  Background: Regions with copy number variations (in germline cells) or copy
number alteration (in somatic cells) are of great interest for human disease
gene mapping and cancer studies. They represent a new type of mutation and are
larger-scaled than the single nucleotide polymorphisms. Using genotyping
microarray for copy number variation detection has become standard, and there
is a need for improving analysis methods. Results: We apply the cumulative plot
to the detection of regions with copy number variation/alteration, on samples
taken from a chronic lymphocytic leukemia patient. Two sets of whole-genome
genotyping of 317k single nucleotide polymorphisms, one from the normal cell
and another from the cancer cell, are analyzed. We demonstrate the utility of
cumulative plot in detecting a 9Mb (9 x 10^6 bases) hemizygous deletion and 1Mb
homozygous deletion on chromosome 13. We also show the possibility to detect
smaller copy number variation/alteration regions below the 100kb range.
Conclusions: As a graphic tool, the cumulative plot is an intuitive and a
scale-free (window-less) way for detecting copy number variation/alteration
regions, especially when such regions are small.
