Is the default threshold of 0.1 for GISTIC2.0 good?

Question

[Avro]

Hi everyone,

I work with human segmented data, and I am using GISTIC2.0. The default log2 threshold is 0.1. Above 0.1 = amplification, lower than 0.1 = deletion. I wanted to ask the community members what they think about this threshold since it is subjective, no?

Thank you

[Jonathan Crowther]

You should note that it is not below 0.1 that is a deletion rather below -0.1.

[Avro]

Hi! Yes, sorry. In gene pattern, 0.1 is automatically converted to -0.1. :)

Answer 1

[Giovanni M Dall'Olio]

In Jerby-Aron et al 2014 they used thresholds of -.3 and .3 for defining deletion/amplification. See the description in the Experimental Procedures:

Of note, the SCNA parameters (-0.3 and 0.3) used here are more stringent cutoffs compared to those used in the literature to define gene amplification and deletion (Beroukhim et al., 2010).