What supplemental variant data is available for human genome analysis?

For human resequencing data, DNASTAR provides access to the Variant Annotation Database, which 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.

Is there an additional cost to access the human variant databases?

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.

Does Lasergene Genomics clinical research software support both Sanger and Illumina sequence data for variant analysis?

Yes, both sequencing platforms are supported for all whole genome and targeted resequencing projects.

How long does it take to go from raw data to analysis for an exome project?

The typical exome assembly and analysis time is approximately one hour, and this includes sequence mapping, variant calling, variant cross-comparing across samples and annotating found variants with variant databases.

Can I use variant calls made in my BWA/GATK pipeline?

Yes, the VCF comparison workflow accessed in SeqMan NGen allows you to compare variants across samples and/or annotate them with the available variant databases to enhance your analysis.

What types of variant analysis are available following assembly?

Lasergene Genomics clinical research software provides a wide variety of tools for analyzing variants, including:

• Large-scale SNP comparisons across individuals and groups
• Advanced gene filtering based on the level of disruption to each gene caused by variations
• Comparison of groups of variants using text filters, tabular data, or graphical representations that include Venn diagrams, scatter plots and heat maps
• The ability to send genes or variants of interest to SeqMan Ultra to view the read alignment at that position; or to GenVision Pro to view the assembly coverage for all samples simultaneously

Can Lasergene Genomics detect structural variations in genomic resequencing data?

Yes, Lasergene Genomics can detect copy number variation (CNV) and other structural variants as part of gene panel, whole exome and whole genome sequence analysis. Simply check the box for Calculate Copy Number Variation during assembly setup in SeqMan NGen. You can then view, filter and analyze CNVs and other structural variants using ArrayStar and SeqMan Pro.

Does Lasergene Genomics support BED or VCF files for targeted sequencing?

Yes. SeqMan NGen can read and utilize BED and VCF files in the assembly and can also create and export a VCF file during assembly. ArrayStar can export BED and VCF files.