Illumina Corporation

Leland Stanford Junior University

Biotage Ab

Qiagen Gmbh

Mostafa Ronaghi

Michael Previte

Molly Min He

Cheng-Yao Chen

Helmy A Eltoukhy

M Shane Bowen

Tarun Kumar Khurana

Jonathan Mark Boutell

Eric T Kool

Rigo Pantoja

Kevin L Gunderson

Ronald W Davis

Kandaswamy Vijayan

Min-Jui Richard Shen

Bala Murali Venkatesan

Kathryn M Stephens

Juan G Santiago

Yir-Shyuan Wu

Thomas Willis

Maneesh Jain

Filiz Gorpe-Yasar

Erich B Jaeger

Paul Hardenbol

Viktor Stolc

Victoria Popic

Yan-You Lin

Xi-Jun Chen

Hesaam Esfandyarpour

Alexandre Persat

Robert D Chambers

Reto B Schoch

Pål Nyren

Annika Tallsjö

Roberto Rigatti

Niall Anthony Gormley

Jason Richard Betley

Foad Mashayekhi

Shane Bowen

Dirk Evers

Amir Ali Haj Hossein Talasaz

Ali Agah

Pal Nyren

Annika Tallsjo

Filiz Gorpe- Yasar

Victoria Popuc

Implementations of a method for seeding sequence libraries on a surface of a sequencing flow cell that allow for spatial segregation of the libraries on the surface are provided. The spatial segregation can be used to index sequence reads from individual sequencing libraries to increase efficiency of subsequent data analysis. In some examples, hydrogel beads containing encapsulated sequencing libraries are captured on a sequencing flow cell and degraded in the presence of a liquid diffusion barrier to allow for the spatial segregation and seeding of the sequencing libraries on the surface of the flow cell. Additionally, examples of systems, methods and compositions are provided relating to flow cell devices configured for nucleic acid library preparation and single cell sequencing. Some examples include flow cell devices having a hydrogel with genetic material disposed therein, and which is retained within the hydrogel during nucleic acid processing.

Spatial indexing of genetic material and library preparation using hydrogel beads and flow cells

A method for synthesizing a nucleic acid includes synthesizing one or more nucleic acid fragments on a substrate. The synthesized one or more nucleic acid fragments may be amplified on the substrate. The method also includes sequencing the synthesized or amplified one or more nucleic acid fragments on the substrate. The sequencing may provide feedback to designs of the one or more nucleic acid fragments. The method further includes harvesting the synthesized or amplified one or more nucleic acid fragments based on sequencing. The synthesized or amplified one or more nucleic acid fragments may be assembled to generate a target nucleic acid.

Nucleic acid synthesis techniques

This disclosure provides a method of determining a sequence of nucleotides for a nucleic acid template. The method can include the steps of contacting the nucleic acid template with a conformationally labeled polymerase and at least four different nucleotide species under conditions wherein the conformationally labeled polymerase catalyzes sequential addition of the nucleotide species to form a nucleic acid complement of the nucleic acid template, wherein the sequential addition of each different nucleotide species produces a conformational signal change from the conformationally labeled polymerase and wherein the rate or time duration for the conformational signal change is distinguishable for each different nucleotide species; detecting a series of changes in the signal from the conformationally labeled polymerase under the conditions; and determining the rates or time durations for the changes in the signal, thereby determining the sequence of nucleotides for the nucleic acid template.

Conformational probes and methods for sequencing nucleic acids

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

Systems, methods, and compositions provided herein relate to preparation of beads encapsulating long DNA fragments for high-throughput spatial indexing. Some embodiments include preparation of nucleic acid libraries within the bead, wherein the bead includes pores that allow diffusion of reagents while retaining genetic material.

DNA sequencing using hydrogel beads

The present method involves sequencing by synthesis in which a template strand having an attached primer is immobilized in a small volume reaction mixture. In one embodiment, the reaction mixture is in contact with a sensitive heat sensor, which detects the heat of reaction from incorporation of a complementary base (dNTP) in the presence of appropriate reagents (DNA polymerase, and polymerase reaction buffer). Alternatively, or in addition, a change in pH resulting from the incorporation of nucleotides in the DNA polymerase reaction is measured. A device is provided having delivery channels for appropriate reagents, including dNTPs, which may be delivered sequentially or in a mixture. Preferably, the dNTPs are added in a predetermined sequence, and the dNTP is incorporated or not depending on the template sequence.

Enthalpy measurements for sequencing of a nucleic acid sample

A method of sequencing nucleic acids, which can include steps of contacting a substrate having spatially distinguishable features with a plurality of nucleic acids to seed a subset of the features, thereby generating a seeded subset; amplifying the nucleic acids in the seeded subset to form nucleic acid colonies; repeating the preceding steps to increase the number of seeded features, thereby generating an array of nucleic acid colonies; and sequencing the array of nucleic acid colonies.

Method of sequencing nucleic acid colonies formed on a patterned surface by re-seeding

Growing community of inventors

San Diego, CA, United States of America

Mostafa Ronaghi