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Category Genomics>Genetic Data Analysis/Tools Abstract GeneSpring GT is a desktop analysis workbench for analyzing high-volume, high-density genotyping data. The software provides a comprehensive set of linkage and association algorithms that allow researchers to discover relationships between genotypes and phenotypes. Researchers can visually explore fully annotated single nucleotide polymorphisms (SNPs) and genes at varying levels of detail. Designed for biologists and statisticians, GeneSpring GT is capable of importing, visualizing, and analyzing hundreds of thousands of variation measurements simultaneously, for rapid localization of disease or phenotype markers. Products features/capabilities include: New! Quantitative Case Control -- Version 2 provides an easy interface for segregating samples into case and control groups based on the values of the quantitative trait. Tools are available for visualizing the distribution of quantitative values and for selecting the boundaries of extreme values. New! ANOVA -- A new analysis of variance (ANOVA) model is available to examine the group means or quantitative traits, where the groups are assigned according to genotypes. Two (2) models of grouping are available, one for single alleles, and one for complete genotypes (diplotypes). New! Multivariant Regression -- The latest release introduces a suite of new regression tools. Regressions can be performed using any number of markers (genotypes or phenotypes) as independent variables. For quantitative phenotypes these regressions can be performed using a logistic regression algorithm. Genetic Linkage Tests -- With user supplied pedigree information, GeneSpring GT enables users to calculate maximum likelihood and estimate recombination frequencies for millions of variations. Linkage can be estimated for combinations of individual measured variations, haplotype blocks that span measured variations, or observed phenotypes. Linkage Disequilibrium (LD) Tests -- When pedigree information is Not available, GeneSpring GT can test for potential association between phenotypes and marker loci. Often called case-control experiments, these analyses are especially useful for researchers who have genotyped hundreds of individuals. GeneSpring GT reports a number of statistics measuring disequilibrium and association including correlation, chi squared values, chi squared p-values, and standardized disequilibrium. Transmission Disequilibrium Tests -- GeneSpring GT includes tools for estimating transmission disequilibrium statistics as well as for haplotype-based haplotype relative risk (HHRR) statistics. When many affected individuals and their parents have been genotyped, transmission disequilibrium can provide high-resolution localization of potential markers. Loss-of-heterozygosity (LOH) Analysis -- LOH analysis is an essential part of performing genotyping studies in cancer research. GeneSpring GT provides specialized methods for identifying and comparing regions of homozygosity across different individuals and populations. Autozygosity Testing -- Utilizing a patent-pending algorithm, GeneSpring GT provides a novel, highly efficient method for identifying regions that result from the autozygous inheritance of a recessive allele. This algorithm provides unparalleled sensitivity when small numbers of inbred individuals are genotyped. In many studies, fine mapping can be achieved with using sample populations of less than ten (10) individuals. Visualize the Complete Human Genome -- Using a variety of visualization methods, researchers can easily superimpose their analysis results directly on a complete representation of the human genome. They can browse through the human chromosomes at various levels of detail, providing visual snapshots of many different types of genomic information: 1) Nucleotide-level sequence data; 2) Genes and their intron/exon structure; 3) Individual variations and their respective alleles; 4) Maternal and paternal haplotypes; 5) Cytogenetic/karyotypic markers. Patient Meta-data, Family Trees, and Clinical Observations -- Rigorous use in a clinical setting demands that all relevant patient data be made available to the geneticist. GeneSpring GT includes templates for enforcing standardized vocabularies and for importing tables of annotation from other applications. In addition GeneSpring GT includes a visual pedigree editor to help users represent familial relationships and disease transmission in a sample population. GeneSpring GT can also infer pedigree structure directly from raw genotypes and haplotype data with a high degree of accuracy. Finally, data in the standard LINKAGE format can be imported directly into GeneSpring GT. Error Detection and Propagation -- GeneSpring GT contains a number of quality control filters that can be employed as standard procedures in the analysis pipeline: 1) Correct pedigree assignment; 2) Hardy- Weinberg equilibrium; 3) Mendelian inheritance errors; 4) Confounding parameters in sample populations. Virtually all of GeneSpring GT's linkage and association tests can utilize haplotype maps. GeneSpring GT can build these maps directly from users' experimental data, or maps can be imported from external sources. By using haplotype map blocks - rather than individual variations - as markers, the penalty for measurement errors is significantly reduced. The Rapid Route to Publication -- In the hands of researchers around the world, GeneSpring GT is already revolutionizing the time from experiment to publication. A standalone workbench would Not be complete if it didn't include tools for producing publication quality images, ready for final submission. Whether a pedigree diagram, a plot of linkage disequilibrium, a variation dendrogram, a Venn diagram, a haplotype map, the intron structure of a given gene, or a simple scatter plot, GeneSpring GT can produce high resolution images in standard vector and rasterized formats. Tools for Ultra High-throughput Analysis -- All of GeneSpring GT's analysis tools are available using Agilent Technologies' scripting engine. Using the GeneSpring GT ScriptEditor, users can automate their most frequent analysis strategies. These scripts can be shared with colleagues so that complex analysis strategies can be repeated exactly. In high throughput environments where repeatability is important, scripts can guarantee that the same analysis is reproduced exactly.
• Windows 2000/XP/Server 2003 • Pentium IV or faster • 1024 MB RAM or higher • 250 MB avilable disk space • 2 - 4 GB of available disk space (for the complete Human and Mouse genome) • 1024 x 768 display Mac Version • Mac OS X (10.4.x or later) • JVM 1.4.2_06r • 1024 MB RAM or higher • 250 MB avilable disk space • 2 - 4 GB of available disk space (for the complete Human and Mouse genome) • 1024 x 768 display Manufacturer Home office; see web site for international locations.
Life Sciences and Chemical Analysis Group 5301 Stevens Creek Boulevard Santa Clara, CA 95051-7201 USA 800-227-9770 Manufacturer's Web Site www.chem.agilent.com/scripts/pds.asp? lpage=34662 Price Contact manufacturer G6G Product Number 20108 G6G Manufacturer Number 100130 |
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