Copy number variation subtypes

Question

[neenu.abraham8]

What is the difference between Gain and amplification ,Loss and deletion in copy number variation ?

How are the above different in somatic and germline data?

[Jimbou]

As Pierre said,

Duplication = Gain = Amplification = insert

Deletion = Loss

Answer 1

[Eric T.]

In oncology it's a common convention that if "deletion" and "amplification" are used in addition to "loss" and "gain", then loss and gain refer to single-copy alterations, while deletion means (homozygous) loss of both copies and amplification means multi-copy gain, most often 5+ copies (i.e. 2.5-fold gain on diploid chromosomes).

Answer 2

[Pierre Lindenbaum]

According to SO, there are only two sub-classes of CNV: http://www.sequenceontology.org/browser/current_svn/term/SO:0001019 copy_number_gain & copy_number_loss. For me gain==insert, loss==del in the context of CNV

[neenu.abraham8]

Thanks for this information.I took ICGC somatic copy number alteration files.In some files they provided the mutation changes as copy neutral ,copy neutral LOH amp LOH, gain and loss.But the mutation type represent as Amplification and deletion in the annotated TCGA somatic copy number alteration files in Sage Bionetwork's Synapse database. Now I am confused with these terms.and also need some more clarifications regarding the terms like copy neutral and copy neutral LOH.please give a reference to clarify this.

[Jimbou]

http://en.wikipedia.org/wiki/Loss_of_heterozygosity+

or

http://www.ncbi.nlm.nih.gov/pubmed/20107230

Answer 3

[Ron]

• log2CopyNumber < -1 : Deep deletion
• log2CopyNumber < -1 to -0.5 :Shallow Deletion
• log2CopyNumber > 0.5 to 1 : Gain
• log2CopyNumber > 1 : Amplification
• Focal deletion: Region < 50 genes
• Large scale deletion : > 50 genes