Copy Number Analysis Module (CNAM)

Powerful New Methods for Whole Genome Copy Number Association Studies

CNAM is the most accurate and advanced tool for whole genome copy number association studies. Together with HelixTree, CNAM offers an end-to-end solution for normalizing your intensity data, correcting for batch effects and stratification, detecting copy number variations with lower false discoveries and greater sensitivity than any other program, and performing association analysis on found copy number variations or log ratios directly.

 

  • What's New
  • Overview
  • Getting Started

New functionality added to make the copy number association workflow more complete

The following processing, analysis, and quality control measures have
been added recently to make the whole genome copy number association workflow
more complete.

weinbar View Tutorial
SNP & Variation Suite 6.1 and 6.2: New Feature Training

Whole Genome Log Ratio Association TestslogR association window
In addition to performing association tests on copy number covariates using segmentation, CNAM now offers a straightforward approach to perform whole genome single marker associations (correlation/trend, t-test, and regression) directly on log ratios. Further, a median smoothing script is available and can be applied to real-value columns (i.e. p-values) to significantly improve signal to noise ratios.
›› Learn more about Log Ratio Association Tests

Correcting for CNV-Based Batch Effects and Stratification
Similar to SNPs in HelixTree, CNAM can correct log ratios for batch effects and stratification using an Eigenstrat-based principal component analysis (PCA) method.
›› Learn more about Batch Effects & Stratification

Affymetrix 500k, 5.0, 6.0 CEL File Processing
CNAM substantially replicates the Affymetrix workflow for converting CEL files to log
ratios, including:

  • Quantile normalization (without gender bias)
  • Virtual Array Generation (merging CN and SNP data, or NSP and STY)
  • Normalizing log ratios against any reference population

This can be done for 500k, SNP 5.0, and SNP 6.0 arrays. Further, it is relatively high
speed and works for thousands of samples. (2,000 samples can be processed
overnight.) If preferred, CNAM can also read CNT and CNCHP files from Affymetrix's
CNAT Batch Analysis and Genotyping Console Software 2.0 Software tools. 
›› Learn more about CEL File Processing

Other Modifications

  • Importing LogRs into HelixTree can now be done directly from the CNAM menu without having to go through the entire copy number segmentation process.
  • The capability to save a LogR DSF as CNT files has been added to the CNAM menu. This makes it computationally viable to export whole genome LogR data for a virtually unlimited number of samples as CNT files which can then be viewed in Affymetrix's GTC Browser. If desired, you can also choose to save selected chromomses rather than the entire DSF file.
  • Two new scripts are available for download:
    • Export Univariate Segment Means to Wiggle Files
    • Export Multivariate Segment Means to Wiggle File
    In case you forget to check the Optional Bookmark File Output box when running Copy Number Segmentation, you can run these scripts to create Wiggle files directly from the resulting segment means spreadsheet. Wiggle files can be opened in supported genome browsers (e.g. UCSC, Affymetrix GTC) to view copy number segments across the genome.

    Visit our Scripts Repository to download.

What is CNAM?

CNAM employs a proprietary optimal segmenting algorithm that can detect copy number variations with astonishing accuracy. In fact, its unique multivariate method can detect copy number variations at single marker resolution! You can also use CNAM to normalize log ratios against a reference set of your choice and correct for batch effects and stratification using an Eigenstrat-based principal component analysis method. It works on virtually unlimited sample and data sizes and is compatible with most major genotyping platforms (incl. Affymetrix 5.0 and 6.0).

 Whole Genome Copy Number Variation Association

Explore Further

Get Started Accelerating Your Quest for Significance!

The following resources are available to help you get started discovering significant
copy number associations in your data:

A more complete copy number association workflow

The following processing, analysis, and quality control measures have
been added recently to make the copy number association workflow more complete:

  • Download Free Trial
  • Whole Genome Association Tutorial
  • Documentation
  • Tutorials and Webinars