summary page contains six figures to describe the QC information in your VCF file, including its Ti/Tv, types of variant, length of indel, quality score of variants, genotype quality and read depth of variants. You can use customized parameters about read depth and genotype quality to filter the VCF file. The filter result can save to do analysis later. In this QuickStart, the GRCh38 version of NA12878.vcf is chosen for uploading.
The final step to running an analysis on the Genomics Analysis Platform is to create an analysis. To do this, click CREATE NEW ANALYSIS(GRCh37/hg19) or CREATE NEW ANALYSIS(GRCh38/hg38) under the ANALYSES tab in the left navigation bar. In this QuickStart, the genome build of the uploading NA12878.vcf is GRCh38/hg38.
You can choose one mode, which are single, case-control and trio family, to do analysis in step1, and assign this analysis to one project.
Here you can view all samples that are all GRCh38/hg38, then you can select one or multiple sample to do single annotation.
In each analysis result, our platform provides 5 categories result: 1) Analysis overview, 2) Cancer related, 3) Disease related, 4) Functional prediction, and 5) Reporting.
6.1 Analysis Overview
In the overview of the analysis, you can see five figures to describe the annotation results including 1) Number of variants and genes, 2) Classification of variants, 3)Disease databases, 4) Chromosome view, 5)Top 5 genes view.
6.2 Cancer Related
Cancer-related results are from International Cancer Genome Consortium (ICGC) and Catalogue of Somatic Mutations in Cancer (COSMIC) that show the top 20 cancer primary sites. The variants table is below the figures and show more cancer-related information including allele frequency of NCI60, ICGC ID, ICGC occurrence, Cosmic ID and Cosmic occurrence in each variant.
6.3 Disease Related
Disease-related results are from ClinVar, ACMG guideline and GWAS Catalog that show incidental report findings, clinical significance and allele origin information. The variants table is below the figures and show more disease-related information including ClinVar ID, clinical significance, allele origin, reviewer status and GWAS Catalog in each variant.
6.4 Functional Prediction
Functional prediction results are from dbNSFP database and our pathogenic score – Three box plot figures can show the distribution of scores. The variants table is below the figures and show Dr. Score in each exonic and splicing variant.
You can use selected variants and fill patient, specimen and clinics information to generate a PDF report.
6.6 Variant Information
In the variant table, you can click one variant to see 3 detail information including 1) Gene information, 2) Frequency, 3) Functional prediction, and 4) Bookmark function to save interested variants.
6.7 Advanced filter
You can set their customizer filter function by the advance filter function. This platform provides AND, OR and NOT condition with different type of categories and value to do flexible filter analysis. In this QuickStart, we use both TruSight Cancer Sequencing Panel, Hight impact, all Cosmic’s primary site and Reviewed by Expert Panel from ClinVar but the AF cannot upper than 0.05. The overview of condition can see below.