Illumina Cambridge Limited

Illumina Corporation

Sengenics Corporation Pte Ltd

Jonathan Mark Boutell

Roberto Rigatti

Niall Anthony Gormley

Geoffrey Paul Smith

Min-Jui Richard Shen

Kevin L Gunderson

M Shane Bowen

Vincent Peter Smith

Mostafa Ronaghi

Matthew William Kellinger

Kandaswamy Vijayan

Colin Lloyd Barnes

Bala Murali Venkatesan

Jason Richard Betley

Gary Mark Skinner

Kathryn M Stephens

Helmy A Eltoukhy

Xiaohai Liu

Robert C Kain

Wenyi Feng

Xiaolin Wu

Bernard Hirschbein

Tobias William Barr Ost

Randall Smith

Eric Hans Vermaas

Kay Klausing

Thomas J Joseph

David Bentley

Graham John Worsley

Claire Bevis-Mott

Carolyn Tregidgo

Alan D Kersey

John A Moon

Boyan Boyanov

Maria Candelaria Rogert Bacigalupo

Jingwei Bai

John M Beierle

Klaus Maisinger

Frank J Steemers

Allen E Eckhardt

Hongji Ren

Erin Bomati

Alex Nemiroski

Isabelle Marie Julia Rasolonjatovo

Susan Shanahan

Peter McInerney

Shaun Hunter

Kenny Chen

Thomas Joseph

Michael Previte

Molly Min He

Stanley S Hong

Sergio Peisajovich

Gerardo Turcatti

Geraint Wyn Evans

Misha Golynskiy

Oliver Jon Miller

Darren James Hart

Jonathan Michael Blackburn

Pietro Gatti-Lafranconi

Dirk Evers

Angela Kalbande

Gareth Jenkins

Alan Kersey

Michael Chesney

Benjamin Leslie James Godber

Gerado Turcatti

Niall Gormley

Benjamin Leslie Godber

Jonathan David Blackburn

Isabelle Marie Rasolonjatovo

Klara Bojanovic Machado

Jared Peace

The present disclosure relates to the field of molecular biology and more specifically to microarrays and methods. In particular, the present disclosure relates to a method for amplifying a nucleic acid on a substrate comprising at least one well, the method includes: depositing a plurality of first capture primer pairs and a plurality of second capture primer pairs in a layer at least partially covering the inner well surface, wherein the primer density of first capture primer pairs is higher than the primer density of second primer pairs; contacting a sample comprising a plurality of target polynucleotides with the substrate under conditions sufficient for a single target polynucleotide per well to hybridize with a capture primer of the second capture primer pair; and performing a kinetic exclusion assay (KEA) to produce a monoclonal population of amplicons from the single target polynucleotide.

Methods and arrays for producing and sequencing monoclonal clusters of nucleic acid

Provided herein is a method for sequencing a polynucleotide molecules. The method includes the steps of providing a plurality of polynucleotide molecules attached to a surface, wherein a first portion of each polynucleotide molecule is attached to a first location of the surface and a second portion of each polynucleotide molecule is attached to a second location of the surface, the relative proximity of the first and second locations being correlated with the probability that the first and second portions are paired, separating the first and second portions of the polynucleotide molecules on the surface, determining the sequences of the first and second portions of the polynucleotide molecules and comparing the relative proximities and the sequences to determine which first and second portions are paired and to determine the sequence of the target polynucleotide molecules.

Methods for sequencing polynucleotides

Presented herein are methods and compositions for concatenating template strands during the bridge amplification process. The methods are useful for surface amplification at improved densities. The methods and compositions provided herein enable creation of clusters that are brighter, but at the same densities as currently achieved using standard cluster amplification.

Surface concatemerization of templates

The present invention relates to methods of imaging template hybridisation for estimating cluster numbers prior to solid phase amplification and sequencing. More particularly, an initial round of imaging is carried out at the single molecule template hybridisation stage which allows a general estimation of cluster numbers prior to clusters being formed. Amplification of the signal allows single molecule imaging to be carried out using standard sequencing imaging apparatus.

Methods for estimating cluster numbers

In an example of the method, a functionalized coating layer is applied in depressions of a patterned flow cell substrate. The depressions are separated by interstitial regions. A primer is grafted to the functionalized coating layer to form a grafted functionalized coating layer in the depressions. A hydrogel is applied on at least the grafted functionalized coating layer.

Flow cells with hydrogel coating

The present invention relates to the field of molecular biology, and more specifically to methods for reducing the complexity of a nucleic acid sample.

Nucleic acid sample enrichment for sequencing applications

The present disclosure provides methods and systems for detecting multiple different nucleotides in a sample. In particular, the disclosure provides for detection of multiple different nucleotides in a sample utilizing fewer detection moieties than the number of nucleotides being detected and/or fewer imaging events than the number of nucleotides being detected.

Methods and compositions for nucleic acid sequencing

A method of characterizing candidate agents including steps of (a) providing a library of candidate agents attached to nucleic acid tags; (b) contacting the library with a solid support to attach the candidate agents to the solid support, whereby an array of candidate agents is formed; (c) contacting the array with a screening agent, wherein one or more candidate agents in the array react with the screening agent; (d) detecting the array to determine that at least one candidate agent in the array reacts with the screening agent; (e) sequencing the nucleic acid tag to determine the tag sequences attached to candidate agents in the array; and (f) identifying the at least one candidate agent in the array that reacts with the screening agent based on the tag sequence that is attached to the at least one candidate agent.

Platform for discovery and analysis of therapeutic agents

The present disclosure relates to the field of molecular biology and more specifically to microarrays and methods, including methods for modifying immobilized capture primers comprising: a) contacting a substrate comprising a plurality of immobilized capture primers with a plurality of template nucleic acids under conditions sufficient for hybridization to produce one or more immobilized template nucleic acids, and b) extending one or more immobilized capture primers to produce one or more immobilized extension products complementary to the one or more template nucleic acid.

The present disclosure is concerned with compositions and methods for reducing the steps used in the generation of monoclonal clusters by combining the enzymes used for linearization and removal of unused surface primers.

Methods and compositions for cluster generation by bridge amplification

An example method includes reacting a first solution and a different, second solution on a flow cell by flowing the first solution over amplification sites on the flow cell and subsequently flowing the second solution over the amplification sites. The first solution includes target nucleic acids and a first reagent mixture that comprises nucleoside triphosphates and replication enzymes. The target nucleic acids in the first solution transport to and bind to the amplification sites at a transport rate. The first reagent mixture amplifies the target nucleic acids that are bound to the amplification sites to produce clonal populations of amplicons originating from corresponding target nucleic acids. The amplicons are produced at an amplification rate that exceeds the transport rate. The second solution includes a second reagent mixture and lacks the target nucleic acids. The second solution is to increase a number of the amplicons at the amplification sites.

Kinetic exclusion amplification of nucleic acid libraries

The present disclosure is concerned with compositions and methods for the paired-end sequencing of target nucleic acids, and more particularly to obtaining nucleotide sequence information from two separate regions of target nucleic acids using amplification sites having a single type of surface primer.

Methods and compositions for paired end sequencing using a single surface primer

The present disclosure provides methods and systems for determining and/or characterizing one or more haplotypes and/or phasing of haplotypes in a nucleic acid sample. In particular, the disclosure provides methods for determining a haplotype and/or phasing of haplotypes in a nucleic acid sample by incorporating synthetic polymorphisms into fragments of a nucleic acid sample and utilizing the synthetic polymorphisms in determining one or more haplotypes and/or phasing of haplotypes.

Methods and systems for determining haplotypes and phasing of haplotypes

The present invention relates to a sequencing method which allows for increased rates of sequencing and an increase in the density of sequencing data. The system may be based on next generation sequencing methods such as sequencing by synthesis (SBS) but uses multiple primers bound at different positions on the same nucleic acid strand.

Sequencing from multiple primers to increase data rate and density

The present invention is concerned with compositions and methods for improving the rate of correct sample identification in indexed nucleic acid library preparations for multiplex next generation sequencing by exonuclease treatment and optionally blocking the 3' ends of pooled indexed polynucleotides from multiple samples prior to amplification and sequencing.

Compositions and methods for improving sample identification in indexed nucleic acid libraries

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Nr Saffron Walden, United Kingdom

Jonathan Mark Boutell