Omniome, Inc.

Illumina Corporation

Plexium, Inc.

Pacific Biosciences of California, Inc.

Bionano Genomics, Inc.

Omnionie, Inc.

Kandaswamy Vijayan

Joseph Franklin Rokicki

Kevin L Gunderson

M Shane Bowen

Bala Murali Venkatesan

Pinar Iyidogan

Eugene Tu

Corey M Dambacher

Andrew Boyd MacConnell

Jonathan Mark Boutell

Arnold Oliphant

Min-Jui Richard Shen

Mostafa Ronaghi

Yir-Shyuan Wu

Maria Candelaria Rogert Bacigalupo

Shengrong Lin

John M Beierle

Lorenzo Berti

James M Tsay

Sang Ryul Park

Kathryn M Stephens

Mark A Bernard

Yi Zhang

John S Vieceli

Sean Stromberg

Kerry Wilson

Keunho Ahn

Pengyu Yang

Brittany Ann Rohrman

Jesse Lu

Alex Price

James Tsay

Steven T Brentano

Han Cao

Parikshit A Deshpande

Michael David Austin

Ming H Xiao

Michael Boyce-Jacino

Michael Nghiem Nguyen

Devon Cayer

Alexey Y Sharonov

Michael Van Nguyen

Mark C Wallen

Ying Lin Liu

Kapil Mahakalkar

Michael Nguyen

Richard LeCoultre

Alexy Y Sharonov

Richard Lecoultre

Shane M Bowen

Michael Austin

Ming Xiao

Method and composition for identifying cognate nucleotides in a Sequencing By Binding™ procedure, wherein one or more labeled nucleotides are detected in ternary complexes but never incorporated. Labeled nucleotides can be incorporable nucleotides that contact preformed blocked primed template nucleic acids. Alternatively, labeled nucleotides are labeled non-incorporable nucleotides. Labeled nucleotides, including labeled non-incorporable nucleotides, can be detected in ternary complexes in the same reaction mixture that incorporates a reversible terminator nucleotide to create a blocked primed template nucleic acid. Detection of ternary complexes can take place in the presence of a catalytic metal ion.

Process for cognate nucleotide detection in a nucleic acid sequencing workflow

A method of determining a nucleic acid sequence that includes steps of: (a) contacting a primed template nucleic acid with a series of mixtures for forming ternary complexes, wherein each of the mixtures includes a polymerase and nucleotide cognates for at least two different base types suspected of being present at the next template position of the template nucleic acid; (b) monitoring the next template position for ternary complexes formed by the series of mixtures, wherein a signal state indicates presence or absence of ternary complex formed at the next template position by each individual mixture, thereby determining a series of signal states that encodes a base call for the next template position; and (c) decoding the series of signal states to distinguish a correct base call for the next template position from an error in the base call.

Methods and apparatus that increase sequencing-by-binding efficiency

This application provides a bead with a covalently attached chemical compound and a covalently attached DNA barcode and methods for using such beads. The bead has many substantially identical copies of the chemical compound and many substantially identical copies of the DNA barcode. The compound consists of one or more chemical monomers, where the DNA barcode takes the form of barcode modules, where each module corresponds to and allows identification of a corresponding chemical monomer. The nucleic acid barcode can have a concatenated structure or an orthogonal structure. Provided are method for sequencing the bead-bound nucleic acid barcode, for cleaving the compound from the bead, and for assessing biological activity of the released compound.

Oligonucleotide encoded chemical libraries

Disclosed is an assay device comprising a high density of wells aligned thereon.

Assay devices for combinatorial libraries

Provided are sequencing-by-binding methods of detecting cognate nucleotides using a crippled DNA polymerizing enzyme that possesses the ability to bind the next correct nucleotide downstream of a primer in a template-dependent fashion, but does not possess the activity needed to promote phosphodiester bond formation. Use of the crippled DNA polymerase permits interrogation of one nucleotide at a time, without incorporation of any nucleotide. Labeled nucleotides, such as fluorescently labeled nucleotides, can be used in conjunction with the crippled DNA polymerase to establish cognate nucleotide identity in a rapid manner.

Method of nucleic acid sequence determination

A method includes forming a patterned substrate including a plurality of base pads, using a nano-imprint lithography process. A capture substance is attached to each of the plurality of base pads, optionally through a linker, the capture substance being adapted to promote capture of a target molecule.

Microarray fabrication system and method

The present disclosure provides compositions, methods and systems for sequencing a template nucleic acid using a polymerase based, nucleic acid binding reaction involving examination of the interaction between a polymerase and template nucleic acid in the presence of one or more unlabeled nucleotides. The methods rely, in part, on identifying a base of a template nucleic acid during nucleic acid synthesis by controlling the sequencing reaction conditions. Template nucleic acid bases may be identified during an examination step followed by an optional incorporation step.

Nucleic acid sequencing methods and systems

The present disclosure provides compositions, methods and systems for quantifying target sequences and identifying target sequence variants.

Methods of quantifying target nucleic acids and identifying sequence variants

A method including (a) providing an amplification reagent including an array of sites, and a solution having different target nucleic acids; and (b) reacting the amplification reagent to produce amplification sites each having a clonal population of amplicons from a target nucleic acid from the solution. The reacting can include simultaneously transporting the nucleic acids to the sites at an average transport rate, and amplifying the nucleic acids that transport to the sites at an average amplification rate, wherein the average amplification rate exceeds the average transport rate. The reacting can include producing a first amplicon from a nucleic acid that transports to each of the sites, and producing subsequent amplicons from the nucleic acid or from the first amplicon, wherein the average rate at which the subsequent amplicons are generated exceeds the average rate at which the first amplicon is generated.

Kinetic exclusion amplification of nucleic acid libraries

Method of identifying a cognate nucleotide (i.e., the 'next correct nucleotide') for a primed template nucleic acid molecule. In some embodiments, an ordered or random array of primed target nucleic acids characterized by different cognate nucleotides can be evaluated using a single imaging step to identify different cognate nucleotides for a collection of different primed template nucleic acid molecules. An optional incorporation step can follow the identifying step. A polymerase different from the ones used in the binding and examination steps can be used to incorporate a nucleotide, such as a reversible terminator nucleotide, preliminary to identification of the next cognate nucleotide.

Method and system employing distinguishable polymerases for detecting ternary complexes and identifying cognate nucleotides

Provided are methods and systems for detecting formation of nucleotide-specific ternary complexes comprising a DNA polymerase, a nucleic acid, and a nucleotide complementary to the templated base of the primed template nucleic acid. The methods and systems facilitate determination of the next correct nucleotide without requiring chemical incorporation of the nucleotide into the primer. These results can even be achieved in procedures employing unlabeled, native nucleotides.

Sequencing method employing ternary complex destabilization to identify cognate nucleotides

Provided are methods and systems for reducing the time needed for sequencing nucleic acids. The approach relies on detecting formation of nucleotide-specific ternary complexes comprising a polymerase (e.g., a DNA polymerizing enzyme), a primed template nucleic acid molecule, and a nucleotide complementary to the templated base of the primed template nucleic acid. The methods and systems facilitate determination of the next correct nucleotide, as well as the subsequent next correct nucleotide from a cycle of examining four different nucleotides without requiring chemical incorporation of any nucleotide into the primer.

Sequencing method for rapid identification and processing of cognate nucleotide pairs

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San Diego, CA, United States of America

Kandaswamy Vijayan