A method for determining the presence of a copy number imbalance in genomic DNA of a test sample, comprising: a) labeling a sample genomic DNA of a human from a test sample, or an amplification product thereof, to form a labeled test DNA; b) hybridizing the labeled test DNA to a first hybridization array; c) labeling a first reference genomic DNA of a male human from a first reference sample, or an amplification product thereof, to form labeled first reference DNA; d) hybridizing the labeled first reference DNA to a second hybridization array; e) labeling a second reference genomic DNA from a second reference sample of a female human, or an amplification product thereof, to form a labeled second reference DNA; f) hybridizing the labeled second reference DNA to a third hybridization array; g) analyzing the first hybridization array after the hybridizing of the labeled test DNA to determine signal intensities produced by hybridization of the labeled test DNA; h) analyzing the second hybridization array after the hybridizing of the labeled first reference DNA to determine signal intensities produced by the hybridization of the labeled first reference DNA; i) analyzing the third hybridization array after the hybridizing of the labeled second reference DNA to determine signal intensities produced by hybridization of the labeled second reference DNA; wherein the steps of g), h) and i) comprise single channel array comparative genomic hybridisation and j) estimating the copy number of at least one region of the sample genomic DNA by comparing the signal intensities of the first hybridization array with the signal intensities of the second hybridization array and the third hybridization array. a) labeling a sample genomic DNA of a human from a test sample, or an amplification product thereof, to form a labeled test DNA; b) hybridizing the labeled test DNA to a first hybridization array; c) labeling a first reference genomic DNA of a male human from a first reference sample, or an amplification product thereof, to form labeled first reference DNA; d) hybridizing the labeled first reference DNA to a second hybridization array; e) labeling a second reference genomic DNA from a second reference sample of a female human, or an amplification product thereof, to form a labeled second reference DNA; f) hybridizing the labeled second reference DNA to a third hybridization array; g) analyzing the first hybridization array after the hybridizing of the labeled test DNA to determine signal intensities produced by hybridization of the labeled test DNA; h) analyzing the second hybridization array after the hybridizing of the labeled first reference DNA to determine signal intensities produced by the hybridization of the labeled first reference DNA; i) analyzing the third hybridization array after the hybridizing of the labeled second reference DNA to determine signal intensities produced by hybridization of the labeled second reference DNA; wherein the steps of g), h) and i) comprise single channel array comparative genomic hybridisation and j) estimating the copy number of at least one region of the sample genomic DNA by comparing the signal intensities of the first hybridization array with the signal intensities of the second hybridization array and the third hybridization array.