the present invention provides methods of detecting and mapping chromosomal or genetic abnormalities associated with various diseases or with predisposition to various diseases , or to detecting the phenomena of large scale copy number variants . in particular , the present invention provides advanced methods of performing array - based comparative hybridization that allow reproducibility between samples and enhanced sensitivity by using the same detectable label for both test sample and reference sample nucleic acids . invention methods are useful for the detection or diagnosis of particular disease conditions such as cancer , and detecting predisposition to cancer based on detection of chromosomal or genetic abnormalities and gene expression level . invention methods are also useful for the detection or diagnosis of hereditary genetic disorders or predisposition thereto , especially in prenatal samples . moreover , invention methods are also useful for the detection or diagnosis of de novo genetic aberrations associated with post - natal developmental abnormalities .