A novel way to divide the genome for CNV detecting in SNP arrays

Copy number variations (CNVs) are the gains or losses on the genomic DNA from several kilo-bases to hundreds of kilo-bases, which has been proven that more than 12% of genomes could be affected by such variants. Newly developed microarray technologies which were allowed to investigate copy number variants in a genome run slowly and are limited to detect small-sized CNV flexibly. Here we propose a novel way to detect CNV regions in the chromosomes quickly, which use the breakpoint method to define the aberration area. This algorithm uses the P-value of the T-test statistic to get breakpoints and defines the alteration segment. We also introduce a rule for stopping early when there is no breakpoint in the region. To detect CNVs smaller, another rule also needs to detect whether the segment needs to be divided or combined. This method is demonstrated availably on the SNP data to detect copy number alterations.