Agilent Technologies, Inc.

Michael Ruvolo

Emily Marine Leproust

Siyuan Chen

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&#x2032;-B&#x2032;-3&#x2032; to provide a population of duplexes. After hybridizing, the 3&#x2032; 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&#x2032;.

Synthesis of pools of probes by primer extension

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 V-B-Vin 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 Vand Vto 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.

Detection of genomic rearrangements by sequence capture

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.

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Santa Clara, CA, United States of America

Michael Ruvolo