fcna

[ho...@mskcc.org]

Hi,

 

Could you please tell me how you calculate FCNA (fraction of copy number alterations, aka fraction of genome altered)? We have done an analysis of whole exome analysis in melanoma and see a much different distribution of FCNA  than using the IMPACT cohort / values, and are trying to understand why.

 

Thanks for any assistance,

Doug

 

__________________________________________

Douglas Hoen, PhD

Senior Bioinformatics Engineer

Immunogenomics and Precision Oncology Platform

Memorial Sloan Kettering Cancer Center

417 E 68th St, New York, NY 10065

T: 646-888-3344   F: 646-888-3406

www.immunegenomics.org

ho...@mskcc.org

 

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[JJ Gao]

Hi Doug,

The fraction of genome altered is the length of segments with log2 or linear CNA value larger than 0.2 divided by the length of all segments measured. It is based on the value from the segment files. For different studies, because the values in the segment may not be comparable, FGA may not be comparable either. 

Best,

-JJ

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