Applied Biosystems, LLC

Applera Corporation

The Perkin-Elmer Corporation

Fluidigm Corporation

Life Technologies Corporation

Pe Corporation (Ny)

Pe Corporation

Pe Applied Biosystems, a Division of Perkin-Elmer

Applied Biosystems Division, Perkin-Elmer Corp.

Kenneth J Livak

Khairuzzaman Bashar Mullah

Andrew J Blasband

Adam L Lowe

Michael W Hunkapiller

Susan J Flood

Mark F Oldham

Michael Egholm

David Ruff

Eugene G Spier

Jeffrey M Marmaro

Jun Wang

Xiaohui Wang

Stacey N Meyers

Jeffrey Mamoro

Federico Goodsaid

Karl J Guegler

Kai Qin Lao

Emily S Winn-Deen

Aldrich N K Lau

Mark R Andersen

Neil A Straus

Hongye Sun

Charles R Connell

Umberto Ulmanella

Junko F Stevens

Yu Wang

Mark Shannon

Jeremy Heil

Ivy McMullen

Kevin Hennessy

Ryan T Koehler

Francisco M De La Vega

John O'Neill

Lily Xu

Susan J A Flood

Christian A Heid

Leila G Smith

Michael Rhodes

Xiaoqing You

Laurent R Bellon

Dawn Madden

Dennis A Gilbert

Marc Alexander Unger

Eric S Nordman

Charles Stuart Vann

Caifu Chen

Michael Ybarra Lucero

Dar Bahatt

Kevin S Bodner

Jason A A West

Nigel P Beard

Maxim G Brevnov

Theofilos Kotseroglou

Robert C Jones

Muhammad A Sharaf

Douglas Greiner

Stephen J Gunstream

Will Bloch

H Pin Kao

Lincoln J McBride

Wanli Bi

Stephen A Glanowski

Adam Broomer

H Michael Wenz

Julie Williams

Kazuko Aoyagi

Susan Eddins

Theo Kotseroglou

Jason E Babcoke

David W Ruff

Aldrich NK Lau

Stacey Myers

John R O'NEILL

Kevin M Hennessy

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.

Methods for placing, accepting, and filling orders for products and services

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 polynucleotide amplification reaction.

Nucleic acid detection using probes

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.

Probe based nucleic acid detection

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.

Hot start reverse transcription by primer design

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. Surface-modified nanopores are provided as are methods of making them. In some embodiments, surfaced-modified nanopores for slowing the translocation of single stranded DNA (ssDNA) through the nanopore are provided, as are nanopores configured to detect each of a plurality of different bases on an ssDNA strand.

DNA sequencing methods and detectors and systems for carrying out the same

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.

Methods, compositions, and kits for detecting protein aggregates

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&#x2032; 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.

Universal probe assay methods

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.

Combinatorial amplification and detection of nucleic acids

Exemplary embodiments provide microfludic devices and methods for their use. The microfluidic device can include an array of M&#xd7;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.

Microfluidic devices and method for their use

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 Tm, 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 Tm, 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 Tmand Tmare higher than the annealing temperature associated with the polynucleotide amplification reaction.

A system for collecting target nucleic acids from a sample can include at least one sample chamber configured to receive a sample containing target nucleic acids and other material, at least one collection chamber removably mountable relative to the at least one sample chamber and configured to collect target nucleic acids separated from the other material, a filter removably mountable relative to the at least one sample chamber and configured to be disposed between the at least one sample chamber and the at least one collection chamber when the at least one collection chamber is mounted relative to the at least one sample chamber. The system may further include a pair of electrodes configured to generate an electric field sufficient to cause target nucleic acids in the at least one sample chamber to migrate via electrophoresis from the at least one sample chamber through the filter into the at least one collection chamber, wherein the filter may be configured to permit passage of target nucleic acids and to block passage of material of a size larger than the target nucleic acids.

Systems and methods for isolating nucleic acids

Growing community of inventors

San Jose, CA, United States of America

Kenneth J Livak