Pacific Biosciences of California, Inc.

Cornell University

Juniper Networks, Inc.

University of California

Pacific Biosciences for California, Inc.

Pacific Biosciense of California, Inc.

Scolr Pharma, Inc.

Stephen Wilson Turner

Jonas Korlach

Paul M Lundquist

Kevin Travers

Benjamin A Flusberg

Harold G Craighead

Nathaniel McCaffrey

Cheryl Heiner

Geoff Otto

Watt W Webb

Denis Zaccarin

Jon M Sorenson

Michael Levene

John Lyle

Ravi Saxena

Jeffrey Wegener

Adrian Nielsen Fehr

John S Eid

Daniel Bernardo Roitman

Annette Claire Grot

Jeremiah Hanes

Mathieu Foquet

Fred C Christians

Paul S Peluso

Thang Pham

David R Rank

Congcong Ma

Lei Sun

Geoffrey Alan Otto

Yves Lacroix

Scott Edward Helgesen

Keith P Bjornson

Tyson A Clark

Yue Xu

Truman Joe

Hans Callebaut

John Dixon

Sanjay Kalra

Hsien-Chung Woo

Shang Wang

Wendy R Cartee

Eric Schadt

Pezhman Monadgemi

Robin A Emig

Kenneth Mark Maxham

Cheng Frank Zhong

Lei Jia

Patrick Marks

Dale R Webster

Devon Murphy

Jeffery Wegener

Gene W Shen

Arek Bibillo

Austin B Tomaney

Igor D Vilfan

Natasha Popovich

Peiqian Zhao

Yu-Chih Tsai

Andrey Kislyuk

Jessica Lee

Yanqiao Huang

Steven Benjamin Warren

Mark Maxham

Ron L Cicero

Satwik Kamtekar

Aaron J Rulison

Ronald L Cicero

David Kagen Hanzel

Mark Chaisson

Joseph Puglisi

Robert Sebra

Gregory Kearns

Ravi Dalal

Dennis C Ferguson

Mark E McDonald

Molly Min He

Joy Roy

David James Ofelt

Andrei Fedorov

Jeremy Gray

Insil Park

Michael Hite

Alan Brunelle

Kevan Samiee

Hovig Bayandorian

Stephen P Dudek

Khai Luong

Kevin Hester

Harold Ray Lee

Eric Olivares

Bidhan P Chaudhuri

Steven Lin

Chen-Shan Chin

Uros Prestor

Cathy Federici

Paul Hagerman

Ali Bashir

Frank Zhong

Optical analytical devices and their methods of use are provided. The devices are useful in the analysis of highly multiplexed optical reactions in large numbers at high densities, including biochemical reactions, such as nucleic acid sequencing reactions. The devices include integrated illumination elements and optical waveguides for illumination of the optical reactions. The devices further provide for the efficient coupling of optical excitation energy from the waveguides to the optical reactions. Optical signals emitted from the reactions can thus be measured with high sensitivity and discrimination using features such as spectra, amplitude, and time resolution, or combinations thereof. The devices of the invention are well suited for miniaturization and high throughput.

Integrated illumination of optical analytical devices

An analytical device including an optically opaque cladding, a sequencing layer including a substrate disposed below the cladding, and a waveguide assembly for receiving optical illumination and introducing illumination into the device. The illumination may be received from a top, a side edge, and a bottom of the device. The waveguide assembly may include a nanoscale aperture disposed in the substrate and extending through the cladding. The aperture defines a reaction cell for receiving a set of reactants. In various aspects, the device includes a sensor element and the illumination pathway is through the sensor element. Waveguides and illumination devices, such as plasmonic illumination devices, are also disclosed. Methods for forming and operating the devices are also disclosed.

Illumination of integrated analytical systems

Optical analytical devices and their methods of use are provided. The devices are useful in the analysis of highly multiplexed optical reactions in large numbers at high densities, including biochemical reactions, such as nucleic acid sequencing reactions. The devices include optical waveguides for illumination of the optical reactions. The devices further provide for the efficient coupling of optical excitation energy from the waveguides to the optical reactions. Optical signals emitted from the reactions can thus be measured with high sensitivity and discrimination using features such as spectra, amplitude, and time resolution, or combinations thereof. The devices of the invention are well suited for miniaturization and high throughput.

Illumination of optical analytical devices

Optics collection and detection systems are provided for measuring optical signals from an array of optical sources over time. Methods of using the optics collection and detection systems are also described.

Optics collection and detection system and method

Methods, compositions, and systems are provided for characterization of modified nucleic acids. In certain preferred embodiments, single molecule sequencing methods are provided for identification of modified nucleotides within nucleic acid sequences. Modifications detectable by the methods provided herein include chemically modified bases, enzymatically modified bases, abasic sites, non-natural bases, secondary structures, and agents bound to a template nucleic acid.

Classification of nucleic acid templates

A circuit comprising a substrate with sectors on the substrate is provided, each sector comprising clock and data lines, a controller in electrical communication with the clock and data lines, a counter bias line, an amplifier input line and nano-electronic measurement devices on the substrate. A source of each device is coupled to the counter bias line and a drain of each device is coupled to the amplifier input line to obtain an electrical signal on the drain, the identity of which is determined by electrical interaction between the device and a charge label. Each device drain is gated by a corresponding switch between an on state, in which the drain is connected to the amplifier input line, and an off state, in which the drain is isolated from the amplifier input line. The controller controls switch states responsive to clock signal line pulses and data input line data.

Systems and methods for selectively addressing sparsely arranged electronic measurement devices

Methods and systems for single molecule sequencing using concatemers of copies of sense and antisense strands. Concatemers are provided, for example, by carrying out rolling circle amplification on a circular molecule having sense and antisense regions to produce repeated copies of the sense and antisense regions connected by linking regions. The circular molecules can be produced by ligating hairpin adapters to each end of a double-stranded nucleic acid having a sense and antisense strand. The ligations can be carried out, for example using blunt end ligation. In some cases, a single molecule consensus sequence for a single template molecule is obtained. A single read from each template molecule can be obtained by comparing the sequence information of the sense and antisense regions.

Sequencing using concatemers of copies of sense and antisense strands

Methods are provided for reducing the complexity of a population of nucleic acids prior to performing an analysis of the nucleic acids, e.g., sequence analysis. The methods result in a subset of the initial population enriched for a target region, which is typically located within one or more target fragments. The methods are particularly useful for analyzing populations having a high degree of complexity, e.g., chromosomal-derived DNA, whole genomic DNA, or mRNA populations.

Compositions and methods for selection of nucleic acids

The present invention provides methods, compositions, and systems for distributing molecules and complexes into reaction sites. In particular, the methods, compositions, and systems of the present invention result in an active loading of molecules and complexes into reaction sites with improved efficiency over loading by passive diffusion methods alone.

Methods and compositions for delivery of molecule and complexes to reaction sites

Provided are pixels, devices, systems, and methods relating to active pixel sensor in which each active pixel puts out a signal that represents a temporal differential. The output of the active pixel represents a comparison or difference between successive frames. The differential can represent the state of the sensor element in the pixel at the end of one frame compared to the state of the sensor element of the frame, at the end of the prior frame.

Temporal differential active pixel sensor

Methods, devices, and systems for performing intermittent detection during analytical reactions are provided. Such methods facilitate collection of reaction data from disparate reaction times. Further, such methods are useful for reducing photo-induced damage of one or more reactants in an illuminated analytical reaction at a given reaction time. In preferred embodiments, the reaction mixture is subjected to at least one illuminated and non-illuminated period and allowed to proceed such that the time in which the reaction mixture is illuminated is less than a photo-induced damage threshold period.

Intermittent detection during analytical reactions

Methods of producing substrates having selected active chemical regions by employing elements of the substrates in assisting the localization of active chemical groups in desired regions of the substrate. The methods may include optical, chemical and/or mechanical processes for the deposition, removal, activation and/or deactivation of chemical groups in selected regions of the substrate to provide selective active regions of the substrate.

Articles having localized molecules disposed thereon and methods of producing same

Sequencing methods, devices, and systems are described. Arrays of nanoscale electronic elements comprising two electrodes separated by an insulating layer are used to provide sequence information about a template nucleic acid in a polymerase-template complex bound proximate to the insulating region. A sequencing reaction mixture comprising nucleotide analogs having impedance labels is introduced to the array of nanoscale electronic elements under conditions of polymerase mediated nucleic acid synthesis. The time sequence of incorporation of nucleotide analogs is determined by identifying the types of labels of the nucleotide analogs that are incorporated into the growing strand using measured impedance.

Nucleic acid sequencing with nanoscale electrode pairs

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Menlo Park, CA, United States of America

Stephen Wilson Turner