gain vs amp in data output files

[Robert Screaton]

hello

thanks for your very helpful website

could you define what you mean by 'gain' and 'amp' in the copy number analyses you provide

many thanks

rob

Robert Screaton, Ph.D.

Canada Research Chair in Apoptotic Signaling

Children's Hospital of Eastern Ontario Research Institute

401 Smyth Rd.

Ottawa, ON

K1H 8L1

CANADA

phone: (613) 738-4180

fax: (613) 738-4833

http://www.cheori.org/screaton_index.html

[Nikolaus Schultz]

Dear Rob,

Sorry for the late reply. Gain typically means a lower-level arm-level gain, a few extra copies. Amplification refers to higher level, usually focal amplifications (many extra copies, ~5 and up). For example, look at EGFR in glioblastoma, which is focally amplified in more than 40% of samples. The nearby gene CDC14C is frequently gained (along with most of the chromosome), but never amplified.

The IGV screenshot below illustrates this.

I hope this is helpful.

Niki.