Often, genetics studies, especially genome wide ones, talk about "focal copy number variations" in genes or regions of the chromosome. I know what a copy number variation is. What does "focal" mean, exactly?

Are there non-focal CNVs? What are they? Where did the term "focal" originate? Is there a specific paper that coined (and hopefully unambiguously defined) the term?

A search for "focal copy number variation" on Google Scholar should turn up plenty of papers about it. The GISTIC algorithm is a popular computational method for finding putative CNVs- so information about this algorithm may have some clues.

A documentation text for one GISTIC implementation on the Broad Institute's website states the following:

(8) Broad or Focal: Identifies whether the region reaches significance due primarily to broad events (called “broad”), focal events (called “focal”), or independently significant broad and focal events (called “both”).

  • $\begingroup$ You could probably even call an aneuploidy (variation in chromosome number) a CNV. So that’s pretty large-scale. $\endgroup$ Commented Sep 4, 2012 at 16:06

1 Answer 1


A copy number variation (CNV) is when the number of copies of a particular gene varies from one individual to the next.

From: the NIH Glossary

Focal CNVs are regions of repeated genetic information that only span a small proportion (<25%) of the chromosome arm (although this does not seem to be a consistent rule), and can contain few genes. CNVs greater than this are termed either 'large-scale' or 'broad'.

Here are some relevant papers I came across (no doubt there are more);

This paper is about a program (VarScan2) the authors have made to robustly detect somatic mutations and CNVs;

To identify SCNAs [somatic copy number alterations], VarScan 2 compares Q20 (base quality >=20) read depths between tumor and normal samples for contiguous regions of coverage ... Therefore, we apply a circular binary segmentation (CBS) algorithm (Seshan and Olshen 2010) to delineate segments by copy number and identify significant change-points. A subsequent joining procedure merged adjacent segments of similar copy number and classified them as either large-scale (>25% of chromosome arm) or focal events.

From: Koboldt D, et al, 2012.

I continued searching, as I wondered whether this was a standard definition, or just one used by the authors.

This paper is reporting bacterial genes that drive focal chromosomal aberrations, but do not give a great definition (as it seem quite arbitrary to me);

Many of these [chromosomal] aberrations concern large chromosomal regions, which makes it difficult to identify actual driver genes. Increased resolution has led to the detection of focal chromosomal aberrations, defined as 3 Mb or smaller in size [5–8]. Inherent to their size, focal aberrations contain a small number of genes, facilitating driver gene identification

From: Brosens R, et al, 2010.

This extract is from one of the studies referenced by the previous paper (when they mention their definition of focal CNVs). This paper is about CNVs in different tumour cells;

Primary tumors contain varying proportions of nonneoplastic cells thereby obscuring focal amplifications, defined by the increased copy number of a small region of the genome, from simple gains of whole chromosome arms.

From: Leary RJ, et al, 2008.


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