Patents by Inventor Kenneth Livak
Kenneth 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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Patent number: 9567635Abstract: 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: March 12, 2015Date of Patent: February 14, 2017Assignee: Life Technologies CorporationInventors: Kai Lao, Neil Straus, Kenneth Livak
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Patent number: 9518296Abstract: The present teachings provide methods, compositions, and kits for detecting the presence of protein aggregates. In some embodiments, the protein aggregate is treated with a labeled precursor, and the labeled precursor is incorporated into the protein aggregate to form a labeled protein aggregate. The labeled protein aggregate is then measured, thus detecting the presence of the protein aggregate. In some embodiments, the labeled protein aggregate is detected by interaction of labeled precursors, for example by a proximity ligation assay.Type: GrantFiled: August 23, 2013Date of Patent: December 13, 2016Assignee: APPLIED BIOSYSTEMS LLCInventors: David Ruff, Mark Shannon, Kenneth Livak, Karl Guegler, Kevin Hennessy
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Publication number: 20150252418Abstract: 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: ApplicationFiled: March 12, 2015Publication date: September 10, 2015Inventors: Kai LAO, Neil Straus, Kenneth Livak
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Publication number: 20140329238Abstract: Methods of detecting a candidate genetic anomaly such as a candidate duplication in a genome are disclosed. The methods comprise quantifying fluorogenic assays for alleles of a genetic locus from a plurality of individual genomes, identifying ranges of fluorescent intensities indicative of individual genomes homozygous for a first allele, homozygous for a second allele, or heterozygous for both alleles, and identifying individual genomes in which the fluorescence intensities are outside the range of intensities indicative of homozygosity or heterozygosity for the genetic locus.Type: ApplicationFiled: March 25, 2014Publication date: November 6, 2014Applicant: APPLIED BIOSYSTEMS, LLCInventors: Kenneth LIVAK, Junko Stevens, Katherine Lazaruk, Janet Ziegle, Lily Wong
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Publication number: 20140303017Abstract: The present teachings provide methods, compositions, and kits for reverse transcribing and amplifying small nucleic acids such as micro RNAs. High levels of multiplexing are provided by the use of a zip-coded stem-loop reverse transcription primer, along with a PCR-based pre-amplification reaction that comprises a zip-coded forward primer. Detector probes in downstream decoding PCRs can take advantage of the zip-code introduced by the stem-loop reverse transcription primer. In some embodiments, further amplification is achieved by cycling the reverse transcription reaction. The present teachings also provide compositions and kits useful for performing the reverse transcription and amplification reactions described herein.Type: ApplicationFiled: March 6, 2014Publication date: October 9, 2014Applicant: APPLIED BIOSYSTEMS, LLCInventors: Kai LAO, Kenneth Livak, Neil Straus
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Publication number: 20140134624Abstract: The present teachings provide methods, compositions, and kits for detecting the presence of protein aggregates. In some embodiments, the protein aggregate is treated with a labeled precursor, and the labeled precursor is incorporated into the protein aggregate to form a labeled protein aggregate. The labeled protein aggregate is then measured, thus detecting the presence of the protein aggregate. In some embodiments, the labeled protein aggregate is detected by interaction of labeled precursors, for example by a proximity ligation assay.Type: ApplicationFiled: August 23, 2013Publication date: May 15, 2014Applicant: LIFE TECHNOLOGIES CORPORATIONInventors: David RUFF, Mark Shannon, Kenneth Livak, Karl Guegler, Kevin Hennessy
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Patent number: 8067165Abstract: Binary probe and clamp compositions conduct methods for target hybridization detection. Where the probe is a substrate for exonuclease cleavage, the composition provides quantitation and detection of PCR products, by real-time and end-point measurements. Where the probe is an amplification primer, the composition provides an improved method for labelling and detection of PCR products. Probes and clamps may be labelled with fluorescent dyes, quenchers, hybridization-stabilizing moieties, chemiluminescent dyes, and affinity ligands. Clamps may be nucleic acid analogs, such as 2-aminoethylglycine PNA.Type: GrantFiled: August 10, 2009Date of Patent: November 29, 2011Assignee: Applied Biosystems, LLCInventors: Kenneth Livak, Michael Egholm, Michael Hunkapiller
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Publication number: 20080050752Abstract: The present disclosure relates to methods of analyzing binding interactions between a binding component and a receptor component by translocating unbound and any bound components through a pore and detecting the unbound and bound components.Type: ApplicationFiled: June 14, 2007Publication date: February 28, 2008Applicant: Applera CorporationInventors: Hongye SUN, Kenneth Livak
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Publication number: 20080003604Abstract: The present teachings provide methods, compositions, and kits for detecting the presence of protein aggregates. In some embodiments, the protein aggregate is treated with a labeled precursor, and the labeled precursor is incorporated into the protein aggregate to form a labeled protein aggregate. The labeled protein aggregate is then measured, thus detecting the presence of the protein aggregate. In some embodiments, the labeled protein aggregate is detected by interaction of labeled precursors, for example by a proximity ligation assay.Type: ApplicationFiled: May 2, 2007Publication date: January 3, 2008Applicant: Applera CorporationInventors: David Ruff, Mark Shannon, Kenneth Livak, Karl Guegler, Kevin Hennessy
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Publication number: 20070264666Abstract: A method for performing PCR on a liquid sample comprising a plurality of polynucleotide targets, wherein each polynucleotide target is present at very low concentration within the sample. The method comprises applying PCR reactants to the surface of a substrate to produce a plurality of reaction spots on the surface of the substrate; loading the liquid sample and a PCR reagent mixture onto the reaction spots; forming a sealed reaction chamber, having a volume of less than about 20 nanoliters, over each of the reaction spots; and amplifying the sample.Type: ApplicationFiled: July 26, 2007Publication date: November 15, 2007Applicant: APPLERA CORPORATIONInventors: Timothy Woudenberg, Robert Jones, Kenneth Livak
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Publication number: 20070219364Abstract: The present invention relates to methods and kits for detecting the presence or absence of (or quantitating) target nucleic acid sequences using ligation and amplification. The invention also relates to methods, reagents, and kits that employ addressable portions and labeled probes.Type: ApplicationFiled: December 22, 2006Publication date: September 20, 2007Applicant: APPLERA CORPORATIONInventors: Mark Andersen, Michael Hunkapiller, Kenneth Livak, Eugene Spier, H. Wenz
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Publication number: 20070190543Abstract: The present disclosure relates to methods of detecting target analytes based on single molecule detection of coded molecules.Type: ApplicationFiled: November 14, 2006Publication date: August 16, 2007Applicant: Applera CorporationInventor: Kenneth Livak
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Publication number: 20070178519Abstract: Disclosed is a method for determining the number of repeat units in a repeat region of a target nucleic acid. In a first aspect, the method of the invention includes the steps of annealing a primer to a target nucleic acid; performing a first primer extension reaction using a first primer extension reagent; separating the target-primer hybrid and unreacted first primer extension reagent; performing a second primer extension reaction using a second primer extension reagent, wherein at least one of the first or second primer extension reagents includes an extendible nucleotide having a label attached thereto; separating the target-primer hybrid from unreacted second primer extension reagent; measuring a signal produced by the label; treating the label so as to render the label undetectable; and repeating the above steps until the signal is substantially less than a signal detected in a previous cycle.Type: ApplicationFiled: March 30, 2007Publication date: August 2, 2007Applicant: Applera CorporationInventors: Kenneth Livak, Adam Lowe, Andrew Blasband
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Publication number: 20070128620Abstract: 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: ApplicationFiled: July 17, 2006Publication date: June 7, 2007Applicant: APPLERA CORPORATIONInventors: Kai Lao, Neil Straus, Kenneth Livak
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Publication number: 20070077570Abstract: The present teachings provide methods, compositions, and kits for reverse transcribing and amplifying small nucleic acids such as micro RNAs. High levels of multiplexing are provided by the use of a zip-coded stem-loop reverse transcription primer, along with a PCR-based pre-amplification reaction that comprises a zip-coded forward primer. Detector probes in downstream decoding PCRs can take advantage of the zip-code introduced by the stem-loop reverse transcription primer. In some embodiments, further amplification is achieved by cycling the reverse transcription reaction. The present teachings also provide compositions and kits useful for performing the reverse transcription and amplification reactions described herein.Type: ApplicationFiled: May 31, 2006Publication date: April 5, 2007Applicant: APPLERA CORPORATIONInventors: Kai Lao, Kenneth Livak, Neil Straus
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Publication number: 20070037184Abstract: Methods and kits are disclosed for determining the degree of methylation of at least one target region. Typically a sample is exposed to a modifying agent to obtain a modified sample comprising a modified nucleotide. At least one target region in the modified sample is amplified. Some of the disclosed methods comprise at least one additional amplification reaction. In some embodiments, at least one mobility shifting analog is incorporated into an amplicon during an amplification reaction. The analogs are analyzed and the degree of methylation of at least one target region is determined.Type: ApplicationFiled: June 14, 2006Publication date: February 15, 2007Applicant: APPLERA CORPORATIONInventors: VICTORIA BOYD, KENNETH LIVAK, GERALD ZON
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Publication number: 20070026429Abstract: Binary probe and clamp compositions conduct methods for target hybridization detection. Where the probe is a substrate for exonuclease cleavage, the composition provides quantitation and detection of PCR products, by real-time and end-point measurements. Where the probe is an amplification primer, the composition provides an improved method for labelling and detection of PCR products. Probes and clamps may be labelled with fluorescent dyes, quenchers, hybridization-stabilizing moieties, chemiluminescent dyes, and affinity ligands. Clamps may be nucleic acid analogs, such as 2-aminoethylglycine PNA.Type: ApplicationFiled: June 5, 2006Publication date: February 1, 2007Applicant: APPLERA CORPORATIONInventors: Kenneth Livak, Michael Egholm, Michael Hunkapiller
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Publication number: 20070015187Abstract: The present teachings provide methods, compositions, and kits for detecting micro RNAs (miRNAs). In some embodiments, the miRNAs are quantified from formalin-fixed paraffin-embedded tissue samples in which messenger RNA is degraded. The present teachings take advantage of the observation that most mature miRNAs in vivo are protected by degradation as a result of their association with RISC. Thus, novel methods of studying nucleic acids in archived tissues containing degraded messenger RNA are provided, wherein RISC-protected miRNAs are liberated, and analyzed.Type: ApplicationFiled: July 17, 2006Publication date: January 18, 2007Applicant: APPLERA CORPORATIONInventors: Kai Lao, Kenneth Livak
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Publication number: 20060035217Abstract: Binary probe and clamp compositions conduct methods for target hybridization detection. Where the probe is a substrate for exonuclease cleavage, the composition provides quantitation and detection of PCR products, by real-time and end-point measurements. Where the probe is an amplification primer, the composition provides an improved method for labelling and detection of PCR products. Probes and clamps may be labelled with fluorescent dyes, quenchers, hybridization-stabilizing moieties, chemiluminescent dyes, and affinity ligands. Clamps may be nucleic acid analogs, such as 2-aminoethylglycine PNA.Type: ApplicationFiled: March 28, 2002Publication date: February 16, 2006Applicant: PE Corporation (NY)Inventors: Kenneth Livak, Michael Egholm, Michael Hunkapiller
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Publication number: 20050260640Abstract: The present invention is directed to methods, reagents, and kits for detecting the presence or absence of (or quantifying) target polynucleotide sequences and proteins in at least one sample using encoding and decoding reactions. When a particular target polynucleotide is present in a sample for example, a reaction product is formed in the encoding reaction that includes addressable primer portions. At least one labeling probe and at least one address primer can be employed in the decoding amplification reaction thereby providing a detectable signal value depending upon whether a sequence is present or absent. In some embodiments, the encoding comprises a ligation reaction with linker probes, and single nucleotide polymorphisms (SNPs) are analyzed.Type: ApplicationFiled: March 24, 2005Publication date: November 24, 2005Applicant: Applera CorportionInventors: Mark Andersen, Kenneth Livak, Adam Broomer, Caifu Chen