Patents by Inventor Robert A. Ach
Robert A. Ach 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: 11535889Abstract: Described herein is an adapter comprising a population of first oligonucleotides, a second oligonucleotide and a third oligonucleotide, wherein the first oligonucleotides, the second oligonucleotide and the third oligonucleotide are hybridized together to produce a complex that comprises: (i) a first end comprising a transposase recognition sequence, (ii) a central single-stranded region of variable sequence and (iii) a second end comprising sequences that are non-complementary. A method, as well as a kit for practicing the method, are also provided.Type: GrantFiled: March 7, 2019Date of Patent: December 27, 2022Assignee: Agilent Technologies, Inc.Inventors: Robert A. Ach, Nicholas M. Sampas, Brian Jon Peter
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Patent number: 11414695Abstract: A method of enriching for a fragment of a genome, as well as corresponding compositions and kits, are provided. In certain embodiments, the method comprises: (a) contacting a sample comprising fragmented DNA with a Cas9-gRNA complex comprising mutant Cas9 protein that has inactivated nuclease activity and a Cas9-associated guide RNA that is complementary to a site in the DNA, to produce a Cas9-fragment complex that comprises a fragment of the fragmented DNA; and (b) isolating the complex. In addition, other methods and compositions for Cas9/CRISPR-mediated nucleic acid manipulation are also provided.Type: GrantFiled: May 29, 2014Date of Patent: August 16, 2022Assignee: Agilent Technologies, Inc.Inventors: Brian Jon Peter, Robert A. Ach
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Publication number: 20220220544Abstract: The present disclosure is generally directed to detecting nucleic acids. In particular, disclosed herein are methods and compositions for determining the sequence (or identity) and location of RNA and other molecules in situ. The present invention is generally related to a method for detecting nucleic acids, the method including providing a tissue sample; providing an array comprising a plurality of oligonucleotide probes attached to a surface of the array, in which each oligonucleotide probe, of the plurality of oligonucleotide probes, includes a location barcode sequence, a primer binding sequence, and a priming sequence; releasing the plurality of oligonucleotide probes from the array surface; contacting the tissue sample with the released oligonucleotide probes; and allowing the released oligonucleotide probes to diffuse into the tissue sample.Type: ApplicationFiled: January 7, 2022Publication date: July 14, 2022Applicant: AGILENT TECHNOLOGIES, INC.Inventors: Robert A. ACH, Nicholas M. SAMPAS, Brian Jon PETER
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Patent number: 10711269Abstract: A method for making an asymmetrically-tagged sequencing library is provided. In some embodiments, the method may comprise: obtaining a symmetrically-tagged library of cDNA or genomic DNA fragments, hybridizing a tailed first primer to the 3? sequence tag of the library and extending the same to produce primer extension products, and amplifying the primer extension products using a pair of tailed primers to produce asymmetrically-tagged library.Type: GrantFiled: January 18, 2017Date of Patent: July 14, 2020Assignee: Agilent Technologies, Inc.Inventors: Brian Jon Peter, David Taussig, Bahram Arezi, Robert A. Ach, Nicholas M. Sampas
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Patent number: 10697006Abstract: In some embodiments, the amplification method may comprise producing a reaction mix comprising: a nucleic acid sample, a polymerase, nucleotides, a forward primer that hybridizes to a sequence in the bottom strand of a fragment in the sample, and a reverse primer. The reverse primer has a hairpin structure comprising a loop, a stem and a 3? overhang of at least 8 nucleotides, wherein the 3? overhang hybridizes to a sequence in the top strand of the fragment. Subjecting the reaction mix at least two rounds of denaturation, renaturation and primer extension conditions results in extension the forward and reverse primers to produce an amplification product that contains: a double stranded region comprising a nick adjacent to the 5? end of the reverse primer, and the loop of the first hairpin primer. Primer sets and kits for performing the methods are also provided.Type: GrantFiled: August 31, 2017Date of Patent: June 30, 2020Assignee: Agilent Technologies, Inc.Inventors: Brian Jon Peter, Robert A. Ach
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Publication number: 20200172959Abstract: A method for fragmenting a genome is provided. In certain embodiments, the method comprises: (a) combining a genomic sample containing genomic DNA with a plurality of Cas9-gRNA complexes, wherein the Cas9-gRNA complexes comprise a Cas9 protein and a set of at least 10 Cas9-associated guide RNAs that are complementary to different, pre-defined, sites in a genome, to produce a reaction mixture; and (b) incubating the reaction mixture to produce at least 5 fragments of the genomic DNA. Also provided is a composition comprising at least 100 Cas9-associated guide RNAs that are each complementary to a different, pre-defined, site in a genome. Kits for performing the method are also provided. In addition, other methods, compositions and kits for manipulating nucleic acids are also provided.Type: ApplicationFiled: January 21, 2020Publication date: June 4, 2020Inventors: Brian Jon Peter, Robert A. Ach, Michael Walter, Bram Herman
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Patent number: 10577644Abstract: A method for fragmenting a genome is provided. In certain embodiments, the method comprises: (a) combining a genomic sample containing genomic DNA with a plurality of Cas9-gRNA complexes, wherein the Cas9-gRNA complexes comprise a Cas9 protein and a set of at least 10 Cas9-associated guide RNAs that are complementary to different, pre-defined, sites in a genome, to produce a reaction mixture; and (b) incubating the reaction mixture to produce at least 5 fragments of the genomic DNA. Also provided is a composition comprising at least 100 Cas9-associated guide RNAs that are each complementary to a different, pre-defined, site in a genome. Kits for performing the method are also provided. In addition, other methods, compositions and kits for manipulating nucleic acids are also provided.Type: GrantFiled: October 31, 2016Date of Patent: March 3, 2020Assignee: AGILENT TECHNOLOGIES, INC.Inventors: Brian Jon Peter, Robert A. Ach, Michael Walter, Bram Herman
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Publication number: 20190194737Abstract: Described herein is an adapter comprising a population of first oligonucleotides, a second oligonucleotide and a third oligonucleotide, wherein the first oligonucleotides, the second oligonucleotide and the third oligonucleotide are hybridized together to produce a complex that comprises: (i) a first end comprising a transposase recognition sequence, (ii) a central single-stranded region of variable sequence and (iii) a second end comprising sequences that are non-complementary. A method, as well as a kit for practicing the method, are also provided.Type: ApplicationFiled: March 7, 2019Publication date: June 27, 2019Inventors: Robert A. Ach, Nicholas M. Sampas, Brian Jon Peter
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Patent number: 10308979Abstract: This disclosure provides a method comprising: a) clamping the top and bottom strands of a double stranded DNA molecule to produce a duplex in which the top and bottom strands are linked; b) denaturing the duplex to produce a denatured product; and c) renaturing the denatured product in the presence of a labeled oligonucleotide that is complementary to a sequence of nucleotides in the double stranded DNA molecule, thereby producing a D-loop-containing product. Kits for performing the method and products made by the method are also provided.Type: GrantFiled: March 14, 2013Date of Patent: June 4, 2019Assignee: AGILENT TECHNOLOGIES, INC.Inventors: Brian Jon Peter, Robert A. Ach, Zoltan Timar, Joel Myerson, Jeffrey Robert Sampson, Holly Hogrefe
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Publication number: 20180201924Abstract: A method for making an asymmetrically-tagged sequencing library is provided. In some embodiments, the method may comprise: obtaining a symmetrically-tagged library of cDNA or genomic DNA fragments, hybridizing a tailed first primer to the 3? sequence tag of the library and extending the same to produce primer extension products, and amplifying the primer extension products using a prior of tailed primers to produce asymmetrically-tagged library.Type: ApplicationFiled: January 18, 2017Publication date: July 19, 2018Inventors: Brian Jon Peter, David Taussig, Bahram Arezi, Robert A. Ach, Nicholas M. Sampas
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Publication number: 20180073068Abstract: In some embodiments, the amplification method may comprise producing a reaction mix comprising: a nucleic acid sample, a polymerase, nucleotides, a forward primer that hybridizes to a sequence in the bottom strand of a fragment in the sample, and a reverse primer. The reverse primer has a hairpin structure comprising a loop, a stem and a 3? overhang of at least 8 nucleotides, wherein the 3? overhang hybridizes to a sequence in the top strand of the fragment. Subjecting the reaction mix at least two rounds of denaturation, renaturation and primer extension conditions results in extension the forward and reverse primers to produce an amplification product that contains: a double stranded region comprising a nick adjacent to the 5? end of the reverse primer, and the loop of the first hairpin primer. Primer sets and kits for performing the methods are also provided.Type: ApplicationFiled: August 31, 2017Publication date: March 15, 2018Inventors: Brian Jon Peter, Robert A. Ach
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Patent number: 9890417Abstract: Among other things, this disclosure provides a method of detecting a target nucleic acid. Aspects of the method include: (a) obtaining a labeled nucleic acid probe that is complementary to a target nucleic acid, wherein the probe comprises a capture tag; (b) hybridizing the probe with the target nucleic in a fixed cell, in situ, to produce a duplex; (c) linking the probe in the duplex to a peroxidase conjugate via the capture tag to produce a peroxidase-labeled duplex; and (d) incubating the peroxidase-labeled duplex with a peroxidase substrate, wherein the peroxidase activity of the peroxidase conjugate catalyzes deposition of the substrate in the vicinity of the duplex, thereby producing a detectable signal.Type: GrantFiled: November 3, 2014Date of Patent: February 13, 2018Assignee: Agilent Technologies, Inc.Inventors: Kristin Bernick, Robert Ach, Mistuni Ghosh, Brian Smart
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Patent number: 9873907Abstract: A method for fragmenting a genome is provided. In certain embodiments, the method comprises: (a) combining a genomic sample containing genomic DNA with a plurality of Cas9-gRNA complexes, wherein the Cas9-gRNA complexes comprise a Cas9 protein and a set of at least 10 Cas9-associated guide RNAs that are complementary to different, pre-defined, sites in a genome, to produce a reaction mixture; and (b) incubating the reaction mixture to produce at least 5 fragments of the genomic DNA. Also provided is a composition comprising at least 100 Cas9-associated guide RNAs that are each complementary to a different, pre-defined, site in a genome. Kits for performing the method are also provided. In addition, other methods, compositions and kits for manipulating nucleic acids are also provided.Type: GrantFiled: May 29, 2014Date of Patent: January 23, 2018Assignee: Agilent Technologies, Inc.Inventors: Gusti Zeiner, Derek Lee Lindstrom, Brian Jon Peter, Robert A. Ach
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Patent number: 9834814Abstract: This disclosure provides, among other things, a method for analyzing a planar cellular sample. In some embodiments, the method comprises: (a) indirectly or directly attaching nucleic acid tags to binding sites in a planar cellular sample; (b) contacting the planar cellular sample with a solid support comprising an array of spatially addressed features that comprise oligonucleotides, wherein each oligonucleotide comprises a molecular barcode that identifies the feature in which the oligonucleotides is present; (c) hybridizing the nucleic acid tags, or a copy of the same, with the oligonucleotides to produce duplexes; and (d) extending the oligonucleotides in the duplexes to produce extension products that each comprises (i) a molecular barcode and (ii) a copy of a nucleic acid tag. Other embodiments, e.g., kits and the like, are also described.Type: GrantFiled: September 22, 2014Date of Patent: December 5, 2017Assignee: Agilent Technologies, Inc.Inventors: Brian Jon Peter, Robert A. Ach, Alicia Scheffer-Wong, Carolina Caffaro
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Publication number: 20170283864Abstract: Described herein, among other things, is an adapter comprising a population of first oligonucleotides, a second oligonucleotide and a third oligonucleotide, wherein the first oligonucleotides, the second oligonucleotide and the third oligonucleotide are hybridized together to produce a complex that comprises: (i) a first end comprising a transposase recognition sequence, (ii) a central single-stranded region of variable sequence and (iii) a second end comprising sequences that are non-complementary. A method, as well as a kit for practicing the method, are also provided.Type: ApplicationFiled: January 17, 2017Publication date: October 5, 2017Inventors: Robert A. Ach, Nicholas M. Sampas, Brian Jon Peter
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Publication number: 20170175182Abstract: Provided herein, among other things, are a variety of methods that comprise inserting a plurality of barcoded transposons into a population of DNA fragments that comprise DNA fragments of less than 1 kb in length, to produce transposon-tagged fragments that each comprise a barcoded transposon. Kits for performing this method are also provided.Type: ApplicationFiled: October 11, 2016Publication date: June 22, 2017Inventors: Brian Jon Peter, Robert A. Ach, Alicia Scheffer-Wong
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Publication number: 20170107560Abstract: A method of enriching for a fragment of a genome, as well as corresponding compositions and kits, are provided. In certain embodiments, the method comprises: (a) contacting a sample comprising fragmented DNA with a Cas9-gRNA complex comprising mutant Cas9 protein that has inactivated nuclease activity and a Cas9-associated guide RNA that is complementary to a site in the DNA, to produce a Cas9-fragment complex that comprises a fragment of the fragmented DNA; and (b) isolating the complex. In addition, other methods and compositions for Cas9/CRISPR-mediated nucleic acid manipulation are also provided.Type: ApplicationFiled: October 26, 2016Publication date: April 20, 2017Inventors: Brian Jon Peter, Robert A. Ach
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Patent number: 9574236Abstract: Provided herein is a method of sample analysis. In certain embodiments, the method comprises: a) cross-linking protein of a cell using a first compound to produce a first cross-linked product comprising cross-linked protein, and RNA; b) contacting the first cross-linked product and a second compound under conditions by which an oligonucleotide portion of the second compound hybridizes to the RNA; c) activating a reaction the first and second compound, thereby covalently crosslinking the oligonucleotide to the cross-linked protein to produce a second cross-linked product; d) isolating the second cross-linked product using an affinity tag; and e) analyzing the isolated second cross-linked product. Compounds for performing the method are also provided.Type: GrantFiled: January 6, 2015Date of Patent: February 21, 2017Assignee: Agilent Technologies, Inc.Inventors: Brian Phillip Smart, Robert A. Ach
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Publication number: 20170044592Abstract: A method for fragmenting a genome is provided. In certain embodiments, the method comprises: (a) combining a genomic sample containing genomic DNA with a plurality of Cas9-gRNA complexes, wherein the Cas9-gRNA complexes comprise a Cas9 protein and a set of at least 10 Cas9-associated guide RNAs that are complementary to different, pre-defined, sites in a genome, to produce a reaction mixture; and (b) incubating the reaction mixture to produce at least 5 fragments of the genomic DNA. Also provided is a composition comprising at least 100 Cas9-associated guide RNAs that are each complementary to a different, pre-defined, site in a genome. Kits for performing the method are also provided. In addition, other methods, compositions and kits for manipulating nucleic acids are also provided.Type: ApplicationFiled: October 31, 2016Publication date: February 16, 2017Inventors: Brian Jon Peter, Robert A. Ach, Michael Walter, Bram Herman
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Patent number: 9416407Abstract: A method of sample analysis is provided. In certain embodiments, the method may comprise: a) contacting under primer extension conditions a genomic sample comprising a test genome with a set of at least ten sequence-specific primers that are complementary to sites in only one strand of a reference chromosomal region, to produce primer extension products, and b) analyzing the primer extension products to identify a chromosomal rearrangement in the test genome.Type: GrantFiled: October 1, 2008Date of Patent: August 16, 2016Assignee: Agilent Technologies, Inc.Inventors: Robert A. Ach, Carsten Carstens, Bernd Buehler