Patents by Inventor Mostafa Ronaghi
Mostafa Ronaghi 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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Publication number: 20150080230Abstract: A method including (a) providing an amplification reagent including an array of sites, and a solution having different target nucleic acids; and (b) reacting the amplification reagent to produce amplification sites each having a clonal population of amplicons from a target nucleic acid from the solution. The reacting can include simultaneously transporting the nucleic acids to the sites at an average transport rate, and amplifying the nucleic acids that transport to the sites at an average amplification rate, wherein the average amplification rate exceeds the average transport rate. The reacting can include producing a first amplicon from a nucleic acid that transports to each of the sites, and producing subsequent amplicons from the nucleic acid or from the first amplicon, wherein the average rate at which the subsequent amplicons are generated exceeds the average rate at which the first amplicon is generated.Type: ApplicationFiled: October 13, 2014Publication date: March 19, 2015Inventors: Min-Jui Richard Shen, Jonathan Mark Boutell, Kathryn M. Stephens, Mostafa Ronaghi, Kevin Gunderson, Bala Murali Venkatesan, M. Shane Bowen, Kandaswamy Vijayan
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Patent number: 8895249Abstract: A method including (a) providing an amplification reagent including an array of sites, and a solution having different target nucleic acids; and (b) reacting the amplification reagent to produce amplification sites each having a clonal population of amplicons from a target nucleic acid from the solution. The reacting can include simultaneously transporting the nucleic acids to the sites at an average transport rate, and amplifying the nucleic acids that transport to the sites at an average amplification rate, wherein the average amplification rate exceeds the average transport rate. The reacting can include producing a first amplicon from a nucleic acid that transports to each of the sites, and producing subsequent amplicons from the nucleic acid or from the first amplicon, wherein the average rate at which the subsequent amplicons are generated exceeds the average rate at which the first amplicon is generated.Type: GrantFiled: March 1, 2013Date of Patent: November 25, 2014Assignee: Illumina, Inc.Inventors: Min-Jui Richard Shen, Jonathan Mark Boutell, Kathryn M. Stephens, Mostafa Ronaghi, Kevin Gunderson, Bala Murali Venkatesan, M. Shane Bowen, Kandaswamy Vijayan
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Patent number: 8846314Abstract: A method and system are presented for fast and efficient isolation, purification and quantitation of nucleic acids from complex biological samples using isotachophoresis in microchannels. In an embodiment, a sieving medium may be used to enhance selectivity. In another embodiment, PCR-friendly chemistries are used to purify nucleic acids from complex biological samples and yield nucleic acids ready for further analysis including for PCR. In another embodiment, small RNAs from biological samples are extracted, isolated, preconcentrated and quantitated using on-chip ITP with a high efficiency sieving medium. The invention enables fast concentration and separation (takes 10s to 100s of seconds) of nucleic acids with high selectivity and using lower volumes of reagents (order of 10s of ?L to focus less than 1 pg/?L of nucleic acid).Type: GrantFiled: March 2, 2010Date of Patent: September 30, 2014Assignee: The Board of Trustees of the Leland Stanford Junior UniversityInventors: Robert D. Chambers, Juan G. Santiago, Alexandre Persat, Reto B. Schoch, Mostafa Ronaghi
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Publication number: 20140255919Abstract: The present technology relates to molecular sciences, such as genomics. More particularly, the present technology relates to methods for obtaining long lengths of sequencing data.Type: ApplicationFiled: March 7, 2014Publication date: September 11, 2014Applicant: ILLUMINA, INC.Inventors: Mostafa Ronaghi, Helmy A. Eltoukhy
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Patent number: 8753816Abstract: The present technology relates to molecular sciences, such as genomics. More particularly, the present technology relates to nucleic acid sequencing.Type: GrantFiled: October 26, 2011Date of Patent: June 17, 2014Assignee: Illumina, Inc.Inventors: Roberto Rigatti, Jonathan Mark Boutell, Jason Richard Betley, Niall Anthony Gormley, Mostafa Ronaghi, Dirk Evers
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Patent number: 8709729Abstract: A method of making an array of nucleic acid colonies, including the steps of (a) providing a substrate having a patterned surface of features, wherein the features are spatially organized in a repeating pattern on the surface of the substrate; (b) contacting the substrate with a solution of different target nucleic acids to seed no more than a subset of the features that contact the solution; (c) amplifying the nucleic acids on the subset of features; and (d) repeating steps (b) and (c) to increase the number of features that are seeded with a nucleic acid, thereby making an array of nucleic acid colonies.Type: GrantFiled: May 29, 2013Date of Patent: April 29, 2014Assignee: Illumina, Inc.Inventors: Mostafa Ronaghi, Helmy Eltoukhy
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Patent number: 8702948Abstract: Disclosed are a method and apparatus that use an electric field for improved biological assays. The electric field is applied across a device having wells, which receive reactants, which carry a charge. The device thus uses a controllable voltage source between the first and second electrodes, which is controllable to provide a positive charge and a negative charge to a given electrode. By controlled use of the electric field charged species in a fluid in a fluid channel are directed into or out of the well by an electric field between the electrodes. The present method involves the transport of fluids, as in a microfluidic device, and the electric field-induced movement of reactive species according to various assay procedures, such as DNA sequencing, synthesis or the like.Type: GrantFiled: September 14, 2012Date of Patent: April 22, 2014Assignee: The Board of Trustees of the Leland Stanford Junior UniversityInventors: Mostafa Ronaghi, Tarun Khurana, Juan G. Santiago
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Publication number: 20130338042Abstract: A method including (a) providing an amplification reagent including an array of sites, and a solution having different target nucleic acids; and (b) reacting the amplification reagent to produce amplification sites each having a clonal population of amplicons from a target nucleic acid from the solution. The reacting can include simultaneously transporting the nucleic acids to the sites at an average transport rate, and amplifying the nucleic acids that transport to the sites at an average amplification rate, wherein the average amplification rate exceeds the average transport rate. The reacting can include producing a first amplicon from a nucleic acid that transports to each of the sites, and producing subsequent amplicons from the nucleic acid or from the first amplicon, wherein the average rate at which the subsequent amplicons are generated exceeds the average rate at which the first amplicon is generated.Type: ApplicationFiled: March 1, 2013Publication date: December 19, 2013Applicant: ILLUMINA, INC.Inventors: Min-Jui Richard Shen, Jonathan Mark Boutell, Kathryn M. Stephens, Mostafa Ronaghi, Kevin Gunderson, Bala Murali Venkatesan, M. Shane Bowen, Kandaswamy Vijayan
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Publication number: 20130338008Abstract: A method of making an array of nucleic acid colonies, including the steps of (a) providing a substrate having a patterned surface of features, wherein the features are spatially organized in a repeating pattern on the surface of the substrate; (b) contacting the substrate with a solution of different target nucleic acids to seed no more than a subset of the features that contact the solution; (c) amplifying the nucleic acids on the subset of features; and (d) repeating steps (b) and (c) to increase the number of features that are seeded with a nucleic acid, thereby making an array of nucleic acid colonies.Type: ApplicationFiled: May 29, 2013Publication date: December 19, 2013Applicant: ILLUMINA, INC.Inventors: Mostafa Ronaghi, Helmy A. Eltoukhy
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Patent number: 8592225Abstract: A nanopore device capable of single molecule detection is described. The nanopores are formed in thin, rigid membranes and modified by a sputtered metal that forms an overhang during application. The overhang causes the pore to be narrower in a certain region, allowing passage of only a single molecule through the pore at a time, or binding to a biomolecule on the pore to be detected by a change in ionic current flow through the nanopore. Embodiments include a silicon nitride membrane formed on a silicon substrate and having a nanopore drilled with a focused ion beam system, followed by gold sputtering onto the membrane. Devices are formed with one or more nanopores and chambers having electrodes on either side of the nanopore.Type: GrantFiled: September 27, 2007Date of Patent: November 26, 2013Assignee: The Board of Trustees of the Leland Stanford Junior UniversityInventors: Mostafa Ronaghi, Amir Ali Haj Hossein Talasaz, Ronald W. Davis
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Publication number: 20130281306Abstract: The present technology relates to molecular sciences, such as genomics. More particularly, the present technology relates to nucleic acid sequencing.Type: ApplicationFiled: October 26, 2011Publication date: October 24, 2013Inventors: Roberto Rigatti, Jonathan Mark Boutell, Jason Richard Betley, Niall Anthony Gormley, Mostafa Ronaghi, Dirk Evers
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Patent number: 8476022Abstract: A method of making an array of nucleic acid colonies, by (a) providing a substrate having a patterned surface of features, wherein the features are spatially separated from each other on the surface of the substrate; (b) contacting the substrate with a solution of different target nucleic acids to seed a subset of the features that contact the solution, wherein each feature in the subset is seeded with a single nucleic acid from the solution, wherein a plurality of the features that contact the solution are not seeded with a nucleic acid from the solution; (c) amplifying the nucleic acids to form a nucleic acid colony at each of the features in the subset; and (d) repeating steps (b) and (c) to increase the number of the features on the surface that have a nucleic acid colony, thereby making an array of nucleic acid colonies.Type: GrantFiled: July 10, 2012Date of Patent: July 2, 2013Assignee: Illumina, Inc.Inventors: Mostafa Ronaghi, Helmy A. Eltoukhy
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Patent number: 8383348Abstract: The invention is directed to novel methods of multiplexing nucleic acid reactions, including amplification, detection and genotyping. The invention relies on the use of precircle probes that are circularized in the presence of the corresponding target nucleic acids, cleaved, and then amplified.Type: GrantFiled: August 9, 2011Date of Patent: February 26, 2013Assignee: Board of Trustees of the Leland Stanford Junior UniversityInventors: Thomas D. Willis, Paul Hardenbol, Maneesh Jain, Viktor Stolc, Mostafa Ronaghi, Ronald W. Davis
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Publication number: 20130008789Abstract: Disclosed are a method and apparatus that use an electric field for improved biological assays. The electric field is applied across a device having wells, which receive reactants, which carry a charge. The device thus uses a controllable voltage source between the first and second electrodes, which is controllable to provide a positive charge and a negative charge to a given electrode. By controlled use of the electric field charged species in a fluid in a fluid channel are directed into or out of the well by an electric field between the electrodes. The present method involves the transport of fluids, as in a microfluidic device, and the electric field-induced movement of reactive species according to various assay procedures, such as DNA sequencing, synthesis or the like.Type: ApplicationFiled: September 14, 2012Publication date: January 10, 2013Applicant: The Board of Trustree of the Leland Stanford Junior UniversityInventors: Mostafa Ronaghi, Tarun Khurana, Juan G. Santiago
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Publication number: 20120295262Abstract: The present technology relates to molecular sciences, such as genomics. More particularly, the present technology relates to methods for obtaining long lengths of sequencing data.Type: ApplicationFiled: July 10, 2012Publication date: November 22, 2012Applicant: ILLUMINA, INC.Inventors: Mostafa Ronaghi, Helmy A. Eltoukhy
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Patent number: 8277628Abstract: Disclosed are a method and apparatus that use an electric field for improved biological assays. The electric field is applied across a device having wells, which receive reactants, which carry a charge. The device thus uses a controllable voltage source between the first and second electrodes, which is controllable to provide a positive charge and a negative charge to a given electrode. By controlled use of the electric field charged species in a fluid in a fluid channel are directed into or out of the well by an electric field between the electrodes. The present method involves the transport of fluids, as in a microfluidic device, and the electric field-induced movement of reactive species according to various assay procedures, such as DNA sequencing, synthesis or the like.Type: GrantFiled: July 10, 2008Date of Patent: October 2, 2012Assignee: The Board of Trustees of the Leland Stanford Junior UniversityInventors: Mostafa Ronaghi, Tarun Khurana, Juan G. Santiago
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Patent number: 8236532Abstract: Methods for obtaining nucleic acid sequence information including the steps of (a) providing a first sequencing reagent to a target nucleic acid in the presence of a polymerase, wherein the first sequencing reagent includes at least two different nucleotide monomers and no more than three nucleotide monomers, wherein the nucleotide monomers are simultaneously in the presence of the target nucleic acid, (b) providing a second sequencing reagent to the target nucleic acid, wherein the second sequencing reagent comprises one or more nucleotide monomers, at least one of the one or more nucleotide monomers being different from the nucleotide monomers present in the first sequencing reagent, and wherein the second sequencing reagent is provided subsequent to providing the first sequencing reagent, and optionally (c) repeating (a) and (b) for said target nucleic acid, whereby sequence information for at least a portion of the target nucleic acid is obtained.Type: GrantFiled: December 17, 2009Date of Patent: August 7, 2012Assignee: Illumina, Inc.Inventors: Mostafa Ronaghi, Helmy A. Eltoukhy
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Publication number: 20120142016Abstract: A nanopore device capable of single molecule detection is described. The nanopores are formed in thin, rigid membranes and modified by a sputtered metal that forms an overhang during application. The overhang causes the pore to be narrower in a certain region, allowing passage of only a single molecule through the pore at a time, or binding to a biomolecule on the pore to be detected by a change in ionic current flow through the nanopore. Embodiments include a silicon nitride membrane formed on a silicon substrate and having a nanopore drilled with a focused ion beam system, followed by gold sputtering onto the membrane. Devices are formed with one or more nanopores and chambers having electrodes on either side of the nanopore.Type: ApplicationFiled: September 27, 2007Publication date: June 7, 2012Inventors: Mostafa Ronaghi, Amir Ali Haj Hossein Talasaz, Ronald W. Davis
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Publication number: 20120065091Abstract: The invention is directed to novel methods of multiplexing nucleic acid reactions, including amplification, detection and genotyping. The invention relies on the use of precircle probes that are circularized in the presence of the corresponding target nucleic acids, cleaved, and then amplified.Type: ApplicationFiled: August 9, 2011Publication date: March 15, 2012Inventors: Thomas D. Willis, Paul Hardenbol, Maneesh Jain, Viktor Stolc, Mostafa Ronaghi, Ronald W. Davis
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Publication number: 20110312529Abstract: This disclosure provides a method of determining a sequence of nucleotides for a nucleic acid template. The method can include the steps of contacting the nucleic acid template with a conformationally labeled polymerase and at least four different nucleotide species under conditions wherein the conformationally labeled polymerase catalyzes sequential addition of the nucleotide species to form a nucleic acid complement of the nucleic acid template, wherein the sequential addition of each different nucleotide species produces a conformational signal change from the conformationally labeled polymerase and wherein the rate or time duration for the conformational signal change is distinguishable for each different nucleotide species; detecting a series of changes in the signal from the conformationally labeled polymerase under the conditions; and determining the rates or time durations for the changes in the signal, thereby determining the sequence of nucleotides for the nucleic acid template.Type: ApplicationFiled: June 16, 2011Publication date: December 22, 2011Applicant: ILLUMINA, INC.Inventors: MOLLY HE, CHENG-YAO CHEN, ERIC KOOL, MOSTAFA RONAGHI, MICHAEL PREVITE, RIGO PANTOJA