What is Copy Number Variation(CNV) and Alteration(CNA)

Question

[akij]

When I search for what is CNV, the term CNA also pop up in every article which makes me confused because I am not from biology background. So far my understanding is, both cnv and cna are duplication, insertion, deletion of base pairs. For example, if GCGATGA appears more than once in a DNA, then it is either CNV or CNA. I also know that copy number must be >1kb. After reading some articles I got this general idea about the terms but not sure if I am correct though. It would be nice if someone explain both terms.

[Chris Miller]

One more comment - the example you give, of GCGATGA appearing more than once, is usually referred to as an indel. Generally speaking, SV/CNVs are bigger than 1kb, indels are smaller than 100bp, and there's also a weird middle range where the terms are often mixed.

Answer 1

[Chris Miller]

Typically, CNV refers to germline events, which are variants in the population. CNA usually refers to somatic events, like those found in tumors. They are sometimes used interchangeably.

Confusingly, this is different from single-nucleotide events, which are SNPs (germline events in the population) and SNVs (somatic events).

No one said the nomenclature had to make sense! (I mean, have you seen how we name genes?!)

[akij]

Well, then why CNV is more studied than CNA? If we look in the TCGA database, each cancer cases have files for CNV but nothing for CNA. If CNA is found in tumor cells, shouldn't we study CNA instead of CNV?

[igor]

As Chris mentioned:

They are sometimes used interchangeably.

TCGA is looking at the somatic copy number differences.

[Chris Miller]

Yes, this is correct. In TCGA, for whatever reason, the nomenclature used was CNV. They're used interchangeably enough that you're pretty much always going to have to look at the context to figure out which one is being discussed.