Problem: How do I take advantage of the new Agilent Custom 2 x 415K human CGH platform supported in v1.3.1?

Topic: caIntegrator Usage

Release: caIntegrator v1.31 and above

Date entered: 01/10/2012

Solution

As of v1.3.1, caIntegrator supports a new in situ oligonucleotide array platform known as Agilent Custom 2 x 415K Human CGH (Comparative Genomic Hybridization), which is an update of the stock Agilent SurePrint G3 Human CGH Microarray Kit 2x400K platform (catalog no. G4448A) adapted by The Cancer Genome Atlas (TCGA) project.  For detailed technical specifications of the platform, please refer to this page on the NCBI site.

This newly supported platform is similar to others in that it generates copy number results as a data type. Unlike SNP-based platforms, however, Agilent Custom 2 x 415K Human CGH does not generate LOH (Loss of Heterozygosity) or SNP (Single Nucleotide Polymorphism) data. For more information about how Agilent Custom 2 x 415K Human CGH compares to other array platforms, please refer to this chart on the TCGA wiki.

Please note that the platform's design file does come bundled with the caIntegrator installation; it must be downloaded separately and manually loaded into caIntegrator by the study manager or other end user. The design file can be download here, courtesy of the Web site of the European Bioinformatics Institute. (The filename of the design file from the download link is 'A-GEOD-13346.adf.txt'; elsewhere on the Internet, the design filename can be found as 'GPL13346_family_tdt.adf'.)

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