SNP Chip Data Analysis for Whole Genome Association Studies I - PowerPoint PPT Presentation

SNP Chip Data Analysis for Whole Genome Association Studies I nforSense Limited Sha Liao , Life Science Application Scientist July 11, 2007 www.inforsense.com

What is GenSense? -- Field: Statistical Genetics -- Focus on: Genome-Wide Association studies -- Subject: SNP Chip Data ~~ Rapid identification of phenotype/genotype associations and predictive biomarkers using GenSense

What can GenSense do? Portal – End user environment Portal – End user environment Data Quality Analysis Results Data Quality Analysis Results Handling Control Methods Interpretation Handling Control Methods Interpretation -- Organise data in projects -- Assess quality of SNPs and samples -- Analyse data using statistical tests -- Annotation services like ‘SNP to gene’ mapping

Example: Affymetrix SNP Chip Data

Duplicate Check

Analysis: SNP, MAF, HWE

Interpret: Map SNPs to Genes

Ingenuity Interpret: Genes to Pathways GeneGO

Why use GenSense? � -- Automatic organization of imported data � -- Effective utilization of analysis approaches � -- Wide integration of related tools � -- Deployable reuse of completed workflows � -- Intuitive visualization of performed results

Automatic organization of imported data Portal – End user environment Portal – End user environment Data Quality Analysis Results Data Quality Analysis Results Control Methods Interpretation Handling Control Methods Interpretation Handling � Affymetrix, Illumina, Linkage, PLINK, HapMap & PrettyBase formats � Generic � SNP major � Sample major � SNP, Sample triple � Data reduction � Flexible import styles

Effective utilization of analysis approaches Portal – End user environment Portal – End user environment Analysis Data Quality Results Analysis Data Quality Results Handling Control Interpretation Methods Handling Control Interpretation Methods � SNP and genotype analysers � Haplotype analysers � Genotype/Phenotype correlation and simulation � Linkage Disequilibrium (LD)

Wide integration of 3rd part tools Portal – End user environment Portal – End user environment Analysis Results Data Quality Analysis Results Data Quality Handling Control Methods Interpretation Handling Control Methods Interpretation � Genome browser (UCSC) � Haploview � PLINK � PHASING

Deployable reuse of completed workflows Portal – End user environment Portal – End user environment

Intuitive visualization of performed results --Spotfire --Haploview --HeatMap …

How to use GenSense? � -- Portal: Deployable service � -- Client: Build application workflows

Portal – Homepage Portal – Homepage

Portal – Create a new project Portal – Create a new project

Portal – Service Links Portal – Service Links

Portal – Duplicate Check Results Portal – Duplicate Check Results

Portal – HeatMap Visualization Portal – HeatMap Visualization

Client: Build workflows

Interaction With Other Plug-in BioSense GeneGO, Ingenuity

ClinicalSense

Thank you! � For more information, please visit: � http://www.inforsense.cn � http://www.inforsense.com � For questions please contact � Sha Liao liaosha@inforsense.com � Ronghua Zeng rhzeng@inforsense.com