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

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snp chip data analysis for whole genome association
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SNP Chip Data Analysis for Whole Genome Association Studies I - - PowerPoint PPT Presentation

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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

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www.inforsense.com

I nforSense Limited Sha Liao, Life Science Application Scientist

July 11, 2007

SNP Chip Data Analysis for Whole Genome Association Studies

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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

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What can GenSense do?

Portal – End user environment Portal – End user environment

Data Handling Data Handling Quality Control Quality Control Analysis Methods Analysis Methods Results Interpretation Results Interpretation

  • - Organise data in projects
  • - Assess quality of SNPs and samples
  • - Analyse data using statistical tests
  • - Annotation services like ‘SNP to gene’ mapping
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Example: Affymetrix SNP Chip Data

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Duplicate Check

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Analysis: SNP, MAF, HWE

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Interpret: Map SNPs to Genes

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Interpret: Genes to Pathways

GeneGO Ingenuity

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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
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Portal – End user environment Portal – End user environment

Data Handling Data Handling

Quality Control Quality Control Analysis Methods Analysis Methods Results Interpretation Results Interpretation

  • Affymetrix, Illumina, Linkage, PLINK,

HapMap & PrettyBase formats

  • Generic
  • SNP major
  • Sample major
  • SNP, Sample triple
  • Data reduction
  • Flexible import styles

Automatic organization of imported data

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Effective utilization of analysis approaches

Portal – End user environment Portal – End user environment Data Handling Data Handling Quality Control Quality Control

Analysis Methods Analysis Methods

Results Interpretation Results Interpretation

  • SNP and genotype analysers
  • Haplotype analysers
  • Genotype/Phenotype correlation and

simulation

  • Linkage Disequilibrium (LD)
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Wide integration of 3rd part tools

Portal – End user environment Portal – End user environment Data Handling Data Handling Quality Control Quality Control

Analysis Methods Analysis Methods Results Interpretation Results Interpretation

  • Genome browser

(UCSC)

  • Haploview
  • PLINK
  • PHASING
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Deployable reuse of completed workflows

Portal – End user environment Portal – End user environment

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Intuitive visualization of performed results

  • -Spotfire
  • -Haploview
  • -HeatMap

…

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How to use GenSense?

  • - Portal: Deployable service
  • - Client: Build application workflows
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Portal – Homepage Portal – Homepage

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

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Portal – Service Links Portal – Service Links

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Portal – Duplicate Check Results Portal – Duplicate Check Results

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Portal – HeatMap Visualization Portal – HeatMap Visualization

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Client: Build workflows

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Interaction With Other Plug-in

BioSense GeneGO, Ingenuity

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ClinicalSense

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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