How do I use the Variant Annotation Database for my project?

To utilize the Variant Annotation Database for your clinical research project, simply click on the “Annotate with the Variant Annotation Database” option in the Analysis Options window of SeqMan NGen when you set up your project.

The Variant Annotation database will automatically be used to annotate the variants identified in your data.

What supplemental variant data is available in the Variant Annotation Database?

DNASTAR’s Variant Annotation Database contains variant information using coordinates from GRCh37 (hg19) and GRCh38. Annotations include information about the frequency of the variant in the general population, in specific populations, and in publications, as well as information concerning the variant’s impact on functionality. The annotation information comes from several sources, including:

• Mastermind, the comprehensive database of genomic literature from Genomenon, providing access to NGS variant data from millions of PubMed publications.
• 1000 Genomes Project and the Exome Sequencing Project (ESP)
• dbNSFP v 4.1 which includes:

• Functional impact predictions from Sorting Intolerant from Tolerant (SIFT), MutationTaster, and the Likelihood Ratio Test (LRT).
• Evolutionary conservation scores from SiPhy, PhyloP, PhastCons and GERP++.
• Pathogenicity and clinical significance impact from ClinVar.
• Basic amino acid sequence information, Database of Single Nucleotide Polymorphism (dbSNP) IDs, and annotations from Uniprot and Interpro.

How can I find citations for a specific variant in current publications?

Our integration with Mastermind provides a seamless way to find publications on a specific variant of interest. In ArrayStar, easily access and link to data from Mastermind in the SNP Table for each of your variants, including:

• MM Count 1: Count of articles in the Mastermind Genomic Search Engine with cDNA matches for a specific variant
• MM Count 2: Count of articles in the Mastermind Genomic Search Engine with variants either explicitly matching at the cDNA level or given only at protein level.
• MM Count 3: Count of Mastermind articles in the Mastermind Genomic Search Engine, including other DNA-level variants resulting in the same amino acid change.
• MM Gene: Genes for a variant from the Mastermind Genomic Search Engine.
• MM HGVS: HGVS genomic notation for a variant from the Mastermind Genomic Search Engine.
• MM ID 3: Variant identifiers in the Mastermind Genomic Search Engine, as gene:key, for MMCNT3.
• MM URI 3: Search URI for articles in the Mastermind Genomic Search Engine, including other DNA-level variants resulting in the same amino acid change.

Is there an additional cost to access the Variant Annotation Database?

No. Access to the variant databases for human genome analysis is included with your purchase of Lasergene Genomics and remains available as long as your service plan is active.