Method To Identify Focal Amplification

Question

[Piv1]

Hi, I am looking for a method/algorithm for the identification of focal amplification ( agilent CGH data or Affymetrix SNP6) in a set of tumors. Any suggestions are welcome. Thanks,

Answer 1

[Chris Miller]

You'll probably want try one or more of these, listed in order of my recommendation:

• JISTIC, which is the successor to GISTIC.
• CMDS (paper)
• RAE (paper)
• GTS

[Rm]

G/JISTIC is good one..

[Chirag Nepal]

Hi @Rm and @Chris Miller,

I am trying to use JISTIC to analyze CNV across large cohort. I am stuck with making probe_location_file, that is used to make input matrix file. I had posted the question here: JISTIC. Make Probe location file to compare copy number among samples

Alternatively, can I just make matrix for gene based, by interesting gene coordinates with CNV coordinates, and assign the CNV(amplification/deletion) value. But not samples will have some value to assign in the output file from DNACopy. So what do I insert in those missing values.

Thank you!

Answer 2

[Rm]

Try Agilent's Genomic Workbench: (you can get a trial version of it from their website)

and try Affy's Genotyping console to handle SNP6 data. ( I think this too freely available for academic use)

For focal (you can define the size) regions write a simple script to extract the information required.