This document discusses the analysis of Affymetrix OncoScan data using Nexus Copy Number software. It outlines researchers' needs such as visualizing data, identifying common aberrations, comparing sample populations, and predictive analysis. It then describes the data processing in Nexus, including algorithms for identifying significant aberrations and dealing with heterogeneity. Finally, it shows examples of data visualization, analysis features for survival, enrichment, and comparing groups that Nexus provides to help researchers analyze and understand OncoScan data.

1. Affymetrix OncoScan™ Data Analysis with
Nexus Copy Number ™
Zhiwei Che, Ph.D.
BioDiscovery, Inc.

2. 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 between
two sample populations
4. How to find common biological themes using Gene
Enrichment Analysis

3. Researchers’ needs with OncoScan™ Data
(cont.)
5. How to identify genomic regions that are predictive of a
numerical value (e.g. age of onset) using Predictive
Power analysis
6. How to identify genomic regions that are predictive of
survival and generate Kaplan-Meier plots
7. How to access public cancer data sets and compare
with their own data

4. Data Processing in Nexus Copy Number
Pre-Processing
Log Ratio
Segmentation
Project
Regions
Genes
Function
CEL
CNCHP
CYCHP
Affy OncoScan™
NimbleScan
GenomeStudio
Agilent FE
ImaGene
GenePix
BlueFuse
Text file

5. 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 analysis
of this power with easy to use interface
• Survival Analysis
– Cox Regression Analysis / Kaplan-Meier Analysis
• Class Comparison
– Fisher Exact test

6. Nexus DB
Project
Project Project
Project
Project
Project
Project
Project ProjectProject
Project
ProjectProject Project
Project
Internet
• Autism
• Cancer
• Autism
• Alzheimer
• Cancer • Cancer• Alzheimer
• Cancer
• Autism
Secure Storage
Cross Project and Platform Search
Global Collaboration
Public Data Sets Access

7. Nexus Copy Number

8. Breast Cancer OncoScan™ Data Set in Nexus

9. Individual Control Sample Genome View

10. Individual Cancer Sample Genome View

11. Genome View for All Samples

12. Genome Heatmap View for All Samples

13. Run GISTIC on All Samples

14. GISTIC Results Genome View

15. Genome View by Conditions

16. Close-up on Her-2

17. Compare Different Groups

18. Significantly Different CNA Regions

19. Enrichment Results for Functions

21. Survival Predictive Power Analysis

22. Kaplan-Meier Plot

23. Query Copy Number Event in Nexus DB