Background: Cancer genomes are evolved from normal genomes by accumulating somatic mutations.Previous researches show that tumor genomes may preferentially have copy number variations at one allele of a heterozygous SNP locus of the normal genome, and this is called allele specific copy number variation (ASCNV).ASCNVs may confer critical survival advantage to tumor cells, and therefore studies on ASCNVs can give insightful information about tumor progression.