Mutations Tab Questions

[Xavier Reilly]

Hello,

We posted this previously, but did not receive any response.

We have several questions about some definitions of terms in the mutations tab.

Q1) What is this program's definition of a splice mutation? What is the difference between a splice site and a splice region?

Q2) Under Copy number, there are several different outcomes. What is the difference between a Gain and an Amplification? Can either result in an increase in chromosome number or chromosome duplication?

Q3) Is Functional Impact biochem based (i.e. is it based on possible changes in protein shape and structure)? Also, why is Functional Impact only provided for missense mutations? Does it not apply to for nonsense mutations, splice mutations, frameshifts, etc?

Thank you,

Xavier Reilly

[Nikolaus Schultz]

Hi Xavier,

Here are some partial answers:

2) Gain and amplification are both increased copy-number … gains are lower level (fewer copies, typically more broad), amplifications are higher level (more copies, typically focal). In the case of TCGA, the data come from the GISTIC algorithm. We typically only consider the amplifications call as biologically relevant for individual genes by default.

3) The predicted functional impact is usually based on conservation of the affected amino acid. By default, truncating variants are considered deleterious, so these algorithms only predict the impact for missense mutations.

Niki.

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