Patents by Inventor Kai Lao
Kai Lao 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: 20110257385Abstract: Provided herein are compositions, materials, methods and kits for immobilizing a template polynucleotide in a first orientation, and immobilizing a complementary sequence of the template polynucleotide in an orientation that is flipped compared to the orientation of the template polynucleotide. Provided herein are adaptive oligonucleotides that can be used in various nucleic acid manipulations to generate immobilized complement polynucleotides that are flipped in orientation compared to the orientation of the immobilized template polynucleotides.Type: ApplicationFiled: February 23, 2011Publication date: October 20, 2011Applicant: LIFE TECHNOLOGIES CORPORATIONInventors: KEVIN MCKERNAN, ALAN BLANCHARD, GERALD ZON, KAI LAO, NEIL STRAUS, EUGENE SPIER, CAIFU CHEN
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Publication number: 20100124765Abstract: The present disclosure relates to the amplification of target nucleic acid sequences for various sequencing and/or identification techniques. This can be accomplished via the use of target primers. The use of these target primers, as described herein, allows for the reduction in the amplification of undesired hybridization events (such as primer dimerization) while allowing for the amplification of the target nucleic acid sequences.Type: ApplicationFiled: October 16, 2009Publication date: May 20, 2010Applicant: LIFE TECHNOLOGIES CORPORATIONInventors: Kai LAO, Neil STRAUS, Nanlan XU
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Publication number: 20070259356Abstract: The present teachings relate to methods, compositions, and kits for detecting one or more target polynucleotide sequences in a sample, and methods compositions and kits for forming concatameric ligation products. In some embodiments of the present teachings, oligonucleotides are hybridized to complementary target polynucleotides and are ligated together to form a concatameric ligation product. In some embodiments of the present teachings, the concatameric ligation product can be amplified, and the identity and quantity of the target polynucleotides determined based on sequence introduced in the ligation reaction. Some embodiments of the present teachings provide methods for removing unligated probes from the reaction mixture. Some embodiments of the present teachings provide for highly multiplexed detection, identification, and quantification of a plurality of target polynucleotides using a variety of analytical procedures.Type: ApplicationFiled: December 12, 2006Publication date: November 8, 2007Applicant: APPLERA CORPORATIONInventors: Caifu Chen, Kevin Hennessy, Kai Lao, Teodoro Paner, Vinod Mirchandani
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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: 20070128654Abstract: The present invention relates to universal-tagged oligonucleotide primers, and to methods of using the primers for amplifying the genome.Type: ApplicationFiled: January 18, 2007Publication date: June 7, 2007Inventors: Kai Lao, Caifu Chen, Ryan Koehler, Charles Scafe, Gary Schroth
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Publication number: 20070128621Abstract: The present teachings provide methods, compositions, and kits for performing primer extension reactions on at least two target polynucleotides in the same reaction mixture. In some embodiments, a reverse transcription reaction is performed on a first target polynucleotide with a hot start primer comprising a self-complementary stem and a loop, and extension products form at high temperatures but extension products form less so at low temperatures since the self-complementary stem of the hot start primer prevents hybridization of the target specific region to the target. However, non-hot start primers with free target specific regions can hybridize to their corresponding targets at the low temperature and extension can happen at the low temperature.Type: ApplicationFiled: July 17, 2006Publication date: June 7, 2007Applicant: APPLERA CORPORATIONInventors: Kai Lao, Neil Straus
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Publication number: 20070099228Abstract: The present teachings relate to methods, compositions, and kits for detecting one or more target polynucleotide sequences in a sample, and methods compositions and kits for forming concatameric ligation products. In some embodiments of the present teachings, oligonucleotides are hybridized to complementary target polynucleotides and are ligated together to form a concatameric ligation product. In some embodiments of the present teachings, the concatameric ligation product can be amplified, and the identity and quantity of the target polynucleotides determined based on sequence introduced in the ligation reaction. Some embodiments of the present teachings provide methods for removing unligated probes from the reaction mixture. Some embodiments of the present teachings provide for highly multiplexed detection, identification, and quantification of a plurality of target polynucleotides using a variety of analytical procedures.Type: ApplicationFiled: December 12, 2006Publication date: May 3, 2007Applicant: APPLERA CORPORATIONInventors: Caifu Chen, Kevin Hennessy, Kai Lao, Teodoro Paner, Vinod Mirchandani
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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: 20070059739Abstract: The present teachings provide novel methods, compositions, and kits for analyzing mature micro RNAs (miRNAs). By taking advantage of the observation that most mature miRNAs in cells are tightly associated with RISCs, the present teachings provide approaches for studying mature miRNAs without the complications of additional nucleic acids. For example, in some embodiments the present teachings provide a method of purifying mature miRNAs comprising heating a sample to form a lysate, and, degrading the additional nucleic acids. The resulting mixture lacks the additional nucleic acids, and contains mature miRNAs associated with RISCs. Liberating the mature miRNAs from RISCs, for example by a protease, a detergent, and/or heat, can result in a pure collection of mature miRNAs.Type: ApplicationFiled: July 17, 2006Publication date: March 15, 2007Applicant: APPLERA CORPORATIONInventor: Kai Lao
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Publication number: 20070048757Abstract: The present teachings provide methods, compositions, and kits for reverse transcribing and amplifying small nucleic acids such as micro RNAs. In some embodiments, the present teachings provide methods of forming micro RNA signatures from single cells, including stem cells. In some embodiments, the present teachings provide methods for determining the identity and/or purity of cells. The present employ performing a multiplexed reverse transcription reaction comprising stem-loop reverse transcription primers, which optionally undergoes temperature cycling, followed by a multiplexed PCR-based pre-amplification reaction, and a subsequently a plurality of lower-plex decoding PCRs.Type: ApplicationFiled: May 31, 2006Publication date: March 1, 2007Applicant: APPLERA CORPORATIONInventors: Kai Lao, Neil Straus, Will Bloch
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Publication number: 20070026430Abstract: The present teachings provide methods, compositions, and kits for detecting target analytes, including proteins. In some embodiments, cleavage reactions are performed in the context of proximity probe reactions that query target proteins, wherein the presence and/or quantity of cleavage products is indicative of the presence and/or quantity of a target protein. In some embodiments, the cleavage fragments are quantitated using a real time PCR assay comprising a stem-loop primer, wherein the stem-loop primer comprises a self-complementary hairpin structure and a free 3? end end complementary to the cleavage product. In some embodiments, polymerase extension approaches are employed in the context of proximity probe reactions.Type: ApplicationFiled: June 30, 2006Publication date: February 1, 2007Applicant: APPLERA CORPORATIONInventors: Mark Andersen, Benjamin Schroeder, Kai Lao
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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: 20070015176Abstract: The present teachings are directed to compositions, methods, and kits for detecting and quantitating small nucleic acid molecules, including small DNA molecules and small RNA molecules. The detector probes of the current teachings, including single-loop detector probes, double-loop detector probes, and bimolecular detector probes, are designed to selectively hybridize with a corresponding small nucleic acid target and to produce, under appropriate conditions, a detectable signal or a detectably different signal. The detector complexes of the current teachings comprise a detector probe comprising a first reporter group and a displaceable sequence comprising a second reporter group, wherein the displaceable sequence is hybridized to the detector probe.Type: ApplicationFiled: February 14, 2006Publication date: January 18, 2007Applicant: Applera CorporationInventors: Kai Lao, Neil Straus
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Publication number: 20060292586Abstract: The present invention relates to the detection of target sequences. Detection can be achieved through the use of ID-tag complexes. These ID-tag complexes are relatively stable in the absence of a target sequence. In the presence of a target sequence, the complexes dissociate and form new complexes or duplexes, which can be purified or eliminated and detected on an ID-tag system.Type: ApplicationFiled: November 30, 2005Publication date: December 28, 2006Inventors: Gary Schroth, Kai Lao, Neil Straus
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Publication number: 20060223066Abstract: The present teachings are generally directed to methods for normalizing at least one species of small nucleic acid that is present in a population of small nucleic acid species, wherein the relative concentration of at least one small nucleic acid species is substantially greater than the relative concentration of at least one other small nucleic acid species in the population. At least one small nucleic acid species is normalized using a multiplicity of primers comprising degenerate sequences. In some embodiments, a small nucleic acid species is identified by inserting at least part of an extension product from a normalized population into a vector and subsequently sequencing the insert. In some embodiments, a small nucleic acid species is identified by determining the sequence of at least part of an extension product.Type: ApplicationFiled: March 29, 2005Publication date: October 5, 2006Applicant: Applera CorporationInventors: Kai Lao, Neil Straus, John Burns
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Publication number: 20060141518Abstract: Methods for detection of nucleic acids such as a cDNA copy of an mRNA are disclosed. The methods comprise using a PCR to form a preamplification product which comprises cDNA sequence as well as primer target sequences and a detection probe sequence, which are introduced by the forward and reverse primers. In a second PCR, preamplification product is amplified using universal primers which hybridize to the primer target sequences or their complements. Amplification can be detected using a detection probe that hybridizes to the detection probe sequence or its complement.Type: ApplicationFiled: December 28, 2005Publication date: June 29, 2006Inventors: Kai Lao, Mark Reed
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Publication number: 20060078906Abstract: The present invention is directed to methods, reagents, kits, and compositions for identifying and quantifying target polynucleotide sequences. A linker probe comprising a 3? target specific portion, a loop, and a stem is hybridized to a target polynucleotide and extended to form a reaction product that includes a reverse primer portion and the stem nucleotides. A detector probe, a specific forward primer, and a reverse primer can be employed in an amplification reaction wherein the detector probe can detect the amplified target polynucleotide based on the stem nucleotides introduced by the linker probe. In some embodiments a plurality of short miRNAs are queried with a plurality of linker probes, wherein the linker probes all comprise a universal reverse primer portion a different 3? target specific portion and different stems. The plurality of queried miRNAs can then be decoded in a plurality of amplification reactions.Type: ApplicationFiled: May 31, 2005Publication date: April 13, 2006Applicant: Applera CorporationInventors: Caifu Chen, Dana Ridzon, Zhaohui Zhou, Kai Lao, Neil Straus
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Publication number: 20060063163Abstract: The present teachings relate to methods, compositions, and kits for detecting one or more target polynucleotide sequences in a sample, and methods compositions and kits for forming concatameric ligation products. In some embodiments of the present teachings, oligonucleotides are hybridized to complementary target polynucleotides and are ligated together to form a concatameric ligation product. In some embodiments of the present teachings, the concatameric ligation product can be amplified, and the identity and quantity of the target polynucleotides determined based on sequence introduced in the ligation reaction. Some embodiments of the present teachings provide methods for removing unligated probes from the reaction mixture. Some embodiments of the present teachings provide for highly multiplexed detection, identification, and quantification of a plurality of target polynucleotides using a variety of analytical procedures.Type: ApplicationFiled: November 4, 2004Publication date: March 23, 2006Applicant: Applera CorporationInventors: Caifu Chen, Kevin Hennessy, Kai Lao, Teodoro Paner, Vinod Mirchandani
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Publication number: 20060057611Abstract: The present disclosure provides methods and composition to detect or quantitate one or more target sequences in a reaction that couples a linear amplification reaction to an exponential amplification reaction.Type: ApplicationFiled: June 30, 2005Publication date: March 16, 2006Applicant: Applera CorporationInventors: H. Kao, Kai Lao, Robert Jones
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Publication number: 20060057595Abstract: Compositions, methods, and kits for identifying and for quantitating polynucleotide targets are disclosed. These compositions, methods, and kits are particularly useful when the polynucleotide target is a small RNA molecule, including without limitation microRNA (miRNA), small interfering RNA (siRNA), and certain other classes of non-coding RNA molecules. The forward and reverse primers of the disclosed first primer sets comprise unusually short target-binding portions that are 6-10 nucleotides long. Certain of the disclosed methods employ one or more multiplex reaction steps to identify, quantitate, or identify and quantitate, a multiplicity of target polynucleotides.Type: ApplicationFiled: September 16, 2004Publication date: March 16, 2006Applicant: Applera CorporationInventors: Kai Lao, Neil Straus