Affymetrix OncoScan™ Data Analysis withNexus Copy Number ™

Zhiwei Che, Ph.D.

BioDiscovery, Inc.

Researchers’ needs with OncoScan™ Data

1. Visualize the data in an easy and straightforward way

2. How to identify common aberrations in group of samples

– Based on set minimum frequency

– Using the STAC algorithm

– Using the GISTIC algorithm

3. How to identify regions of significant difference betweentwo sample populations

4. How to find common biological themes using GeneEnrichment Analysis

Researchers’ needs with OncoScan™ Data(cont.)

5. How to identify genomic regions that are predictive of anumerical value (e.g. age of onset) using PredictivePower analysis

6. How to identify genomic regions that are predictive ofsurvival and generate Kaplan-Meier plots

7. How to access public cancer data sets and comparewith their own data

Data Processing in Nexus Copy NumberPre-Processing

Log Ratio

Segmentation

Project

Regions

Genes

Function

CEL

CNCHP

CYCHP

Affy OncoScan™

NimbleScan

GenomeStudio

Agilent FE

ImaGene

GenePix

BlueFuse

Text file

Enabling researchers to take advantage

Incorporation of State-of-the-Art Methodologies

• Identification of statistically significant common aberrations– STAC Algorithm from Upenn

– GISTIC Algorithm from Broad Inst.

• Dealing with sample aneuploidy and heterogeneity– ASCAT Algorithm from U of Oslo

– Tumor with matched normal analysisof this power with easy to use interface

• Survival Analysis– Cox Regression Analysis / Kaplan-Meier Analysis

• Class Comparison– Fisher Exact test

Nexus DB

ProjectProject Project

Project

Project

Project

ProjectProject ProjectProject

Project

ProjectProject ProjectProject

Internet

• Autism• Cancer

• Autism• Alzheimer

• Cancer • Cancer• Alzheimer• Cancer

• Autism

Secure StorageCross Project and Platform SearchGlobal CollaborationPublic Data Sets Access

Nexus Copy Number

Breast Cancer OncoScan™ Data Set in Nexus

Individual Control Sample Genome View

Individual Cancer Sample Genome View

Genome View for All Samples

Genome Heatmap View for All Samples

Run GISTIC on All Samples

GISTIC Results Genome View

Genome View by Conditions

Close-up on Her-2

Compare Different Groups

Significantly Different CNA Regions

Enrichment Results for Functions

Survival Predictive Power Analysis

Kaplan-Meier Plot

Query Copy Number Event in Nexus DB