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What is recurrent somatic copy-number alterations?

Hi there,

I was performing GISTIC2.0 to find so-called "recurrent" somatic copy number alterations (SCNA). However, I am not quite understand what the term "recurrent" means here.

In fact in my region-level CNA file estimated by GISTIC, there is a deletion peak with only one sample positive. Therefore, how can we say this is a "recurrent" SCNA?

scna gistic
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updated by Kevin Blighe Kevin Blighe • written by Xiaofan • Xiaofan

Hello! I haven't used GISTIC myself so I cannot answer with 100% confidence, but could it mean that the given SCNA you found in your sample takes place in a region already described to be prone to CNAs?

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written by iraun iraun

1 answer

Hello,

A recurrent somatic copy number alteration (recurrent sCNA) is a copy number alteration that occurs at a statistically-significantly high frequency in a set of tumour samples. GISTIC and GAIA are two algorithms / programs that detect these.

As an example, we could say that ERBB2 / HER2 gene amplification is a recurrent sCNA in Her2-positive breast cancer - the gene can be amplified x17 in this cancer histology sub-type.

As it can be inferred, through the detection of recurrent sCNA with very low p-values and high penetrance, one could use these in clinical diagnostic tests.

Kevin

NB - deletions can also be recurrent sCNA

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written by Kevin Blighe Kevin Blighe

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