With mapped DNA-Seq data, Array Studio allows users to identify, visualize and annotate sequence, mutations and copy number variations. In this article, we walk you through a few important DNA-Seq analysis modules.
- Identify DNA Sequence Variation
- Generate and Annotate VCF Variant Data
- Identify Somatic and Germline Mutations in Matched-Pair Data
- Summarize NGS Coverage Data to Detect Copy Number Variants
- Visualize NGS Copy Number Variations
- Integrate CNV chip and DNA-seq Visualizations in the Omicsoft Genome Browser
Users can run Summarize Variant Data module to identify SNPs, insertions and deletions. It also automatically runs in DNA-Seq pipeline. The output Variant Report can be annotated with Mutation Annotator databases.
Variant Call Format (VCF) data is the most common format for reporting sequence variation. Array Studio variant detection can output merged or individual VCF files, and can organize and annotate these data for efficient filtering in Array Studio. and public database-based annotators, please check out our wiki page on Annotate Variant Files. Array Studio provides a large number of classifiers and annotators to improve the identification of interesting variants. Examples include: 1000Genomes, ClinVar, GERP++, dbNSFP (database for nonsynonymous SNPs' functional predictions), GRASP : Genome-Wide Repository of Associations between SNPs and Phenotypes, GWAVA, Haploreg, RegulomeDB.
If you have matched pair DNA-Seq data between tumor and normal from the same subject, you can run the Var Scan 2 matched pair analysis. this annotates somatic mutations that compare two samples from the same subject such as tumor or normal for differences in genotype. It will generate calls for genotype of the samples and flag germline versus somatic mutations.
DNAseq Whole-Genome and Whole-Exome data can be processed in Array Studio to detect amplification and deletion events. By comparing the relative signal between samples from the same subject, regions with unusually high or low signal in the disease sample will be flagged as a potential Copy Number Variation (CNV) event. The result can be visualized in a few ways, including scatter plot, segment chromosome view, or in genome browser.