“As next-gen sequencing investigations begin to yield results, the need for analytical tools capable of exploring and representing those data has grown,” says Josh Forsythe, Golden Helix Vice President of Sales and Marketing. “SVS 7.5 meets this need by providing researchers a complete suite of tools to support DNA resequencing and variant analysis workflows, and also includes performance upgrades requested by our active user community.”

SVS 7.5 contains a selection of powerful new rare variant analysis and statistical workflows, as well as flexible visualization tools and enhanced control over annotation track searches. Combined with regular web-based updates and committed customer support, SVS 7.5 is an optimal analytical solution for researchers grappling with intensive data output from complex genomic studies.

Rare Variant Analysis

Golden Helix’ latest offering expands on the Sequence Analysis Module first included in SVS 7.4 by offering several new collapsing methods for sequence analysis in addition to features capable of importing, managing, and visualizing large sets of variants.

Rare variant analysis workflows in SVS 7.5 have been augmented by the addition of the Kernel-Based Adaptive Cluster (KBAC) test as well as the latest regression-based versions of both Combined Multivariate and Collapsing (CMC) and KBAC methods. These statistical methods, integrated into SVS 7.5 with guidance from their developer, Suzanne Leal of Baylor College of Medicine, can be applied to detect associations between complex disease phenotypes and rare variants while correcting for confounding variables, or even to glean more information from prior GWAS studies.

SVS 7.5 also features improved support for variant classification which helps bring order to large lists of variants and includes support for insertions and deletions regardless of format. SVS also offers more options when importing VCF files to capture all input file details, as well as the ability to import Complete Genomics VAR files. Moreover, researchers interested in coding resequencing data for SNP analysis can take advantage of a novel bi-allelic expansion feature.

Single Nucleotide Variants (SNVs), along with Insertions/Deletions (InDels), can be further visualized with the Variant Map feature included in SVS 7.5. Variant Maps present color representations of SNVs, InDels, and mix substitution variants by analyzing each marker in the source spreadsheet, comparing alleles to a reference base. As Gabe Rudy, Golden Helix’ Vice President of Product Development, explains:

“By capitalizing on the human eye’s knack for pattern recognition, the Variant Map feature allows to you to quickly drill down to chromosomes or genes that have a high mutation burden for one group of samples or another. This empowers you to start looking at data in a very exploratory way.”

Enhanced Visualization Techniques

Data exploration in SVS 7.5 has been enhanced by upgrades to its fully integrated Genome Browser, developed to provide gene and genetic position context information through the incorporation of numerous data repositories. Contextual web links are also available for connecting to the Internet for information about a specific range or position in a chromosome with the click of a button.

In this release, the Genome Browser is now able to conduct global and track-based searches, allowing quick navigation to annotated gene features. Updated coloring and grouping controls, applicable to Variant Maps, Heat Maps, and other plots, extend control over graph visualizations and empower researchers to filter, color, and split results as desired.

Additional Features

SVS 7.5 features many new statistical and visual tools to bring order to data, including:

Variant classification features optimized for large-scale lists of variants

Collapsing methods for sequence analysis, including regression-based CMC and KBAC

Ability to filter by PolyPhen2 functional effects prediction score

Ability to handle Complete Genomics VAR file formats

Bi-allelic expansion to encode resequencing data

Variant maps for introspective data visualization

Genome Browser search interface for annotation tracks

Coloring, grouping, and filtering controls

Additional support for the GFF/GTF annotation format

About SNP & Variation Suite

SNP & Variation Suite is the most powerful and integrated collection of high-performance analytic tools for managing, analyzing, and visualizing large-scale, complex genomic data. It’s fast, easy-to-use, and runs on conventional desktop computers enabling researchers to interact with their data as never before. Both statistically and visually, researchers can explore the relationships among vast amounts of clinical patient data, environmental factors, and genetic variants to understand the cause of disease and other inherited traits — all without writing a single line of code or buying expensive hardware. Applications include candidate gene analysis, genome-wide association studies, copy number analysis, cytogenetic research, and next-generation sequencing studies.

About Golden Helix

Golden Helix is a leading bioinformatics organization, specializing in sequence and array-based SNP and copy number analysis, genetic association software, and analytic services. Our innovative technologies empower scientists to determine the genetic causes of disease, transform drug discovery, develop genetic diagnostics, and advance the quest for personalized medicine. Used by hundreds of researchers at the world’s top pharmaceutical, biotech, and academic research organizations, Golden Helix products and services have been cited in over 500 peer-reviewed publications.