Illumina Corporation

Illumina Cambridge Limited

Encodia, Inc.

Illumina Singapore Pte. Ltd.

John M Beierle

Kevin L Gunderson

Maria Candelaria Rogert Bacigalupo

James M Tsay

Sang Ryul Park

M Shane Bowen

Kandaswamy Vijayan

Yir-Shyuan Wu

Shengrong Lin

Bala Murali Venkatesan

Lorenzo Berti

Mark S Chee

Lei Shi

Michael Phillip Weiner

Boyan Boyanov

Jonathan Mark Boutell

Roberto Rigatti

Matthew William Kellinger

Jingwei Bai

Klaus Maisinger

David Louis Heiner

Bradley Kent Drews

Alexandre Richez

Randall Smith

David Elliott Kaplan

Sean M Ramirez

Beng Keong Ang

Kevan Samiee

Ludovic Vincent

Xiaohai Liu

Wayne N George

Xiaolin Wu

Timothy J Merkel

Peyton Shieh

Norihito Muranaka

Robert C James

Luca Monfregola

Naiqian Zhan

Tyler Jamison Dill

Anmiv Prabhu

Yuxiang Huang

Valerie Uzzell

Kristina Munoz

Michael S Graige

Michel Perbost

Wei Wei

Scott William Bailey

Heng Kuang Cheng

Robert Yang

Edwin Li

Samantha Schmitt

Sunmin Ahn

Leonid Malevanchik

Maria Candelaria Bacigalupo

James Tsay

Alexander Fuhrmann

Jie Mao

Elliot John Lawrence

Xavier Von Hatten

Shane M Bowen

Heng Huang

Vicky V Lam

Nilda Juan

Nicole Lee

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

Kits and methods of using the kits for analyzing macromolecules, including peptides, polypeptides, and proteins, employing nucleic acid encoding are disclosed. The sample analysis kits employ nucleic acid encoding and/or nucleic acid recording of a molecular interaction and/or reaction, such as recognition events (e.g., between an antigen and an antibody, between a modified terminal amino acid residue, or between a small molecule or peptide therapeutic and a target, etc.). Additional barcoding reagents, such as those for cycle-specific barcoding (e.g., 'clocking'), compartment barcoding, combinatorial barcoding, spatial barcoding, or any combination thereof, may be included in the kits. The sample may comprise macromolecules, including peptides, polypeptides, and proteins, and the recording may generate molecular interaction and/or reaction information, and/or polypeptide sequence information. The kits may be used in high-throughput, multiplexed, and/or automated analysis, and are suitable for analysis of a proteome or subset thereof.

Kits for analysis using nucleic acid encoding and/or label

Embodiments of the present disclosure relate to methods of preparation of templates for polynucleotide sequencing. In particular, the disclosure relates to linearization of clustered polynucleotides in preparation for sequencing by cleavage of one or more first strands of double-stranded polynucleotides immobilized on a solid support by a transition metal complex, for example, a palladium complex or a nickel complex. Further disclosure relate to linearization of clustered polynucleotides by cleaving one or more second strands of double double-stranded polynucleotides immobilized on a solid support comprising azobenzene linker by NaSO. Nucleotides and oligonucleotides comprising a 3' phosphate moiety blocking group, and methods of removing the same using a fluoride reagent are also disclosed.

Compositions and methods for chemical cleavage and deprotection of surface-bound oligonucleotides

An array includes a support including a plurality of discrete wells, a gel material positioned in each of the plurality of discrete wells, and a quality control tracer grafted to the gel material in each of the plurality of discrete wells. The quality control tracer comprises (a) a cleavable nucleotide sequence comprising a cleavage site and (b) a detectable label; and in some aspects, is a cleavable nucleotide sequence with a detectable label and a non-reactive nucleotide sequence or a primer nucleotide sequence.

Arrays with quality control tracers

A flow cell package includes first and second surface-modified patterned wafers and a spacer layer. The first surface-modified patterned wafer includes first depressions separated by first interstitial regions, a first functionalized molecule bound to a first silane or silane derivative in at least some of the first depressions, and a first primer grafted to the first functionalized molecule in the at least some of the first depressions. The second surface-modified patterned wafer includes second depressions separated by second interstitial regions, a second functionalized molecule bound to a second silane or silane derivative in at least some of the second depressions, and a second primer grafted to the second functionalized molecule in the at least some of the second depressions. The spacer layer bonds at least some first interstitial regions to at least some second interstitial regions, and at least partially defines respective fluidic chambers of the flow cell package.

Flow cell package and method for making the same

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

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.

Detection apparatus includes a microfluorometer having an objective, an excitation radiation source, and a detector. The detection apparatus also includes a fluidic system for delivering reagents from a reagent cartridge to a flow cell. The fluidic system includes a manifold body having a plurality of fluidic channels configured for fluid communication between the reagent cartridge and the flow cell. The fluidic system also includes a plurality of reagent sippers. The fluidic system also includes a valve configured to mediate fluid between reagent reservoirs and the flow cell. The detection apparatus also includes a flow cell latch clamp module having a clamp cover for holding the flow cell. The objective is configured to direct excitation radiation from the radiation source to the flow cell and to direct emission from the flow cell to the detector. The microfluorometer is movable to acquire wide-field images of different areas of the flow cell.

Detection apparatus having a microfluorometer, a fluidic system, and a flow cell latch clamp module

Embodiments of the present disclosure relate to methods for capturing and amplifying target polynucleotides on a solid surface, in particular in a well in a microarray, wherein the microarray may comprise a) a substrate comprising at least one well, a surface surrounding the well and an inner well surface; b) a first layer covering the inner well surface and comprising at least one first capture primer pair; and c) a second layer covering the first layer and the surface surrounding the well.

A microarray is designed capture one or more molecules of interest at each of a plurality of sites on a substrate. The sites comprise base pads, such as polymer base pads, that promote the attachment of the molecules at the sites. The microarray may be made by one or more patterning techniques to create a layout of base pads in a desired pattern. Further, the microarrays may include features to encourage clonality at the sites.

Growing community of inventors

Laguna Niguel, CA, United States of America

John M Beierle