Genome-Wide Association

Virtually Unlimited Data. Unparalleled Performance

Anticipating association studies with possibly hundreds of millions of markers generated per sample by next generation sequencing, the core architecture of SVS 7 has been completely reinvented to efficiently handle datasets of virtually any size on a desktop computer. Smart memory management and data caching ensures you will experience accelerated performance at every step. Further, SNP data is stored in a remarkably sparse data storage format enabling you to rapidly import large-scale whole-genome data, analyze it with conventional hardware, and efficiently share projects among collaborators. Your entire GWAS study can fit on a single USB Flash drive!

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Comprehensive Genetic Association Testing

Find more associations with the most extensive collection of genetic association tests, including allele, genotype, haplotype, copy number variation (CNV), runs of homozygosity (ROH), multi-locus, LD, and regression-based testing. Many tests can be run individually or simultaneously while also controlling for false positives by employing multiple testing corrections and permutation testing. Plus, it's easy to compare association results from different biomarkers simultaneously with a genome browser.

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Unprecedented Whole Genome Visualization

Seeing is believing with an intuitive interface that puts your data in genomic context at every step. Discover how rewarding it is to navigate whole genome data live within a spreadsheet - complete with genomic annotations - or visually in a genome browser. A new dynamic analytic visualization tool with integrated genome browser offers exceptional flexibility in how you visualize data and present results. Gain greater insights with unprecedented whole genome views and navigation control.

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Streamlined Import of Whole Genome Arrays

SVS 7 supports the direct import of most common genotyping platform file format. For Affymetrix, you can import CEL, CHP, CNT, and CNCHP files for all human mapping arrays including 5.0 and 6.0. Illumina is supported by a custom DSF export plug-in for the BeadStudio and GenomeStudio software programs. A new Agilent import tool reads Agilent text files created with the Agilent Feature Extraction software.

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Real-Time Editing, Manipulation, and Enrichment

The sheer size and complexity of whole genome data makes it extremely difficult to work with. SVS 7 eliminates the hassles with real-time spreadsheet manipulation, data editing, and enrichment. Easily combine multiple sample sets and data of different types, from different arrays, or even platforms. Quickly recode genotypes based on a specified genetic model, flip DNA strands, transcode from AB to AGCT formats, and more. Further, an integrated spreadsheet editor facilitates data editing and transformation on a grand scale.

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Comprehensive Quality Assurance

The more time you spend enhancing the quality of your GWAS data, the higher the chance you'll have of a successful study. SVS delivers the most comprehensive set of conventional and state-of-the-art quality assurance tools to ensure your data is of the highest quality, including every measure outlined in the definitive paper from Laurie, et.al. in Genetic Epidemiology. Here's a sample of what you can do:

• LD pruning
• One-step SNP filtering on call rates, HWE, and MAF
• Relatedness checks
• Population stratification
• SNP concordance
• Gender misidentification
• Multidimensional outlier detection
• Autosome heterozygosity
• Visual inspection of allele intensities
• Chromosomal aberration screening
• And more...

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