PBAT COPY NUMBER ASSOCIATION TESTING

Performing copy number association in PBAT is in many ways similar to performing SNP association in PBAT in that most FBAT tests for SNP analysis are supported for copy number analysis as well. The big differences are in data preparation and handling. Whereas SNP genotypes can be called with a great deal of accuracy, current genotyping technology does not enable us to make unambiguous integer copy number calls. Therefore, PBAT performs association using log2 ratios (from now on referred to as LogRs) as covariates rather than integer copy number values.

Using LogRs as covariates presents data handling challenges, because on a whole genome scale, a LogR file can be tens of gigabytes in size and cannot be stored in computer memory. Rather than loading all the LogRs into a spreadsheet and joining them with pedigree information, as done in SNP analysis, Golden Helix PBAT analyzes the LogR file directly and matches it “behind the scenes” with a pedigree spreadsheet.

This tutorial will lead you through performing PBAT CNV association assuming a LogR DSF file has been created. For help creating LogR DSF files using the Copy Number Analysis Module (CNAM) see Steps 1-3 of the Whole Genome Copy Number Association Tutorial.

This tutorial can be generalized for any data set. To follow along exactly, it is recommended you first download and unzip the ZIP file below. It contains a LogR DSF file containing ~500k LogRs on 30 samples and a corresponding CSV pedigree spreadsheet.

Overview:

1. 1. Prepare a LogR DSF file
2. 2. Prepare and import a pedigree spreadsheet
3. 3. Run PBAT CNV analysis
   

REQUIREMENTS

To complete this tutorial, you will need the following:

• Golden Helix PBAT
• Copy Number Analysis Module (CNAM)
• 30common_pbat_cnv.zip (contains a LogR DSF file containing ~500k LogRs on 30 samples and a corresponding CSV pedigree spreadsheet)

Prerequisite Knowledge:
Intermediate CNAM and Golden Helix PBAT functionality