Provided is a method of genome-wide testing of gene copy number at the genetically most important loci to determine whether the gene and/or its selected larger surrounding chromosome region is rearranged to result in an unbalanced abnormality in one or more subjects. The method includes selecting multiple gene loci of the DNAs to be examined in the test, conducting the test, and comparing the number of copies at each locus tested by quantification of total gene target number to determine the relative number of each polymorphic sequence detected to assure that each important tested sequence is distinguished from the other alleles at the same locus. A method of detecting the highest number of abnormal patients possible based upon the number of test sites available in a protocol is also provided. Depending upon the state of the life cycle, both of the methods can be done together or in sequence.