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: 20110246084Abstract: The present technology relates to the methods and systems for analysis of sequencing data. In particular, methods and systems for characterizing a target nucleic acid while determining the nucleotide sequence of the target nucleic acid are described. Certain embodiments include methods and systems for identifying the source of a target nucleic acid by comparing the accumulating nucleotide sequence of a target nucleic acid to a population of reference nucleotide sequences.Type: ApplicationFiled: November 24, 2009Publication date: October 6, 2011Inventors: Mostafa Ronaghi, Helmy A. Etoukhy
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Patent number: 7993880Abstract: 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: February 19, 2010Date of Patent: August 9, 2011Assignee: The 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: 20110171655Abstract: The present method involves sequencing by synthesis in which a template strand having an attached primer is immobilized in a small volume reaction mixture. In one embodiment, the reaction mixture is in contact with a sensitive heat sensor, which detects the heat of reaction from incorporation of a complementary base (dNTP) in the presence of appropriate reagents (DNA polymerase, and polymerase reaction buffer). Alternatively, or in addition, a change in pH resulting from the incorporation of nucleotides in the DNA polymerase reaction is measured. A device is provided having delivery channels for appropriate reagents, including dNTPs, which may be delivered sequentially or in a mixture. Preferably, the dNTPs are added in a predetermined sequence, and the dNTP is incorporated or not depending on the template sequence.Type: ApplicationFiled: March 16, 2011Publication date: July 14, 2011Applicant: THE BOARD OF TRUSTEES OF THE LELAND STANFORD JUNIOR UNIVERSITYInventors: Hesaam Esfandyarpour, Mostafa Ronaghi
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Patent number: 7932034Abstract: The present method involves sequencing by synthesis in which a template strand having an attached primer is immobilized in a small volume reaction mixture. In one embodiment, the reaction mixture is in contact with a sensitive heat sensor, which detects the heat of reaction from incorporation of a complementary base (dNTP) in the presence of appropriate reagents (DNA polymerase, and polymerase reaction buffer). Alternatively, or in addition, a change in pH resulting from the incorporation of nucleotides in the DNA polymerase reaction is measured. A device is provided having delivery channels for appropriate reagents, including dNTPs, which may be delivered sequentially or in a mixture. Preferably, the dNTPs are added in a predetermined sequence, and the dNTP is incorporated or not depending on the template sequence.Type: GrantFiled: December 18, 2007Date of Patent: April 26, 2011Assignee: The Board of Trustees of the Leland Stanford Junior UniversityInventors: Hesaam Esfandyarpour, Mostafa Ronaghi
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Publication number: 20100330619Abstract: 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: February 19, 2010Publication date: December 30, 2010Inventors: Thomas D. Willis, Paul Hardenbol, Maneesh Jain, Viktor Stolc, Mostafa Ronaghi, Ronald W. Davis
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Publication number: 20100279882Abstract: The present technology relates to molecular sciences, such as genomics. More particularly, the present technology relates to nucleic acid sequencing.Type: ApplicationFiled: April 30, 2010Publication date: November 4, 2010Inventors: Mostafa Ronaghi, Dirk Evers, Jason Richard Betley
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Publication number: 20100224494Abstract: 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: ApplicationFiled: March 2, 2010Publication date: September 9, 2010Applicant: 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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Patent number: 7782237Abstract: An error-corrected representation of an input signal, such as a bioluminescence signal, is generated. An analog representation of the input signal is oversampled and quantized to provide a first-stage digital output and a residual error. The residual error is provided as a second-stage digital output using successive approximation. The first-stage and second-stage digital outputs are used to generate an error-corrected representation of the bioluminescence signal.Type: GrantFiled: June 13, 2008Date of Patent: August 24, 2010Assignee: The Board of Trustees of the Leland Stanford Junior UniversityInventors: Mostafa Ronaghi, Ali Agah
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Publication number: 20100173303Abstract: 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: December 17, 2009Publication date: July 8, 2010Inventors: Mostafa Ronaghi, Helmy A. Eltoukhy
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Patent number: 7700323Abstract: 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: April 15, 2004Date of Patent: April 20, 2010Assignee: The 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: 20100075340Abstract: The present disclosure encompasses the manufacture and use of rapid and inexpensive electrical biosensors comprising microelectrodes in a micro-channel. The devices of the disclosure can be used to detect and quantify target cells, protein biomarkers, and nucleic acid biomarkers, and the like, by measuring instantaneous changes in ionic impedance. The micro-channel devices of the disclosure are also suitable for the detection of target protein and oligonucleotide, and small molecule target biomarkers using protein-functionalized micro-channels for the rapid electrical detection and quantification of any type of target protein biomarker in a sample.Type: ApplicationFiled: September 21, 2009Publication date: March 25, 2010Inventors: Mehdi Javanmard, Mostafa Ronaghi, Ron W. Davis
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Patent number: 7648824Abstract: The present invention provides a method of identifying a base at a target position in a sample nucleic acid sequence, said method comprising: subjecting a primer hybridised to said sample nucleic acid immediately adjacent to the target position, to a polymerase primer extension reaction in the presence of a nucleotide, whereby the nucleotide will only become incorporated if it is complementary to the base in the target position, and determining whether or not said nucleotide is incorporated by detecting whether PPi is released, the identity of the target base being determined from the identity of any nucleotide incorporated, wherein, where said nucleotide comprises an adenine base, an ?-thio triphosphate analogue of said nucleotide is used, ant the Rp isomer of said analogue and/or the degradation products of said analogue are eliminated from the polymerase reaction step.Type: GrantFiled: November 26, 2008Date of Patent: January 19, 2010Assignee: Qiagen GmbHInventors: Pal Nyren, Mostafa Ronaghi, Annika Tallsjo
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Publication number: 20090309773Abstract: An error-corrected representation of an input signal, such as a bioluminescence signal, is generated. An analog representation of the input signal is oversampled and quantized to provide a first-stage digital output and a residual error. The residual error is provided as a second-stage digital output using successive approximation. The first-stage and second-stage digital outputs are used to generate an error-corrected representation of the bioluminescence signal.Type: ApplicationFiled: June 13, 2008Publication date: December 17, 2009Inventors: Mostafa Ronaghi, Ali Agah
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Publication number: 20090298064Abstract: Genomic sequencing is implemented for high throughput applications that can include short reads. In one example, whole-genome sequencing involves a method in which a subset of fragments of a target genome are selected as a random function, and each fragment is replicated into clones. The clones are ordered into clone contigs based on sets of overlapping clones, and potential read overlaps are determined from clone read data. The method can also involve reading local assemblies of contigs from regions smaller than a clone length and assembling the local assemblies into read sets, combining the assembled read sets into clone-sized regions and assembling the clone-sized regions, and assembling the clone-sized regions into clone contigs. Overlapping sets of clones and their ordering can be determined computationally from read data, with a high depth of clone coverage to provide a large number of boundaries on which the assemblies can be segmented into overlapping regions of pooled reads.Type: ApplicationFiled: May 29, 2008Publication date: December 3, 2009Inventors: Serafim Batzoglou, Mostafa Ronaghi, Andreas Sundquist
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Patent number: 7622281Abstract: Described herein are methods and compositions relating to amplifying nucleic acid. In certain embodiments, the invention provides methods for labeling and amplifying a nucleic acid molecule.Type: GrantFiled: May 19, 2005Date of Patent: November 24, 2009Assignee: The Board of Trustees of the Leland Stanford Junior UniversityInventors: Mostafa Ronaghi, Foad Mashayekhi
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Publication number: 20090286299Abstract: DNA sequencing techniques are important for a variety of research and diagnostic applications. Pyrosequencing is a “sequencing by synthesis” technique that makes use of luciferase. Modified luciferase enzymes and methods of DNA pyrosequencing are provided. Means of preparing and producing mutant luciferases that have enhanced selectivity for ATP or dATP are described.Type: ApplicationFiled: May 15, 2009Publication date: November 19, 2009Inventors: Mostafa Ronaghi, Helmy A. Eltoukhy, Leila Bazargan
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Publication number: 20090155801Abstract: The present invention provides a method of identifying a base at a target position in a sample nucleic acid sequence, said method comprising: subjecting a primer hybridised to said sample nucleic acid immediately adjacent to the target position, to a polymerase primer extension reaction in the presence of a nucleotide, whereby the nucleotide will only become incorporated if it is complementary to the base in the target position, and determining whether or not said nucleotide is incorporated by detecting whether PPi is released, the identity of the target base being determined from the identity of any nucleotide incorporated, wherein, where said nucleotide comprises an adenine base, an ?-thio triphosphate analogue of said nucleotide is used, ant the Rp isomer of said analogue and/or the degradation products of said analogue are eliminated from the polymerase reaction step.Type: ApplicationFiled: November 26, 2008Publication date: June 18, 2009Applicant: Biotage ABInventors: Pal Nyren, Mostafa Ronaghi, Annika Tallsjo
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Publication number: 20090032401Abstract: 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: July 10, 2008Publication date: February 5, 2009Applicant: The Board of Trustees of the Leland Stanford Junior UniversityInventors: Mostafa Ronaghi, Tarun Khurana, Juan G. Santiago
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Patent number: 7459311Abstract: The present invention provides a method of identifying a base at a target position in a sample nucleic acid sequence, said method comprising: subjecting a primer hybridised to said sample nucleic acid immediately adjacent to the target position, to a polymerase primer extension reaction in the presence of a nucleotide, whereby the nucleotide will only become incorporated if it is complementary to the base in the target position, and determining whether or not said nucleotide is incorporated by detecting whether Ppi is released, the identity of the target base being determined from the identity of any nucleotide incorporated, wherein, where said nucleotide comprises an adenine base, an ?-thio triphosphate analogue of said nucleotide is used, and the Rp isomer of said analogue and/or the degradation products of said analogue are eliminated from the polymerase reaction step.Type: GrantFiled: September 7, 2001Date of Patent: December 2, 2008Assignee: Biotage ABInventors: Pål Nyren, Mostafa Ronaghi, Annika Tallsjö
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Publication number: 20080166727Abstract: The present method involves sequencing by synthesis in which a template strand having an attached primer is immobilized in a small volume reaction mixture. In one embodiment, the reaction mixture is in contact with a sensitive heat sensor, which detects the heat of reaction from incorporation of a complementary base (dNTP) in the presence of appropriate reagents (DNA polymerase, and polymerase reaction buffer). Alternatively, or in addition, a change in pH resulting from the incorporation of nucleotides in the DNA polymerase reaction is measured. A device is provided having delivery channels for appropriate reagents, including dNTPs, which may be delivered sequentially or in a mixture. Preferably, the dNTPs are added in a predetermined sequence, and the dNTP is incorporated or not depending on the template sequence.Type: ApplicationFiled: December 18, 2007Publication date: July 10, 2008Applicant: The Board of Trustees of the Leland Stanford Junior UniversityInventors: Hesaam Esfandyarpour, Mostafa Ronaghi