Question

What is recurrent somatic copy-number alterations?

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2.1 years ago

Xiaofan ▴ 10

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 • 656 views

ADD COMMENT • link updated 2.1 years ago by Kevin Blighe 87k • written 2.1 years ago by Xiaofan ▴ 10

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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?

ADD REPLY • link 2.1 years ago by iraun 6.2k

score 2 · Accepted Answer · 2022-03-25

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