A method for detecting a variance in the frequency of a genomic region in a genetic sample, comprising the steps of: providing a genetic sample; introducing at least first and second sets of first and second fixed sequence oligonucleotides to the genetic sample under conditions that allow the sets of fixed sequence oligonucleotides to specifically hybridize to complementary regions in nucleic acid regions of interest, wherein each set comprises an oligonucleotide associated with a different optically detectable label, and wherein each set comprises a target-non complementary sequence that binds selectively to the same single array feature; wherein each set is selective for a different chromosome, for a different locus on the same chromosome or for a different allele of the same locus; introducing one or more bridging oligonucleotides for each set under conditions that allow the bridging oligonucleotides to hybridize to complementary regions in the nucleic acid regions of interest between the first and second fixed sequence oligonucleotides to create hybridization products; ligating the hybridized oligonucleotides to create contiguous ligation products complementary to nucleic acid regions of interest, wherein the contiguous ligation products from each set comprise sequences that are complementary to the single array feature; introducing the contiguous ligation products from each set to an array comprising one or more features complementary to the contiguous ligation products; detecting hybridization of the contiguous ligation products from each set to the array by detection of the optically detectable labels, wherein contiguous ligation products from each set are evaluated competitively on the single array feature; wherein the relative frequency of the optically detectable labels on the array is indicative of the presence or absence of a variance in the frequency of a nucleic acid region of interest in the genetic sample, wherein the variance is detected by an increased or decreased level of hybridization of one set of contiguous ligation products as compared to a second set of contiguous ligation products. providing a genetic sample; introducing at least first and second sets of first and second fixed sequence oligonucleotides to the genetic sample under conditions that allow the sets of fixed sequence oligonucleotides to specifically hybridize to complementary regions in nucleic acid regions of interest, wherein each set comprises an oligonucleotide associated with a different optically detectable label, and wherein each set comprises a target-non complementary sequence that binds selectively to the same single array feature; wherein each set is selective for a different chromosome, for a different locus on the same chromosome or for a different allele of the same locus; introducing one or more bridging oligonucleotides for each set under conditions that allow the bridging oligonucleotides to hybridize to complementary regions in the nucleic acid regions of interest between the first and second fixed sequence oligonucleotides to create hybridization products; ligating the hybridized oligonucleotides to create contiguous ligation products complementary to nucleic acid regions of interest, wherein the contiguous ligation products from each set comprise sequences that are complementary to the single array feature; introducing the contiguous ligation products from each set to an array comprising one or more features complementary to the contiguous ligation products; detecting hybridization of the contiguous ligation products from each set to the array by detection of the optically detectable labels, wherein contiguous ligation products from each set are evaluated competitively on the single array feature; wherein the relative frequency of the optically detectable labels on the array is indicative of the presence or absence of a variance in the frequency of a nucleic acid region of interest in the genetic sample, wherein the variance is detected by an increased or decreased level of hybridization of one set of contiguous ligation products as compared to a second set of contiguous ligation products.