title: Copy-number-variation and copy-number-alteration region detection by cumulative plots.
abstract: 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 317 k 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 9 Mb (9 x 10(6) bases) hemizygous deletion and 1 Mb homozygous deletion on chromosome 13. We also show the possibility to detect smaller copy number variation/alteration regions below the 100 kb 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.
authors.affiliation: The Robert S Boas Center for Genomics and Human Genetics, Feinstein Institute for Medical Research, North Shore LIJ Health System, Manhasset, NY 11030, USA. wli@nslij-genetics.org
authors.forename: Wentian
authors.initials: W
authors.lastname: Li
authors.forename: Annette
authors.initials: A
authors.lastname: Lee
authors.forename: Peter K
authors.initials: PK
authors.lastname: Gregersen
mesh_terms: D000465:Algorithms; D018628:Gene Dosage / Q000235:genetics*; D014644:Genetic Variation; D015894:Genome, Human; D005838:Genotype; D006720:Homozygote; D006801:Humans; D009154:Mutation