Illumina Corporation

Leland Stanford Junior University

Illumina Cambridge Limited

General Electric Company

Illumina Singapore Pte. Ltd.

Illumina France Sarl

Tarun Kumar Khurana

Poorya Sabounchi

Yir-Shyuan Wu

M Shane Bowen

Ali Agah

Craig M Ciesla

Aathavan Karunakaran

Helmy A Eltoukhy

Stanley S Hong

Arnaud Rival

Merek C Siu

Bernard Hirschbein

Wenyi Feng

Arvin Emadi

Jeffrey S Fisher

Cyril Delattre

Majid Aghababazadeh

Tracy Helen Fung

Yan-You Lin

Boyan Boyanov

Robert C Kain

Mostafa Ronaghi

Dale Buermann

Hai Quang Tran

Joseph Francis Pinto

Alex Aravanis

Dajun Yuan

Arash Jamshidi

Randall Smith

Kevin L Gunderson

Juan G Santiago

Sebastian Bohm

Paul Crivelli

Mark R Pratt

Dietrich A Dehlinger

Maria Candelaria Rogert Bacigalupo

Min-Jui Richard Shen

Steven Mark Barnard

Philip Y Paik

Amirali Kia

Robert Scott Duthie

Jian Gong

Wei-Cheng Tian

Darren Segale

AmirAli Talasaz

Gordon M Cann

Jay Taylor

Frank J Steemers

Bradley Kent Drews

Fiona Kaper

Bala Murali Venkatesan

Behnam Javanmardi

Xi-Jun Chen

Lewis J Kraft

Filiz Gorpe-Yasar

Alexander Hsiao

Jennifer Olivia Foley

Mathieu Lessard-Viger

Victoria Popic

Erich B Jaeger

Reto Schoch

Yasaman Farshchi

Hui Han

Liangliang Qiang

Justin Fullerton

Wesley A Cox-Muranami

Fabien Abeille

Minsoung Rhee

Xuance Zhou

Chetanya Jain

Gregory Suematsu

Eric Hans Vermaas

Kay Klausing

Byoungsok Jung

Gary J Watts

Kenneth M Kuhn

Sz-Chin Steven Lin

Oliver Jon Miller

Clifford Lee Wang

Lea Pickering

Foad Mashayekhi

Farnaz Absalan

George Sakaldasis

Yan-you Lin

Sarah Stuart

Brian Douglas Mather

Xavier Von Hatten

Charles Lin

Yin Nah Teo

Daniel Leonard Fuller

Wesley A Cox-muranami

Hamed Amini

Eliane H Trepagnier

Hongxia Xu

Sebastien Georg Gabriel Ricoult

Chenlu Hou

Rajiv Bharadwaj

Andrew J Price

Elisabet Rosas

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

An example of a flow cell includes a substrate and a cationic polymeric hydrogel on the substrate. The cationic polymeric hydrogel includes a cationic moiety that is i) integrated into a monomeric unit of an initial polymeric hydrogel or ii) attached to the monomeric unit of the initial polymeric hydrogel through a linker. The flow cell further includes an amplification primer attached to the cationic polymeric hydrogel.

Flow cells

In an example, a target material is immobilized on two opposed sequencing surfaces of a flow cell using first and second fluids. The first fluid has a density less than a target material density and the second fluid has a density greater than the target material density; or the second fluid has a density less than the target material density and the first fluid has a density greater than the target material density. The first fluid (including the target material) is introduced into the flow cell, whereby at least some of the target material becomes immobilized by capture sites on one of the sequencing surfaces. The first fluid and non-immobilized target material are removed. The second fluid (including target material) is introduced into the flow cell, whereby at least some of the target material becomes immobilized by capture sites on another of the sequencing surfaces.

Immobilization in flow cells

An apparatus includes one or more valves adapted to be coupled to corresponding reagent reservoirs and a flow cell interface adapted to be coupled to a flow cell. The apparatus includes a sample cartridge interface having one or more ports and adapted to be coupled to a sample cartridge carrying a sample of interest. The sample cartridge interface positioned downstream of the flow cell interface. The apparatus includes a pump adapted to load a channel of the flow cell with the sample of interest via the flow cell interface associated with an outlet of the flow cell and a corresponding port of the sample cartridge interface.

Systems and related sample loading manifold assemblies

Actuation systems and methods are disclosed. An apparatus includes a system including a flow cell receptacle and a valve drive assembly including a shape memory alloy actuator including a pair of shape memory alloy wires and a flow cell disposable within the flow cell receptacle and having a membrane valve. The system actuates the membrane valve, via the shape memory alloy actuator, by causing a voltage to be applied to a first one of the shape memory alloy wires and the system not applying the voltage to a second one of the shape memory alloy wires.

Actuation systems and methods

Devices, systems, and methods for non-volatile storage include a well activation device operable to modify one or more wells from a plurality of wells of a flow cell to provide a set of readable wells. Readable wells are configured to allow exposure of a well to substances from nucleotide sequencing fluids, and prevent exposure to other substances and fluids, such as nucleotide synthesizing fluids. The well activation device may also modify wells to provide a set of writeable wells. This set of wells is configured to allow exposure to the nucleotide synthesizing fluids and substances; and prevent exposure to the nucleotide sequencing fluids and substances. There may also be provisions made for risk mitigation for data errors such as generating commands to write specified data to a nucleotide sequence associated with a particular location in a storage device, reading the nucleotide sequence and performing a comparison.

System and method for storage

A biosensor is provided including a detection device and a flow cell mounted to the detection device. The detection device has a detector surface with a plurality of reaction sites. The detection device also includes a filter layer. A method is providing including obtaining signal data from an array of light detectors; determining a crosstalk function for each of the light detectors of the array of light detectors; and determining characteristics of analytes of interest based on the signal data using the crosstalk functions.

Biosensors for biological or chemical analysis and systems and methods for 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.

An example of a biotin-streptavidin cleavage composition includes a formamide reagent and a salt buffer. The formamide reagent is present in the biotin-streptavidin cleavage composition in an amount ranging from about 10% to about 50%, based on a total volume of the biotin-streptavidin cleavage composition. The salt buffer makes up the balance of the biotin-streptavidin cleavage composition. In some examples, the biotin-streptavidin cleavage composition is used to cleave library fragments from a solid support. In other examples, other mechanisms are used to cleave library fragments from a solid support.

Biotin-streptavidin cleavage composition and library fragment cleavage

There is set forth herein a device comprising structure defining a detector surface configured for supporting biological or chemical substances, and a sensor array comprising light sensors and circuitry to transmit data signals using photons detected by the light sensors. The device can include one or more features for reducing fluorescence range noise in a detection band of the sensor array.

Detector with reduced fluorescence range noise

A system writes input data to a storage device as machine-written polynucleotides; and reads machine written polynucleotides from the storage device as output data. The storage device includes a flow cell including a plurality of storage wells in which machine written polynucleotides may be stored. The storage device may include a set of electrodes corresponding to the storage wells that allow for selective interactions with wells across the surface of a flow cell. Operation of the storage device may include receiving a read request associated with a particular location in the storage device, creating a copy of a nucleotide sequence located at the particular location in the storage device, transferring the copy of the nucleotide sequence to a read location, and reading the copy of the nucleotide sequence at the read location.

Storage device, system, and method

A flow cell including inlet and outlet ports in fluid communication with each other through a flow channel that extends therebetween. The flow channel includes a diffuser region and a field region that is located downstream from the diffuser region. The field region of the flow channel directs fluid along reaction sites where desired reactions occur. The fluid flows through the diffuser region in a first flow direction and through the field region in a second flow direction. The first and second flow directions being substantially perpendicular.

Microdevices and biosensor cartridges for biological or chemical analysis and systems and methods for the same

In accordance with embodiments herein a method for capturing cells of interest in a digital microfluidic system is provided, comprising utilizing a droplet actuator to transport a sample droplet to a microwell device. The microwell device includes a substrate having a plurality of microwells that open onto a droplet operations surface of the microwell device. The sample droplet includes cells of interest that enter the microwells. The method introduces capture beads to the microwells, and the capture elements are immobilized on the capture beads. The method utilizes the droplet actuator to transport a cell lysis reagent droplet to the microwell device. Portions of the cell lysis reagent droplet enter the microwells and, during an incubation period, cause the cells of interest to release analyte that is captured by the capture elements on the capture beads.

Digital microfluidic system for single-cell isolation and characterization of analytes

An example method includes connecting a flow cell to an instrument. The flow cell includes a flow channel including a manifold section having a manifold section swept volume and a detection section having a detection section swept volume. A ratio of the detection section swept volume to manifold section swept volume is at least 10 to 1. A first reagent is pumped through the flow channel. A first chemical reaction is performed between the first reagent and analytes positioned in the detection section. A subsequent reagent is pumped through the flow channel to flush out the remaining reagent. A concentration of at least 99.95 percent of reagent positioned in the detection section is the subsequent reagent, after pumping a total volume of the subsequent reagent through the flow channel that is equal to or less than 2.5 times a total swept volume of the manifold section plus the detection section.

Flow cell with integrated manifold

Growing community of inventors

Menlo Park, CA, United States of America

Tarun Kumar Khurana