Abstract: The present invention is drawn to a flexible oligonucleotide hybridization system for detecting polymorphisms among sequences sharing high sequence homology, utilizing capture and reporter probes which provide for allelic discrimination and selection of target from among the homologous sequences.

Abstract: Methods and compositions are provided for detecting the presence or absence of methylation at methylation sites in a target nucleic acid sequence, utilizing probe sets complementary to first and second binding domains located upstream and downstream of one or more methylation sites of interest in a nucleic acid sequence. Methylation determination may be combined with the detection of additional polymorphisms, such as single nucleotide polymorphisms and/or gene dosage determinations, to provide a more complete genetic profile at a locus or loci of interest.

Abstract: Methods and compositions are provided for determining the dosage of target nucleic acid sequences. Probes comprising a crosslinking agent are combined with a sample that may comprise a target sequence that is complementary to a probe. Hybridization is allowed to occur between complementary sequences. The crosslinking agent is activated. Covalent bonds are formed between a probe and a target sequence if they are hybridized to each other, and a high-stringency wash step is employed to significantly lower background contamination. The crosslinked nucleic acids can then be detected and the resulting signal compared against a known diploid locus to determine the dosage of the target sequence. Dosage detection may be combined with the detection of polymorphisms, such as single nucleotide polymorphisms, to provide a more complete genetic profile at a locus or loci of interest.