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!