Abstract: The present disclosure is directed to a single-end sequencing method for improved detection of genomic rearrangements such as deletions, insertions, inversions, and translocations that are present in a polynucleotide. A first priming event allows for sequencing of a target sequence, and a second priming event on an adapter allows for identification of the sequences amplified and tagged by selective amplification. The combination of priming events in the same direction facilitates read alignment and the identification of any genomic rearrangements.

Abstract: The present disclosure is directed to a single-end sequencing method for improved detection of genomic rearrangements such as deletions, insertions, inversions, and translocations that are present in a polynucleotide. A first priming event allows for sequencing of a target sequence, and a second priming event on an adapter allows for identification of the sequences amplified and tagged by selective amplification. The combination of priming events in the same direction facilitates read alignment and the identification of any genomic rearrangements.

Abstract: The present disclosure is directed to a single-end sequencing method for improved detection of genomic rearrangements such as deletions, insertions, inversions, and translocations that are present in a polynucleotide. A first priming event allows for sequencing of a target sequence, and a second priming event on an adapter allows for identification of the sequences amplified and tagged by selective amplification. The combination of priming events in the same direction facilitates read alignment and the identification of any genomic rearrangements.

Abstract: A method of selecting a set of normalization probes for use on a comparative genome hybridization array is provided. In certain embodiments, the method includes: a) selecting a first region of a genome to be evaluated by comparative genome hybridization to produce data; b) selecting a second region of the genome for normalization of the data, and c) selecting from a set of candidate probes a sub-set of normalization probes that detect the second region.

Abstract: A method of selecting a set of normalization probes for use on a comparative genome hybridization array is provided. In certain embodiments, the method includes: a) selecting a first region of a genome to be evaluated by comparative genome hybridization to produce data; b) selecting a second region of the genome for normalization of the data, and c) selecting from a set of candidate probes a sub-set of normalization probes that detect the second region.

Abstract: In some embodiments, control nucleic acid constructs useful as spiking reagents are provided which comprise a nucleic acid vector having an insert comprising a control nucleic acid molecule. In some embodiments, the insert contains at least one methyltransferase recognition site, such as a CpG dinucleotide. In some embodiments, the insert has a sequence complementary to a negative control probe of a microarray. Methods and kits for using the control nucleic acid constructs as spiking reagents in methylation analysis are disclosed.

Abstract: Methods for detecting the integration of viral nucleic acids into a host cell, and methods for determining the locus of integration using microarrays are described. The methods can also be used in conjunction with viral vectors used in gene therapy.

Abstract: The present invention generally relates to the determination of the state of one or more locations within a nucleic acid and, in particular, to the determination of the methylation state of one or more methylation sites within a nucleic acid such as DNA. In one aspect of the invention, a nucleic acid, such as DNA, that is suspected of being methylated is exposed to a nucleic acid probe able to hybridize the nucleic acid at or near the methylation site. After hybridization, the nucleic acid-probe hybrid is exposed to a methylation-sensitive restriction endonuclease able to bind at or near the methylation site. The restriction endonuclease is not able to cleave the nucleic acid-probe hybrid if the DNA is methylated at the methylation site, but is able to cleave the nucleic acid-probe hybrid if the nucleic acid is not methylated at the methylation site. Determination of the cleavage state of the probe can thus be used to determine the state of the methylation site.

Abstract: A method for determining chromatin accessibility of nucleic acids in a cell by expressing an effective amount of a nuclease in a cell to digest chromatin at chromatin accessible sites to form chromatin fragments; isolating chromatin fragments from the cell; and hybridizing the chromatin fragments on a microarray to determine the location and/or sequence of the chromatin fragments.