Patents by Inventor Kenneth J. Livak
Kenneth J. Livak 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: 20200392571Abstract: Methods and systems for ordering assays which detect SNPs or gene expression are provided. The methods use PCR and RT-PCR procedures. Collections of stock assays are assembled using pre- and post-manufacturing quality control procedures and made available to consumers via the Internet. In addition, custom assays are prepared upon order from the consumer and these assays are also prepared using pre- and post-manufacturing quality control procedures. The assays are then delivered to the consumer.Type: ApplicationFiled: June 5, 2020Publication date: December 17, 2020Applicant: APPLIED BIOSYSTEMS, LLCInventors: Ryan T. KOEHLER, Kenneth J. LIVAK, Junko STEVENS, Francisco M. DE LA VEGA, Michael RHODES, Laurent R. BELLON, Dawn MADDEN, Dennis A. GILBERT, Yu N. WANG, Eugene G. SPIER, Xiaoqing YOU, Lily XU, Jeremy HEIL, Emily S. WINN-DEEN, Ivy McMULLEN, Susan EDDINS, Leila G. SMITH
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Patent number: 10689692Abstract: Methods and systems for ordering assays which detect SNPs or gene expression are provided. The methods use PCR and RT-PCR procedures. Collections of stock assays are assembled using pre- and post-manufacturing quality control procedures and made available to consumers via the Internet. In addition, custom assays are prepared upon order from the consumer and these assays are also prepared using pre- and post-manufacturing quality control procedures. The assays are then delivered to the consumer.Type: GrantFiled: September 6, 2016Date of Patent: June 23, 2020Assignee: APPLIED BIOSYSTEMS, LLCInventors: Ryan T. Koehler, Kenneth J. Livak, Junko Stevens, Francisco M. De La Vega, Michael Rhodes, Laurent R. Bellon, Dawn Madden, Dennis A. Gilbert, Yu N. Wang, Eugene G. Spier, Xiaoqing You, Lily Xu, Jeremy Heil, Emily S. Winn-Deen, Ivy McMullen, Susan Eddins, Leila G. Smith
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Publication number: 20170268051Abstract: Methods and systems for ordering assays which detect SNPs or gene expression are provided. The methods use PCR and RT-PCR procedures. Collections of stock assays are assembled using pre- and post-manufacturing quality control procedures and made available to consumers via the Internet. In addition, custom assays are prepared upon order from the consumer and these assays are also prepared using pre- and post-manufacturing quality control procedures. The assays are then delivered to the consumer.Type: ApplicationFiled: September 6, 2016Publication date: September 21, 2017Inventors: Ryan T. Koehler, Kenneth J. Livak, Junko STEVENS, Francisco M. DE LA VEGA, Michael RHODES, Laurent R. BELLON, Yu N. WANG, Xiaoqing YOU, Michael W. HUNKAPILLER, Janet S. ZIEGLE, Julie WILLIAMS, Dawn MADDEN, Dennis A. GILBERT, Charles R. SCAFE, Hadar I. ISAAC, Eugene G. SPIER, Lily XU, Leila G. SMITH, Jeremy HEIL, Stephen GLANOWSKI, John SCOTT, Emily S. WINN-DEEN, Ivy MCMULLEN, Lini WU, Harold Carey GIRE, Susan EDDINS
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Patent number: 9644231Abstract: The invention provides a method for detecting a target nucleotide sequence by tagging the nucleotide sequence with a nucleotide tag, providing a probe oligonucleotide with a melting temperature Tm1, comprising a regulatory sequence and a nucleotide tag recognition sequence; incorporating the probe oligonucleotide into the tagged polynucleotide in a polynucleotide amplification reaction, providing a regulatory oligonucleotide with a melting temperature Tm2, comprising a sequence segment that complementary to the regulatory sequence and a tail segment that does not hybridize to the probe nucleotide when the sequence segment and the regulatory sequence are annealed, amplifying the tagged target nucleic acid sequence in a PCR amplification reaction using the probe oligonucleotide as a primer, and using a DNA polymerase with high strand displacement activity and low 5?-nuclease activity, and detecting the amplification product; wherein Tm1 and Tm2 are higher than the annealing temperature associated with the polynType: GrantFiled: May 15, 2015Date of Patent: May 9, 2017Assignee: Fluidigm CorporationInventors: Kenneth J. Livak, Stacey N. Meyers, Xiaohui Wang, Jun Wang
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Patent number: 9587272Abstract: The invention provides a method for detecting a target nucleotide sequence by tagging the nucleotide sequence with a nucleotide tag, providing a probe oligonucleotide with a melting temperature Tm1, comprising a regulatory sequence and a nucleotide tag recognition sequence; incorporating the probe oligonucleotide into the tagged polynucleotide in a polynucleotide amplification reaction, providing a regulatory oligonucleotide with a melting temperature Tm2, comprising a sequence segment that is at least partially complementary to the regulatory sequence, amplifying the tagged target nucleic acid sequence in a PCR amplification reaction using the probe oligonucleotide as a primer, and detecting the amplification product; wherein Tm1 and Tm2 are higher than the annealing temperature associated with the polynucleotide amplification reaction.Type: GrantFiled: July 24, 2014Date of Patent: March 7, 2017Assignee: Fluidigm CorporationInventors: Kenneth J. Livak, Stacey N. Meyers, Jun Wang, Xiaohui Wang
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Patent number: 9528152Abstract: In some embodiments, an analyte detection system is provided that includes a nanochannel, an electrode arrangement, and a plurality of nanoFET devices disposed in the nanochannel. A plurality of nucleic acid base detection components can be used that include a plurality of nanopores, a plurality of nanochannels, a plurality of hybridization probes, combinations thereof, and the like. According to other embodiments of the present teachings, different coded molecules are hybridized to a target DNA molecule and used to detect the presence of various sequences along the target molecule. A kit including mixtures of coded molecules is also provided. In some embodiments, devices including nanochannels, nanopores, and the like, are used for manipulating movement of DNA molecules, for example, in preparation for a DNA sequencing detection. Nanopore structures and methods of making the same are also provided as are methods of nucleic acid sequencing using the nanopore structures.Type: GrantFiled: December 2, 2014Date of Patent: December 27, 2016Assignee: Life Technologies CorporationInventors: Hongye Sun, Mark F. Oldham, John O'Neill, Charles R. Connell, Umberto Ulmanella, Aldrich N. K. Lau, Theo Kotseroglou, Kenneth J. Livak
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Publication number: 20160348149Abstract: Reagents and methods are provided for detecting the presence of a target polynucleotide in a sample are disclosed. In one aspect, a method for producing a labeled amplification product by amplifying a target nucleic acid sequence to produce an amplification product comprising the target sequence, a first probe-binding sequence 5? to the target sequence, and a second probe-binding sequence 3? to the target sequence, thereby producing an amplification product; and hybridizing a first detection probe to the amplification product, the first detection probe comprising a first segment that hybridizes to the first probe-binding sequence and a second segment that hybridizes to the second probe-binding sequence, thereby producing a labeled amplification product is disclosed.Type: ApplicationFiled: May 2, 2016Publication date: December 1, 2016Inventors: Kenneth J. Livak, Jason A. A. West, Robert C. Jones
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Patent number: 9464320Abstract: Methods and systems for ordering assays which detect SNPs or gene expression are provided. The methods use PCR and RT-PCR procedures. Collections of stock assays are assembled using pre- and post-manufacturing quality control procedures and made available to consumers via the Internet. In addition, custom assays are prepared upon order from the consumer and these assays are also prepared using pre- and post-manufacturing quality control procedures. The assays are then delivered to the consumer.Type: GrantFiled: April 27, 2012Date of Patent: October 11, 2016Assignee: Applied Biosystems, LLCInventors: Ryan T. Koehler, Kenneth J. Livak, Junko Stevens, Francisco M. De La Vega, Michael Rhodes, Laurent R. Bellon, Julie Williams, Dawn Madden, Dennis A. Gilbert, Yu N. Wang, Eugene G. Spier, Xiaoqing You, Lily Xu, Jeremy Heil, Stephen Glanowski, Emily S. Winn-Deen, Ivy McMullen, Leila G. Smith
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Publication number: 20160153026Abstract: High throughput methods are used that combine the features of using a matrix-type microfluidic device, labeled nucleic acid probes, and homogenous assays to detect and/or quantify nucleic acid analytes. The high throughput methods are capable of detecting nucleic acid analyses with high PCR and probe specificity, producing a low fluorescence background and therefore, a high signal to noise ratio. Additionally, the high throughput methods are capable of detecting low copy number nucleic acid analyte per cell.Type: ApplicationFiled: October 9, 2015Publication date: June 2, 2016Inventors: Kenneth J. Livak, Marc Unger
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Patent number: 9353406Abstract: Reagents and methods are provided for detecting the presence of a target polynucleotide in a sample are disclosed. In one aspect, a method for producing a labeled amplification product by amplifying a target nucleic acid sequence to produce an amplification product comprising the target sequence, a first probe-binding sequence 5? to the target sequence, and a second probe-binding sequence 3? to the target sequence, thereby producing an amplification product; and hybridizing a first detection probe to the amplification product, the first detection probe comprising a first segment that hybridizes to the first probe-binding sequence and a second segment that hybridizes to the second probe-binding sequence, thereby producing a labeled amplification product is disclosed.Type: GrantFiled: October 24, 2011Date of Patent: May 31, 2016Assignee: Fluidigm CorporationInventors: Kenneth J. Livak, Jason A. A. West, Robert C. Jones
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Publication number: 20150361486Abstract: The invention provides a method for detecting a target nucleotide sequence by tagging the nucleotide sequence with a nucleotide tag, providing a probe oligonucleotide with a melting temperature Tm1, comprising a regulatory sequence and a nucleotide tag recognition sequence; incorporating the probe oligonucleotide into the tagged polynucleotide in a polynucleotide amplification reaction, providing a regulatory oligonucleotide with a melting temperature Tm2, comprising a sequence segment that complementary to the regulatory sequence and a tail segment that does not hybridize to the probe nucleotide when the sequence segment and the regulatory sequence are annealed, amplifying the tagged target nucleic acid sequence in a PCR amplification reaction using the probe oligonucleotide as a primer, and using a DNA polymerase with high strand displacement activity and low 5?-nuclease activity, and detecting the amplification product; wherein Tm1 and Tm2 are higher than the annealing temperature associated with the polynType: ApplicationFiled: May 15, 2015Publication date: December 17, 2015Applicant: FLUIDIGM CORPORATIONInventors: Kenneth J. Livak, Stacey N. Meyers, Xiaohui Wang, Jun Wang
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Patent number: 9157116Abstract: High throughput methods are used that combine the features of using a matrix-type microfluidic device, labeled nucleic acid probes, and homogenous assays to detect and/or quantify nucleic acid analytes. The high throughput methods are capable of detecting nucleic acid analyes with high PCR and probe specificity, producing a low fluorescence background and therefore, a high signal to noise ratio. Additionally, the high throughput methods are capable of detecting low copy number nucleic acid analyte per cell.Type: GrantFiled: February 9, 2009Date of Patent: October 13, 2015Assignee: Fluidigm CorporationInventors: Kenneth J. Livak, Marc Unger
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Publication number: 20150238919Abstract: Exemplary embodiments provide microfluidic devices and methods for their use. The microfluidic device can include an array of M×N reaction sites formed by intersecting a first and second plurality of fluid channels of a flow layer. The flow layer can have a matrix design and/or a blind channel design to analyze a large number of samples under a limited number of conditions. The microfluidic device can also include a control layer including a valve system for regulating solution flow through fluid channels. In addition, by aligning the control layer with the fluid channels, the detection of the microfluidic devices, e.g., optical signal collection, can be improved by piping lights to/from the reaction sites. In an exemplary embodiment, guard channels can be included in the microfluidic device for thermal cycling and/or reducing evaporation from the reaction sites.Type: ApplicationFiled: January 30, 2015Publication date: August 27, 2015Inventors: Mark F. OLDHAM, Dar BAHATT, Kenneth J. LIVAK, Jason E. BABCOKE, H. Pin KAO, Stephen J. GUNSTREAM, Kevin S. BODNER, Douglas P. GREINER, Nigel P. BEARD
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Publication number: 20150218630Abstract: In some embodiments, an analyte detection system is provided that includes a nanochannel, an electrode arrangement, and a plurality of nanoFET devices disposed in the nanochannel. A plurality of nucleic acid base detection components can be used that include a plurality of nanopores, a plurality of nanochannels, a plurality of hybridization probes, combinations thereof, and the like. According to other embodiments of the present teachings, different coded molecules are hybridized to a target DNA molecule and used to detect the presence of various sequences along the target molecule. A kit including mixtures of coded molecules is also provided. In some embodiments, devices including nanochannels, nanopores, and the like, are used for manipulating movement of DNA molecules, for example, in preparation for a DNA sequencing detection. Nanopore structures and methods of making the same are also provided as are methods of nucleic acid sequencing using the nanopore structures.Type: ApplicationFiled: December 2, 2014Publication date: August 6, 2015Inventors: Hongye SUN, Mark F. Oldham, John O'Neill, Charles R. Connell, Umberto Ulmanella, Aldrich N.K. Lau, Theo Kotseroglou, Kenneth J. Livak
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Publication number: 20150147755Abstract: The invention provides a method for detecting a target nucleotide sequence by tagging the nucleotide sequence with a nucleotide tag, providing a probe oligonucleotide with a melting temperature Tm1, comprising a regulatory sequence and a nucleotide tag recognition sequence; incorporating the probe oligonucleotide into the tagged polynucleotide in a polynucleotide amplification reaction, providing a regulatory oligonucleotide with a melting temperature Tm2, comprising a sequence segment that is at least partially complementary to the regulatory sequence, amplifying the tagged target nucleic acid sequence in a PCR amplification reaction using the probe oligonucleotide as a primer, and detecting the amplification product; wherein Tm1 and Tm2 are higher than the annealing temperature associated with the polynucleotide amplification reaction.Type: ApplicationFiled: July 24, 2014Publication date: May 28, 2015Inventors: Kenneth J. Livak, Stacey N. Myers, Jun Wang, Xiaohui Wang
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Patent number: 8993240Abstract: The present teachings provide methods, compositions, and kits for performing primer extension reactions. In some embodiments, a reverse transcription reaction is performed on a target polynucleotide with a hot start primer comprising a blunt-ended self-complementary stem, and a loop, and extension products form at high temperatures but reduce extension product formation at low temperatures.Type: GrantFiled: July 16, 2009Date of Patent: March 31, 2015Assignee: Applied Biosystems, LLCInventors: Kai Qin Lao, Neil A. Straus, Kenneth J. Livak
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Patent number: 8969090Abstract: In some embodiments, an analyte detection system is provided that includes a nanochannel, an electrode arrangement, and a plurality of nanoFET devices disposed in the nanochannel. A plurality of nucleic acid base detection components can be used that include a plurality of nanopores, a plurality of nanochannels, a plurality of hybridization probes, combinations thereof, and the like. According to other embodiments of the present teachings, different coded molecules are hybridized to a target DNA molecule and used to detect the presence of various sequences along the target molecule. A kit including mixtures of coded molecules is also provided. In some embodiments, devices including nanochannels, nanopores, and the like, are used for manipulating movement of DNA molecules, for example, in preparation for a DNA sequencing detection. Nanopore structures and methods of making the same are also provided as are methods of nucleic acid sequencing using the nanopore structures.Type: GrantFiled: January 4, 2011Date of Patent: March 3, 2015Assignee: Life Technologies CorporationInventors: Hongye Sun, Eric S. Nordman, Mark F. Oldham, John R. O'Neill, Charles Connell, Umberto Ulmanella, Aldrich N. K. Lau, Theofilos Kotseroglou, Kenneth J. Livak
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Patent number: 8945481Abstract: Exemplary embodiments provide microfludic devices and methods for their use. The microfluidic device can include an array of M×N reaction sites formed by intersecting a first and second plurality of fluid channels of a flow layer. The flow layer can have a matrix design and/or a blind channel design to analyze a large number of samples under a limited number of conditions. The microfluidic device can also include a control layer including a valve system for regulating solution flow through fluid channels. In addition, by aligning the control layer with the fluid channels, the detection of the microfluidic devices, e.g., optical signal collection, can be improved by piping lights to/from the reaction sites. In an exemplary embodiment, guard channels can be included in the microfluidic device for thermal cycling and/or reducing evaporation from the reaction sites.Type: GrantFiled: June 24, 2008Date of Patent: February 3, 2015Assignee: Applied Biosystems, LLCInventors: Mark F. Oldham, Kenneth J. Livak, Jason E. Babcoke, H. Pin Kao, Stephen J. Gunstream, Kevin S. Bodner, Douglas P. Greiner, Nigel P. Beard, Dar Bahatt
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Publication number: 20140315197Abstract: Methods and reagents for detection and analysis of nucleic acids are provided. Certain methods involves an encoding amplification in which a target sequence is associated with probe-binding sequences and optionally with indexing sequences, (2) an optional distribution step in which the product of the encoding amplification is split into multiple aliquots, and (3) a decoding and detection step in which the presence, absence, quantity, or relative amount of the target sequence in the aliquots is determined. The detection step makes use of a multifunctional “self-digesting” molecular probe comprising a primer polynucleotide and a probe oligonucleotide, linked in a 5?-5? orientation.Type: ApplicationFiled: February 19, 2014Publication date: October 23, 2014Inventor: Kenneth J. Livak
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Patent number: 8809238Abstract: The invention provides a method for detecting a target nucleotide sequence by tagging the nucleotide sequence with a nucleotide tag, providing a probe oligonucleotide with a melting temperature Tm1, comprising a regulatory sequence and a nucleotide tag recognition sequence; incorporating the probe oligonucleotide into the tagged polynucleotide in a polynucleotide amplification reaction, providing a regulatory oligonucleotide with a melting temperature Tm2, comprising a sequence segment that is at least partially complementary to the regulatory sequence, amplifying the tagged target nucleic acid sequence in a PCR amplification reaction using the probe oligonucleotide as a primer, and detecting the amplification product; wherein Tm1 and Tm2 are higher than the annealing temperature associated with the polynucleotide amplification reaction.Type: GrantFiled: May 9, 2012Date of Patent: August 19, 2014Assignee: Fluidigm CorporationInventors: Kenneth J. Livak, Stacey N. Meyers, Jun Wang, Xiaohui Wang