Illumina Corporation

Cellanome, Inc.

Illumina Cambridge Limited

Yir-Shyuan Wu

Tarun Kumar Khurana

M Shane Bowen

Kevin L Gunderson

Xi-Jun Chen

Jeffrey S Fisher

Maria Candelaria Rogert Bacigalupo

Shengrong Lin

Arnaud Rival

Yan-You Lin

Kandaswamy Vijayan

Dajun Yuan

Bala Murali Venkatesan

John M Beierle

Lewis J Kraft

Lorenzo Berti

James M Tsay

Sang Ryul Park

Filiz Gorpe-Yasar

Ali Agah

Filiz Gorpe Yasar

Mostafa Ronaghi

Cyril Delattre

Mathieu Lessard-Viger

Victoria Popic

Yasaman Farshchi

Erich B Jaeger

John A Moon

Poorya Sabounchi

Arash Jamshidi

Hui Han

Justin Fullerton

Fabien Abeille

Steven Mark Barnard

Gordon M Cann

Clifford Lee Wang

Farnaz Absalan

Yan-you Lin

Sarah Stuart

Robert C Kain

Frank J Steemers

Bernard Hirschbein

Fiona Kaper

Behnam Javanmardi

Brian Douglas Mather

Byoungsok Jung

Xavier Von Hatten

Liangliang Qiang

Charles Lin

Daniel Leonard Fuller

Hamed Amini

Hongxia Xu

Foad Mashayekhi

Burak Okumus

Victor J Quijano

Pallavi Daggumati

Chenlu Hou

Andrew J Price

Elisabet Rosas

Sebastien Georg Gabriel Ricoult

Dan Cao

Tong Liu

Shi Min Xiao

James Tsay

Falko Noe

Shane M Bowen

Filiz Gorpe- Yasar

Victoria Popuc

Falko Noé

Described herein are systems and methods for analyzing biological samples. Including a method for processing an analyte, comprising providing a fluidic device comprising the analyte and one or more polymer precursors; selecting a discrete area within said fluidic device; providing an energy source in optical communication with fluidic device; and selectively supplying a unit of energy generated from the energy source to the fluidic device to generate a polymer matrix within the fluidic device, wherein the polymer matrix is within the discrete area or adjacent to the discrete area.

Devices and methods for analyzing biological samples

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 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.

Provided is a surface having metal regions and an interstitial region having a composition that differs from the metal regions, wherein a continuous gel layer coats the surface across the metal regions and the interstitial regions. Nucleic acids or other analytes can be attached to the continuous gel layer such that a greater amount is attached over the metal regions than over the interstitial region. Also provided are methods for making such surfaces. Methods are also provided for making an array of nucleic acids or other analytes using such surfaces.

Patterned flow-cells useful for nucleic acid analysis

Methods for analyzing biological samples in a fluidic device comprising generating a polymer matrix from precursors at specific locations comprising biological components

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

Methods for analyzing biological samples in a fluidic device comprising generating a polymer matrix from precursors at discrete areas

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

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

An example of a flow cell includes a substrate, which includes nano-depressions defined in a surface of the substrate, and interstitial regions separating the nano-depressions. A hydrophobic material layer has a surface that is at least substantially co-planar with the interstitial regions and is positioned to define a hydrophobic barrier around respective sub-sets of the nano-depressions.

Flow cells with a hydrophobic barrier

Flow cells using sequencing-ready nucleic acid fragments attached to carrier beads immobilized at capture sites of a plurality of chambers

Embodiments provided herewith are directed to self-assembled methods of preparing a patterned surface for sequencing applications including, for example, a patterned flow cell or a patterned surface for digital fluidic devices. The methods utilize photolithography to create a patterned surface with a plurality of microscale or nanoscale contours, separated by hydrophobic interstitial regions, without the need of oxygen plasma treatment during the photolithography process. In addition, the methods avoid the use of any chemical or mechanical polishing steps after the deposition of a gel material to the contours.

Self assembled patterning using patterned hydrophobic surfaces

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Albany, CA, United States of America

Yir-Shyuan Wu