Patents by Inventor Emily Marine Leproust
Emily Marine Leproust has filed for patents to protect the following inventions. This listing includes patent applications that are pending as well as patents that have already been granted by the United States Patent and Trademark Office (USPTO).
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Patent number: 11390907Abstract: 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?.Type: GrantFiled: March 5, 2013Date of Patent: July 19, 2022Assignee: Agilent Technologies, Inc.Inventors: Michael Ruvolo, Emily Marine Leproust
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Patent number: 10072260Abstract: 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.Type: GrantFiled: October 3, 2013Date of Patent: September 11, 2018Assignee: AGILENT TECHNOLOGIES, INC.Inventors: Scott Robert Happe, Emily Marine Leproust, Julia Barboza, Joseph Hoang Hai Ong
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Patent number: 10017820Abstract: 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.Type: GrantFiled: March 5, 2013Date of Patent: July 10, 2018Assignee: AGILENT TECHNOLOGIES, INC.Inventors: Michael Ruvolo, Emily Marine Leproust
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Patent number: 9580746Abstract: 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.Type: GrantFiled: January 2, 2014Date of Patent: February 28, 2017Assignee: Agilent Technologies, Inc.Inventors: Emily Marine Leproust, Siyuan Chen, Michael Ruvolo
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Publication number: 20160258002Abstract: 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?.Type: ApplicationFiled: March 5, 2015Publication date: September 8, 2016Inventors: Michael RUVOLO, Emily Marine LEPROUST
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Publication number: 20160017425Abstract: 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.Type: ApplicationFiled: March 5, 2013Publication date: January 21, 2016Inventors: Michael RUVOLO, Emily Marine LEPROUST
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Publication number: 20150307875Abstract: 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.Type: ApplicationFiled: October 3, 2013Publication date: October 29, 2015Inventors: Scott Robert Happe, Emily Marine Leproust, Julia Barboza, Joseph Hoang Hai Ong
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Patent number: 9163329Abstract: 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.Type: GrantFiled: January 19, 2012Date of Patent: October 20, 2015Assignee: Agilent Technologies, Inc.Inventors: Emily Marine Leproust, Gusti Zeiner, Petula N. D'andrade
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Patent number: 8889851Abstract: A reagent for oligonucleotide synthesis or purification, wherein the reagent has a structure of: X—C—L—H??(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 —Ca—Cb—; 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.Type: GrantFiled: November 6, 2012Date of Patent: November 18, 2014Assignee: Agilent Technologies, Inc.Inventors: Emily Marine Leproust, Jeremy Lackey
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Publication number: 20140256575Abstract: 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.Type: ApplicationFiled: January 2, 2014Publication date: September 11, 2014Inventors: Emily Marine Leproust, Siyuan Chen, Michael Ruvolo
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Publication number: 20120122702Abstract: 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.Type: ApplicationFiled: January 19, 2012Publication date: May 17, 2012Inventors: Emily Marine Leproust, Gusti Zeiner, Petula N. D'andrade
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Patent number: 8074802Abstract: 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.Type: GrantFiled: June 26, 2009Date of Patent: December 13, 2011Assignee: Agilent Technologies, Inc.Inventors: Peter G. Webb, Alan Schenck, Robert E. Woodworth, Emily Marine Leproust, Eric Lin, Jeffrey M. McMillan
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Publication number: 20100326862Abstract: 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.Type: ApplicationFiled: June 26, 2009Publication date: December 30, 2010Inventors: Peter G. Webb, Alan Schenck, Robert E. Woodworth, Emily Marine Leproust, Eric Lin, Jeffrey M. McMillan
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Publication number: 20100029513Abstract: In some embodiments, the present disclosure provides methods of making a mixture of nucleic acid molecules, the methods comprising the steps of: synthesizing on a substrate a population of nucleic acid molecules wherein each synthesized nucleic acid molecule comprises a substrate-attached proximal nucleic acid molecule, a distal nucleic acid molecule, and a cleavable linker linking the proximal nucleic acid molecule to the distal nucleic acid molecule, and harvesting distal nucleic acid molecules from the substrate by cleaving the cleavable linker under conditions that do not release the proximal nucleic acid molecule. Related compositions and kits are also provided.Type: ApplicationFiled: February 23, 2009Publication date: February 4, 2010Inventors: Joel Myerson, Emily Marine Leproust
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Publication number: 20090075840Abstract: In some embodiments, the present disclosure provides methods of making a mixture of nucleic acid molecules, the methods comprising the steps of: synthesizing on a substrate a population of nucleic acid molecules wherein each synthesized nucleic acid molecule comprises a substrate-attached proximal nucleic acid molecule, a distal nucleic acid molecule, and a cleavable linker linking the proximal nucleic acid molecule to the distal nucleic acid molecule, and harvesting distal nucleic acid molecules from the substrate by cleaving the cleavable linker under conditions that do not release the proximal nucleic acid molecule. Related compositions and kits are also provided.Type: ApplicationFiled: September 18, 2007Publication date: March 19, 2009Inventors: Joel Myerson, Emily Marine Leproust