Abstract: An oligonucleotide composition is provided. The subject composition comprises: a mixture of at least 10 of sets of oligonucleotides, wherein each of the sets of oligonucleotides comprises at least 100 different oligonucleotides of the following formula: X1—V—X2, wherein: X1 and X2 provide binding sites for a pair of PCR primers and V is a variable region that has a variable nucleotide sequence that is complementary to one or more discrete regions of a mammalian genome; the nucleotide sequences of X1 and X2 are the same for each oligonucleotide of a set and different for oligonucleotides of different sets; and the variable regions of each set are complementary to different discrete regions of said mammalian genome. Methods of using the composition and kits containing the composition are also provided.

Abstract: A method and a system for selecting a set of FISH probe oligonucleotide sequences from a plurality of overlapping tiled candidate FISH probe oligonucleotide sequences are provided. A composition that includes FISH probes with sequences from the set of FISH probe oligonucleotide sequences is also provided.

Abstract: A method of sample analysis is provided. The method comprises: a) contacting a genomic sample comprising a plurality of intact chromosomes, i.e., metaphase or interphase chromosomes, with a first set of labeled oligonucleotide probes under in situ hybridization conditions to produce a contacted sample comprising labeled chromosomes, where i. each of the labeled oligonucleotide probes is complementary to a non-repetitive, unique sequence in a region that flanks the centromere of a single chromosome of the plurality of chromosomes; and ii. hybridization of the labeled oligonucleotide probes to the chromosomes produces a distinct labeling pattern for each hybridized chromosome, thereby allowing each of the labeled chromosomes to be distinguished from one another; b) imaging the hybridized chromosomes to provide an image showing the labeling pattern for each labeled chromosome; and c) enumerating a labeled chromosome based on the labeling pattern of said labeled chromosome.

Abstract: A method of sample analysis is provided. In certain embodiments, the method may comprise: a) contacting a sample comprising a microbe with a set of at least two labeled oligonucleotides under in situ hybridization conditions to produce a contacted sample, where the labeled oligonucleotides i. hybridize to different RNA molecules of the microbe at sites that are unique to the microbe, ii. provide a predetermined optically detectable signature that identifies the microbe when the labeled oligonucleotides are hybridized to the different RNA molecules of the microbe, and iii. do not hybridize to ribosomal RNA of the microbe; b) reading the contacted sample to detect hybridization of the labeled oligonucleotides; and c) determining the identity of the microbe on the basis of the predetermined optically detectable signal, where the predetermined optically detectable signal indicates the identity of the microbe in the sample.

Abstract: A method of sample analysis is provided. In certain embodiments, the method may involve a) contacting a genomic sample comprising a test chromosome with a plurality of sets of labeled oligonucleotide probes under in situ hybridization conditions to produce a contacted sample having an oligonucleotide binding pattern; b) imaging the contacted sample to provide an image showing the oligonucleotide binding pattern; and c) analyzing the oligonucleotide binding pattern to identify a chromosomal rearrangement in the test chromosome relative to a reference chromosome.

Abstract: An oligonucleotide composition is provided. The subject composition comprises: a mixture of at least 10 of sets of oligonucleotides, wherein each of the sets of oligonucleotides comprises at least 100 different oligonucleotides of the following formula: X1—V—X2, wherein: X1 and X2 provide binding sites for a pair of PCR primers and V is a variable region that has a variable nucleotide sequence that is complementary to one or more discrete regions of a mammalian genome; the nucleotide sequences of X1 and X2 are the same for each oligonucleotide of a set and different for oligonucleotides of different sets; and the variable regions of each set are complementary to different discrete regions of said mammalian genome. Methods of using the composition and kits containing the composition are also provided.