Illumina Corporation

Illumina Cambridge Limited

Illumina France Sarl

Moon, John A.

M Shane Bowen

Dajun Yuan

Tarun Kumar Khurana

Maria Candelaria Rogert Bacigalupo

Yir-Shyuan Wu

Bala Murali Venkatesan

Andrew Antony Brown

Wayne N George

Arnaud Rival

Lewis J Kraft

Kevin L Gunderson

Kandaswamy Vijayan

Jeffrey S Fisher

Hui Han

Boyan Boyanov

Poorya Sabounchi

Alex Nemiroski

Sang Ryul Park

Jonathan Mark Boutell

Steven Mark Barnard

James M Tsay

Bala Murali K Venkatesan

John A Moon

Mostafa Ronaghi

John S Vieceli

Stephen Tanner

Justin Fullerton

Hai Quang Tran

Dale Buermann

Min-Jui Richard Shen

Dietrich A Dehlinger

Alex Aravanis

Robert Ezra Langlois

Shengrong Lin

Alexandre Richez

John M Beierle

Behnam Javanmardi

Lorenzo Berti

Xi-Jun Chen

Paul Belitz

Kevan Samiee

Kathryn M Stephens

Danny Yuan Chan

Sahngki Hong

Alexander Hsiao

Brian Douglas Mather

Arthur Pitera

Craig M Ciesla

Stanley S Hong

Ali Agah

Joseph Francis Pinto

Cyril Delattre

Tracy Helen Fung

Yan-You Lin

Sean M Ramirez

Gary Mark Skinner

Fabien Abeille

Yasaman Farshchi

Raymond Campos

Danilo Condello

Jason Richard Betley

Ryan Christopher Smith

Ludovic Vincent

Michael S Graige

Audrey Rose Zak

Mathieu Lessard-Viger

John Gerhardt Earney

Steven Modiano

Sebastian Bohm

Michael Previte

Molly Min He

Cheng-Yao Chen

Ryan M Smith

Mark R Pratt

Michal Lebl

Majid Aghababazadeh

Hongji Ren

Niall Anthony Gormley

Frank J Steemers

Arash Jamshidi

Merek C Siu

Frederick G Erie

Michel Perbost

Marco A Krumbuegel

Yinghua Sun

Anthony Lam

Bojan Obradovic

Aaron Liu

Kenny Chen

Randall Smith

Geraint Wyn Evans

Andrew Slatter

Liangliang Qiang

Jennifer Olivia Foley

Steven H Modiano

Hamed Amini

Maxwell Zimmerley

Sang Park

Sharis Minassian

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

An example of an array includes a support, a cross-linked epoxy polyhedral oligomeric silsesquioxane (POSS) resin film on a surface of the support, and a patterned hydrophobic polymer layer on the cross-linked epoxy POSS resin film. The patterned hydrophobic polymer layer defines exposed discrete areas of the cross-linked epoxy POSS resin film, and a polymer coating is attached to the exposed discrete areas. Another example of an array includes a support, a modified epoxy POSS resin film on a surface of the support, and a patterned hydrophobic polymer layer on the modified epoxy POSS resin film. The modified epoxy POSS resin film includes a polymer growth initiation site, and the patterned hydrophobic polymer layer defines exposed discrete areas of the modified epoxy POSS resin film. A polymer brush is attached to the polymer growth initiation site in the exposed discrete areas.

Arrays including a resin film and a patterned polymer layer

A structured substrate includes a substrate body having an active side. The substrate body includes reaction cavities that open along the active side and interstitial regions that separate the reaction cavities. The structured substrate includes an ensemble amplifier positioned within each of the reaction cavities. The ensemble amplifier includes a plurality of nanostructures configured to at least one of amplify electromagnetic energy that propagates into the corresponding reaction cavity or amplify electromagnetic energy that is generated within the corresponding reaction cavity.

Structured substrates for improving detection of light emissions and methods relating to the same

Systems and methods for conducting designated reactions utilizing a base instrument and a removable cartridge. The removable cartridge includes a fluidic network that receives and fluidically directs a biological sample to conduct the designated reactions. The removable cartridge also includes a flow-control valve that is operably coupled to the fluidic network and is movable relative to the fluidic network to control flow of the biological sample therethrough. The removable cartridge is configured to separably engage a base instrument. The base instrument includes a valve actuator that engages the flow-control valve of the removable cartridge. A detection assembly held by at least one of the removable cartridge or the base instrument may be used to detect the designated reactions.

Systems and methods for biochemical analysis including a base instrument and a removable cartridge

An example of a flow cell includes a substrate, a plurality of chambers defined on or in the substrate, and a plurality of depressions defined in the substrate and within a perimeter of each of the plurality of chambers. The depressions are separated by interstitial regions. Primers are attached within each of the plurality of depressions, and a capture site is located within each of the plurality of chambers.

Flow cells

Provided in one example is a method of manufacturing a flowcell that includes: forming a core layer, the core layer disposed between a substrate and a nanowell layer, the nanowell layer having nanowells to receive a sample, the core layer having a higher refractive index than the substrate and the nanowell layer; and forming a grating to couple light to the core layer.

Manufacturing a flowcell with a planar waveguide

Substrates comprising a functionalizable layer, a polymer layer comprising a plurality of micro-scale or nano-scale patterns, or combinations thereof, and a backing layer and the preparation thereof by using room-temperature UV nano-embossing processes are disclosed. The substrates can be prepared by a roll-to-roll continuous process. The substrates can be used as flow cells, nanofluidic or microfluidic devices for biological molecules analysis.

Substrates comprising nano-patterning surfaces and methods of preparing thereof

Substrates comprising dual functional polymer layered surfaces and the preparation thereof by using UV nano-imprinting processes are disclosed. The substrates can be used as flow cells, nanofluidic or microfluidic devices for biological molecules analysis.

Selective surface patterning via nanoimprinting

One example of a flow cell includes a base support and a multi-layer stack positioned over the base support. The multi-layer stack includes a resin layer positioned over the base support; and a hydrophobic layer positioned over the resin layer. A depression is defined in the multi-layer stack through the hydrophobic material and through a portion of the resin.

An interposer for a flow cell comprises a base layer having a first surface and a second surface opposite the first surface. The base layer comprises black polyethylene terephthalate (PET). A first adhesive layer is disposed on the first surface of the base layer. The first adhesive layer comprises methyl acrylic adhesive. A second adhesive layer is disposed on the second surface of the base layer. The second adhesive layer comprises methyl acrylic adhesive. A plurality of microfluidic channels extends through each of the base layer, the first adhesive layer, and the second adhesive layer.

Interposer with first and second adhesive layers

A system includes: an objective lens; a first light source to feed first illuminating light through the objective lens and into a flowcell (e.g., with a relatively thin film waveguide) to be installed in the system, the first illuminating light to be fed using a first grating on the flowcell; and a first image sensor to capture imaging light using the objective lens, wherein the first grating is positioned outside a field of view of the first image sensor. Dual-surface imaging can be performed. Flowcells with multiple swaths bounded by gratings can be used. An auto-alignment process can be performed.

Illumination for fluorescence imaging using objective lens

An example of a flow cell includes a substrate; a first primer set attached to a first region on the substrate, the first primer set including an un-cleavable first primer and a cleavable second primer; and a second primer set attached to a second region on the substrate, the second primer set including a cleavable first primer and an un-cleavable second primer.

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

Fiducial markers are provided on patterned arrays of the type that may be used for molecular analysis, such as sequencing. The fiducials may have configurations that enhance their detection in image or detection data, that facilitate or improve processing, that provide encoding of useful information, and so forth. Examples of the fiducials may include an 'always on' type that respond to multiple frequencies of radiation used during processing and detection so as to return signals during successive cycles of imaging.

System and method with fiducials responding to multiple excitation frequencies

Growing community of inventors

Encinitas, CA, United States of America

M Shane Bowen