WHOLE GENOME COPY NUMBER ASSOCIATION

The Copy Number Analysis Module (CNAM), in conjunction with HelixTree, offers several methods for determining where regions of copy number variation occur and performing association analysis either on log2 ratios directly or on found regions of copy number variation. This tutorial breaks down the overall approach into seven steps, each consisting of one or more processes. They are:

1. 1. Generate log ratios versus reference samples
2. 2. Identify markers to exclude
3. 3. Correct for batch effects and stratification
4. 4. Perform whole genome log ratio association tests
5. 5. Run segmenting algorithm
6. 6. Discretize copy number segment covariates
7. 7. Perform association analysis on copy number segment covariates
8. 8. Visualize segmenting results

Depending on your particular dataset and research goals, it may not always be optimal to perform each step sequentially. To guide you, recommendations for how to proceed are provided at the end of each section.

REQUIREMENTS

To complete this tutorial, you will need the following:

• HelixTree
• Copy Number Analysis Module (CNAM)
• Whole Genome Association Module

Prerequisite Knowledge:
Basic Golden Helix SVS functionality