G6G

InforSense GenSense

Category Genomics>Genetic Data Analysis/Tools

Abstract InforSense GenSense provides a complete and flexible solution that enables the analysis of data from the latest generation of high-throughput genotyping platforms. It has been specifically designed to aid the user with complex analysis to quickly find interesting single nucleotide polymorphisms (SNP’s) and produce reports with easy to understand visualizations. GenSense supports data from Illumina BeadChips and Affymetrix GeneChip Mapping arrays as well as from HapMap, PrettyBase and Pedigree formats. Products features/capabilities include:

GenSense allows you to analyze genome wide association data, including:

1) Case Control and Candidate gene studies.

2) Identify associations between genotypic and phenotypic data.

3) Provide tools to support data management and analysis of genotypic and phenotypic data to automatically detect these associations.

4) Rank the most significant associations among case control studies.

5) Looking at frequencies of alleles in a sample population.

6) Identify predictive and diagnostic biomarkers from significant associations.

7) Provide intuitive and easily absorbed statistical and graphical summaries of large data sets.

8) Compatibility with other InforSense solutions.

9) Link to current genomics data sources -- Entrez Gene, HapMap, SNP’s, Online Mendelian Inheritance in Man (OMIM), Pathways -- for in-silico target identification and validation, toxicogenomics, interpretation of clinical trial data.

10) Graphical traversal of genomic data.

GenSense workflows give you a flexible way of customizing the way in which you test, plan and run your analysis. The solution assists you all the way from data import, through quality control and filtering to data analysis and annotation.

Data Importing and Exporting --

1) Affymetrix GeneChip Mapping Array [Bayesian Robust Linear Model with Mahalanobis distance classifier (BRLMM) and BRLMM-P (-Perfect match probes) output;

2) HapMap genotype format;

3) Illumina BeadStudio (Standard Final Report);

4) Linkage format;

5) PrettyBase format;

6) Generic Sample or SNP major format.

Data Quality Control --

1) Genotype call score filtering;

2) Genotype Completion analysis by sample, locus;

3) Duplicate detection;

4) Test for deviation from Hardy-Weinberg Equilibrium;

5) Mendelian Inheritance Check.

Data Analysis --

A) SNP Analyzer --

• 1) Reference/alternative base;
• 2) Minor Allele Frequency (MAF);
• 3) Allelic and genotype counts;
• 4) Entropy;
• 5) Deviation from Hardy-Weinberg Equilibrium (HWE) chi-square (Chi2) test with p-value (asymptotic and exact).

B) Genotype Analysis --

• 1) Genotype Analyzer node;
• 2) Cluster genotypes;
• 3) Calculate linkage disequilibrium (LD) between all pairs of markers/SNP’s.

C) Case-Control/Genotype/Phenotype Association Tests --

• 1) Trend, Genotypic, Allelic, Dominant-Recessive tests;
• 2) Odds Ratio, Relative Risk;
• 3) Fisher’s exact test.

D) Haplotype Statistics --

• 1) List alleles based on frequency, calculate marker variability;
• 2) Cluster haplotypes.

E) Correspondence analysis (CA) --

• 1) Display association between alleles in multi-allelic markers;
• 2) Multiple CA - display associations between all alleles simultaneously.

F) Association between Genes --

• 1) Linkage Disequilibrium (LD);
• 2) Likelihood ratio;
• 3) Logistic Regression;
• 4) Genotype-Phenotype simulation and correlation.

Annotation and Tool Integration --

1) SNP to Gene mapping using NetAffx, Single Nucleotide Polymorphism database (dbSNP) and EntrezGene.

2) Query and visualize in the University of California at Santa Cruz (UCSC) Genome Browser.

3) HaploView integration;

4) PLINK integration;

5) Optional R-genetics integration.

InforSense GenSense also enables SNPs of interest to be further characterized and interpreted using the genome annotation tools in InforSense BioSense (see G6G Abstract Number 20033). The data can be integrated with sequence analysis workflows to further investigate the genes associated with disease relevant SNPs. The results may also be analyzed with InforSense TextSense (see G6G Abstract Number 20034) to collect and prioritize the most appropriate scientific articles. For complex phenotypic information InforSense ClinicalSense gives the user the ability to design experiments and answer complex questions involving sample stratification.

System Requirements

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Manufacturer

• ID Business Solutions Ltd., London Office (InforSense location)
• Colet Court, 100 Hammersmith Road
• London, W6 7JP
• United Kingdom
• Tel: +44 208 237 8440
• Fax: +44 208 237 8441

Manufacturer Web Site InforSense GenSense

Price Contact manufacturer.

G6G Abstract Number 20106

G6G Manufacturer Number 101430