The difference between Copy Number Alterations, Copy Number Aberrations (CNAs) and Copy Number Variations (CNVs).

Question

[Ward Weistra]

Dear all,

I would like your views on the definitions for copy number alterations, copy number aberrations (CNAs) and copy number variations (CNVs).

This is my current understanding:

1. Copy number alterations and copy number aberrations are synonyms. See for example:

• Bioinformatics (2014) 30 (12):i195-i203 uses copy number aberrations (CNAs) in paper and both terms in titles of references.
• Bioinformatics (2007) 23 (13):i450-i458 uses copy number alterations (CNAs) in paper and both terms in titles of references.

2a. Copy number alterations/aberrations (CNAs) are changes in copy number that have arisen in somatic tissue (for example, just in a tumor), copy number variations (CNVs) originated from changes in copy number in germline cells (and are thus in all cells of the organism). See for example:

• BMC Bioinformatics 2009, 10(Suppl 1):S67: "copy number variations (in germline cells) or copy number alteration (in somatic cells)"
• Genome Med 2009, 1:62: "So far we have focused here on CNVs and cancer predisposition, but similar high-resolution approaches have also driven recent studies on acquired (somatic) copy number alterations (CNAs)"

2b. However some articles seem to use copy number alterations/aberrations (CNAs) as the term encompassing both germline and somatic copy number changes and use somatic copy number alterations/aberrations (SCNAs) as the term for somatic copy number changes:

• Bioinformatics (2014) 30 (12):i195-i203 explains: "Copy number aberrations (CNAs) are gains and losses of large segments of the genome-ranging in size from a few kilobases to whole chromosomes. Somatic CNAs (SCNAs) that occur during the lifetime of an individual are a major contributor to cancer development, particularly for solid tumors [...]."
• Nature Genetics 45, 1134-1140 (2013): "somatic copy number alterations (SCNAs)" and "germline copy number variations (CNVs)"

Wikipedia's 'Copy-number variation' article just mentions "Copy-number variations (CNVs) - a form of structural variation - are alterations of the DNA of a genome [...]". There is no article on alterations/aberrations.

3. Comments on preferred spelling (eg hyphen or no hyphen) are also welcome as side notes :)

Thank you in advance for your answers!

Best regards,
Ward

Answer 1

[DG]

Yeah, basically all of the terms get used synonymously, but within subfields of genetics and genomics you'll notice some preferred nomenclature used. And basically that is exactly how you laid it out. CNA is used in the Cancer Genomics speciality usually when referring to somatic mutations. However you will also still see them in that context referred to as CNVs or just SVs (Structural Variants) quite frequently.

As the side note I prefer no hyphens. I think in English language writing in general there is a move away from hyphenating words for a variety of reasons, particularly when they can be written as two separate words. But really that is mostly down to preference.

Answer 2

[yukselmek]

This paper uses as 2a.

http://www.nature.com/nature/journal/v486/n7403/full/nature10983.html