Copy-number-variation and copy-number-alteration region detection by cumulative plots
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 (9×106 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 200kb range.Conclusions: As a graphic tool, the cumulative plot is an intuitive and a scale-free (windowless) way for detecting copy number variation/alteration regions, especially when such regions are small.
Wentian Li Annette Lee Peter K Gregersen
The Robert S Boas Center for Genomics and Human Genetics, Feinstein Institute for Medical Research, North Shore LIJ Health System, Manhasset, NY 11030, USA
国际会议
The 7th Asia-Pacific Bioinformatics Conference(第七届亚太生物信息学大会)
北京
英文
717-728
2009-01-01（万方平台首次上网日期，不代表论文的发表时间）