Genome-Wide Association

Webcasts: Genome-Wide Association Analysis

Check out our webcasts page for a series of recordings on genome-wide SNP and CNV association studies. Topics range from best practices in study design and quality assurance to analysis and analytic methodologies.

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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.

» More about SNP Analysis and CNV Analysis

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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Robust Quality Assurance

Having collaborated on dozens of SNP and CNV genome-wide association studies, we understand how critical high quality data is for achieving quality results. Therefore, considerable effort has been made to enhance quality assurance at every step. You can now easily generate a number of genotype statistics, view cluster plots of allele intensities, check gender and marker concordance, perform variance analysis on log ratios, filter poor quality markers and samples, and more.

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