Silicon Genetics Introduces Varia, A Software Workbench For High Throughput Genetic Variation Analysis 
10/19/2005 5:10:38 PM

REDWOOD CITY, Calif.--(BUSINESS WIRE)--March 30, 2004--Silicon Genetics today announced Varia(TM), a new generation of genetic analysis software designed to meet the requirements of life science researchers involved in high volume genetic variation analysis. Designed as a standalone workbench incorporating a wealth of integrated analysis algorithms, Varia has been designed to smoothly handle the millions of SNP measurements generated by whole genome genotyping measurement platforms.

"Over the last twelve months, we've worked closely with more than 20 leading research organizations and genotyping platform vendors during our design and development of Varia," said Kevin Wandryk, vice president of marketing and business development for Silicon Genetics. "From day one, our design goal has been to build a tool capable of handling the large volumes of genetic information generated by major research facilities that are taking advantage of recent developments in high throughput SNP measurement platforms."

"The high density and genome-wide coverage of the Affymetrix(R) GeneChip(R) Mapping 10K Array has changed the way our customers do linkage analysis," said John Sowatsky, vice president of the Systems Business Unit for Affymetrix. "Today's researchers use our genotyping tools for whole genome scans and need better software packages that can handle and analyze the large amounts of data generated. Silicon Genetics Varia can apply a wealth of analytical and visualization tools to data sets measuring tens of thousands of SNPs, spanning the entire human genome."

"The Varia technology addresses a number of key issues in genotype analysis," said Dr. Dietrich Stephan, senior investigator & director of the Neurogenomics Division of the Translational Genomics Research Institute. "At TGen, we use high-density SNP technologies to study the genetic mechanisms behind different types of neurological and immunological disorders. In single experiments with remarkably small sample populations, Varia allowed us to quickly identify and localize regions and genes responsible for several disease phenotypes."

Silicon Genetics Varia includes a range of tools designed to assist all applications of genotyping analysis. Major product features include:

-- The complete genome -- navigable displays of the complete human genome at the nucleotide scale, including over 7 million variations.

-- Linkage analysis tools -- validated algorithms for the association of variation-to-variation or of variation-to-disease, including linkage disequilibrium and transmission disequilibrium tests, genetic linkage scores, and case control calculations.

-- Automated tools for building haplotype maps and constructing pedigrees from user-supplied genotype data.

-- Flexible visualization tools -- pedigree diagrams, GOLD plots, haplotype maps, and plots of linkage statistics, useful for data exploration and for producing publication quality images.

-- Patent-pending algorithms for identifying regions of autozygosity likely to represent transmissible markers of recessive diseases.

-- Dedicated interfaces for managing and analyzing data from large families including tools for pedigree import and quality control filters to identify incorrect pedigree assignments and unlikely allele calls.

-- A simple file format for importing variation measurements from virtually any genotyping technology, including Affymetrix, Illumina, Sequenom, and Parallele. Drag and drop data loading from numerous genotyping technologies, and efficient tools for recording the associated clinical metadata.

For more information on Silicon Genetics Varia, or to download a fully functional trial version, go to:

About Silicon Genetics

Silicon Genetics is the leading provider of software solutions for life science discovery. With combined expertise in biostatistics, molecular biology, and information technology, Silicon Genetics is the only company to offer scalability that meets the demands of both high throughput sample volumes and increasing numbers of users. Thousands of scientists at hundreds of organizations, including 12 of the world's top 13 pharmaceutical companies, currently use Silicon Genetics desktop and enterprise solutions to advance their research. Additional information about Silicon Genetics and its products and services can be found at


Silicon Genetics Kevin Wandryk, 650-367-9600