Abstract: The present disclosure provides methods and compositions for analyzing enriched populations of cells or target chromosomes, for example cells in metaphase and methods and compositions for two-dimensional spatial arrangement of cells and chromosomes. Furthermore, methods are disclosed for the detection of structural variations and/or repair events in chromosomes by labeling of single-stranded chromatids with probes, which in illustrative embodiments are of different colors. The hybridization pattern of the labeled probes produces a spectral pattern that provides high-resolution detection of structural variations and/or repair events, which for example can facilitate distinction of benign structural variations from deleterious structural variations. Further, the spectral pattern provides information regarding complex structural variations where more than one rearrangement of chromosomal segments may have occurred.

Abstract: Methods are disclosed for the detection of structural variations and/or repair events in chromosomes by labeling of single-stranded chromatids with probes, which in illustrative embodiments are of different colors. The hybridization pattern of the labeled probes produces a spectral pattern that provides high-resolution detection of structural variations and/or repair events, which for example can facilitate distinction of benign structural variations from deleterious structural variations. Further, the spectral pattern provides information regarding complex structural variations where more than one rearrangement of chromosomal segments may have occurred. Spectral information can be used to generate data tables upon which nodal analysis can be applied to identify structural features of interest.

Abstract: A kit for the characterization of chromosomal inversions using single-stranded probes that are either all identical or all complementary to a single-stranded chromatid is described. Reporter species are attached to oligonucleotide strands designed such that they may hybridize to portions of only one of a pair of single-stranded sister chromatids which may be prepared by the CO-FISH procedure. If an inversion has occurred, these marker probes will be detected on the second sister chromatid at the same location as the inversion on the first chromatid. The kit includes non-repetitive probes that are either all identical or all complementary to at least a portion of a target DNA sequence of only one DNA strand of only one chromatid and may in some embodiments include reagents suitable for performing CO-FISH and/or reagents for hybridizing the probes to the target DNA sequence.

Abstract: A method for the characterization of chromosomal inversions using anti-parallel probes is described. Reporter species are attached to oligonucleotide strands designed such that they may hybridize to portions of only one of a pair of single-stranded sister chromatids which may be prepared by the CO-FISH procedure. If an inversion has occurred, these marker probes will be detected on the second sister chromatid at the same location as the inversion on the first chromatid. Further, one or more reporter species are replaced with anti-parallel probes that hybridize at known locations along the second sister chromatid such that the position and size of the inversion may be identified/estimated.

Abstract: A method and a kit for the identification of chromosomal inversions are described. Chromosomal inversions are difficult to detect unless they are quite large. The improved ability to detect chromosomal inversions is important to a number of medical applications, such as cancer and birth defects, as examples. Reporter species are attached to oligonucleotide strands designed such that they may hybridize to portions of only one of a pair of single-stranded sister chromatids prepared by the CO-FISH procedure, as an example. If an inversion has occurred, these marker probes will be detected on the sister chromatid at the same location as the inversion on the first chromatid.

Abstract: Methods, compositions, and assays are described which are useful in identifying point mutations, identifying cancer cells, and diagnosing cancer.