Abstract: Provided herein is a method for making a pool of probes by primer extension. In certain embodiments, the method comprises hybridizing a first population of oligonucleotides comprising a top strand sequence having the following formula V1-B-3? with a second population of oligonucleotides comprising a bottom strand sequence having the following formula V2?-B?-3? to provide a population of duplexes. After hybridizing, the 3? ends of the oligonucleotides in the duplexes are extended to produce a population of double stranded products comprising a top strand sequence having the following formula V1-B-V2, where V2 is complementary to V2?.

Abstract: In alternative embodiments, provided are methods comprising use of FISH, IHC or equivalent gene fusion detection protocols, and gene sequencing, wherein optionally the gene sequencing is high throughput or next generation gene sequencing, for the identification and characterization of gene abnormalities such as gene breakages; optionally gene breakages comprise gene translocation, gene rearrangements and/or gene inversions. In alternative embodiments, genes or transcripts are analyzed from individuals suspected of having cancer, and the analysis is carried out on biological samples taken from these individuals. This identification and characterization of gene abnormalities can be used in the diagnosis and treatment of a cancer.

Abstract: Provided herein is a method of sample analysis. In some embodiments, the method comprises hybridizing fragmented genomic DNA from a test genome with a population of first oligonucleotides of the formula V1-B-V2 in the presence of one or more second oligonucleotides; contacting the product with ligase to join the ends of the fragmented genomic DNA that are hybridized to V1 and V2 to the one or more second oligonucleotides; and subjecting the product to polymerase chain reaction conditions using amplification primers that hybridize to sites that are provided by the one or more second oligonucleotides, wherein production of a product indicates that the test genome contains a chromosomal rearrangement relative to the reference genome.

Abstract: A probe system is provided. In some embodiments, the probe system may comprise: a first labeled probe that hybridizes to one side of a potential translocation breakpoint in a first locus; a second labeled probe that hybridizes to the other side of the potential translocation breakpoint in the first locus; a third labeled probe that hybridizes to one side of a potential translocation breakpoint in a second locus; a fourth labeled probe that hybridizes to the other side of the potential translocation breakpoint in the second locus; and a fifth labeled probe that hybridizes to both sides of the potential translocation breakpoint in either the first locus or the second locus, but not both. The fifth probe is distinguishably labeled from the first, second, third and fourth probes. Methods for detecting a chromosomal rearrangement in the first and second loci using the probe system are also provided.

Abstract: A method comprising: synthesizing a set of overlapping oligonucleotides that comprises probe sequences that hybridize to unique sequences in a chromosome, assembling the overlapping oligonucleotides in a way that produces one or more double stranded polynucleotides that each comprises multiple probe sequences, labeling the one or more double stranded polynucleotides to produce one or more labeled probes, and hybridizing the labeled probes to an intact chromosome, in situ, is provided.

Abstract: Provided herein is a method for making a pool of probes by primer extension. In certain embodiments, the method comprises hybridizing a first population of oligonucleotides comprising a top strand sequence having the following formula V1-B-3? with a second population of oligonucleotides comprising a bottom strand sequence having the following formula V2?-B?-3? to provide a population of duplexes. After hybridizing, the 3? ends of the oligonucleotides in the duplexes are extended to produce a population of double stranded products comprising a top strand sequence having the following formula V1-B-V2, where V2 is complementary to V2?.

Abstract: Provided herein is a method of sample analysis. In some embodiments, the method comprises hybridizing fragmented genomic DNA from a test genome with a population of first oligonucleotides of the formula V1-B-V2 in the presence of one or more second oligonucleotides; contacting the product with ligase to join the ends of the fragmented genomic DNA that are hybridized to V1 and V2 to the one or more second oligonucleotides; and subjecting the product to polymerase chain reaction conditions using amplification primers that hybridize to sites that are provided by the one or more second oligonucleotides, wherein production of a product indicates that the test genome contains a chromosomal rearrangement relative to the reference genome.

Abstract: A method comprising: synthesizing a set of overlapping oligonucleotides that comprises probe sequences that hybridize to unique sequences in a chromosome, assembling the overlapping oligonucleotides in a way that produces one or more double stranded polynucleotides that each comprises multiple probe sequences, labeling the one or more double stranded polynucleotides to produce one or more labeled probes, and hybridizing the labeled probes to an intact chromosome, in situ, is provided.

Abstract: Methods are provide for determining the relative amounts of individual polynucleotides in a complex mixture. The polynucleotides, after fluorescent labeling, are contacted under hybridization conditions with an array having element disposed at discrete locations on a substrate. The elements comprise two or more distinct polynucleotides that are combined prior to arraying. The level of fluorescence associated with each element provides a measure of its relative amount in the mixture.

Abstract: Methods are provide for determining the relative amounts of individual polynucleotides in a complex mixture. The polynucleotides, after fluorescent labeling, are contacted under hybridization conditions with an array having element disposed at discrete locations on a substrate. The elements comprise two or more distinct polynucleotides that are combined prior to arraying. The level of fluorescence associated with each element provides a measure of its relative amount in the mixture.