Agilent Technologies, Inc.

Emily Marine Leproust

Michael Ruvolo

Siyuan Chen

Gusti Zeiner

Peter G Webb

Alan L Schenck

Jeremy Lackey

Scott Robert Happe

Jeffrey M McMillan

Robert E Woodworth

Joseph Hoang Hai Ong

Petula N D'andrade

Julia Barboza

Eric Lin

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 are various methods for enriching a target fragment that is present in randomly sheared genomic DNA. In some embodiments, the method may involve hybridizing randomly sheared genomic DNA to a halo probe to produce a first circular complex, and then enzymatically digesting the overhanging ends of the genomic fragment. Other embodiments may include hybridizing randomly sheared genomic DNA to an RNA oligonucleotide that comprises a region that hybridizes to a fragment of the randomly sheared genomic DNA to produce an RNA/DNA duplex. The overhanging ends of the genomic fragment in the RNA/DNA duplex can then be enzymatically digested.

Target enrichment of randomly sheared genomic DNA fragments

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.

Synthesis of long fish probes

A method of sample analysis is provided. In certain embodiments, the method involves: a) obtaining a fragmented RNA sample comprising fragments of long RNA molecules and short RNA molecules; b) ligating an adaptor to an end of the RNA of the fragmented RNA sample to produce an adaptor-ligated sample; c) hybridizing said adaptor-ligated sample to an array of nucleic acid probes; and d) reading said array to obtain an estimate of the abundance of a long RNA in the RNA sample and an estimate of the abundance a small RNA in the RNA sample.

RNA labeling method

A reagent for oligonucleotide synthesis or purification, wherein the reagent has a structure of:X&#x2014;C&#x2014;L&#x2014;H&#x2003;&#x2003;(Formula A)wherein X is a phosphoramidite group, an H-phosphonate group, an acetal group, or an isocyanate; C is a direct bond or a cleavable adaptor represented by &#x2014;C&#x2014;C&#x2014;; L is a hydrocarbyl chain; and H is a terminal alkyne or an activated cyclooctyne. The reagent of Formula (A) can be used in the synthesis and purification of oligonucleotides.

Methods for the synthesis and purification of oligomers

A slide cover for enclosing a region comprising an active region on a slide is provided. A slide cover and a slide are also provided. A slide cover for enclosing a region comprising an active region on a slide, where the slide is placed in a clamshell slide holder is also provided.

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San Jose, CA, United States of America

Emily Marine Leproust