Illumina Corporation

Encodia, Inc.

Affymetrix, Inc.

Illumina Cambridge Limited

University of California

Kevin L Gunderson

Frank J Steemers

Mark S Chee

Jeffrey G Mandell

Robert C Kain

David Louis Heiner

Boyan Boyanov

Chanfeng Zhao

John M Beierle

Jingwei Bai

Michael Phillip Weiner

M Shane Bowen

Kandaswamy Vijayan

Yir-Shyuan Wu

Sasan Amini

Shengrong Lin

Bala Murali Venkatesan

Jens H Gundlach

Jonathan Mark Boutell

Maria Candelaria Rogert Bacigalupo

Lei Shi

Norihito Muranaka

Kerri York

Jeffrey S Fisher

Igor Yu Goryshin

Christian Gloeckner

Robert C James

Natasha Pignatelli

John R Stuelpnagel

Min-Jui Richard Shen

Mostafa Ronaghi

Lorenzo Berti

Sang Ryul Park

Liangliang Qiang

Kathryn M Stephens

Tarun Kumar Khurana

Roberto Rigatti

Jian-Bing Fan

Ian M Derrington

Todd Alan Dickinson

Thomas Royce

Eric Stava

Don O'Neil

Luca Monfregola

Hosein Mohimani

John A Moon

David J Lockhart

Molly Min He

Matthew William Kellinger

Cheng-Yao Chen

Amirali Kia

Klaus Maisinger

Dmitry K Pokholok

Nicholas Caruccio

Bradley Baas

Helmy A Eltoukhy

Jerome J Jendrisak

Cyril Delattre

Fiona Kaper

Neil A Straus

Kay Klausing

Stephen Verespy, Iii

Lea Pickering

Kevin Desai

Niall Anthony Gormley

Maureen T Cronin

Michal Lebl

Thomas R Gingeras

Charles Garrett Miyada

Kai Wu

Sergio Peisajovich

Jason Richard Betley

Philip G Collins

Rigo Pantoja

Hajime Matsuzaki

Qing Yang

Xi-Jun Chen

Ryan Christopher Smith

James M Tsay

Trina Faye Osothprarop

Michel Perbost

Gregory A Weiss

Huu Minh Tran

Duc Do

Mark A Maffitt

Lisa Wodicka

Filiz Gorpe-Yasar

Fan Zhang

Natalie Morrell

Charles Lin

Melissa Shults Won

Wouter Meuleman

Rosamond Jackson

Foad Mashayekhi

Carsten Rosenow

Eric Okerberg

Gareth Jenkins

A technique for sequencing nucleic acids in an automated or semi-automated manner is disclosed. Sample arrays of a multitude of nucleic acid sites are processed in multiple cycles to add nucleotides to the material to be sequenced, detect the nucleotides added to sites, and to de-block the added nucleotides of blocking agents and tags used to identify the last added nucleotide. Multiple parameters of the system are monitored to enable diagnosis and correction of problems as they occur during sequencing of the samples. Quality control routines are run during sequencing to determine quality of samples, and quality of the data collected.

Independently removable nucleic acid sequencing system and method

A system for sequencing nucleic acid comprising a plurality of stations and a system control. The system control configured to direct the first substrate to progress and retrogress between the first processing station and the imaging station, direct the second substrate to progress and retrogress between the second processing station and the imaging station, and direct a chemistry cycle of a first sequencing procedure to occur within one of the first processing station or the second processing station while an imaging cycle of a second sequencing procedure occurs within the imaging station.

Nucleic acid sequencing system

The present disclosure relates to methods and kits for generating single cell barcodes and imparting them to the constituent molecules within a single cell. Additionally, methods to overlay sample barcode and spatial barcode information onto the single cell barcodes are also described. Generation of single cell barcodes is achieved by labeling the genomic DNA of a cell/nucleus with a small handful, preferably just a one or two cellular barcode probes (CBP) that can be amplified and propagated to label the constituent molecules within the cell. The disclosure finds utility in applications such as characterization of cellular heterogeneity, comprehensive profiling of tissue composition, characterization of adherent cells, discovery of new cell subtypes and functions of individual cells in the context of its microenvironment, and others.

Methods for barcoding macromolecules in individual cells

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

Embodiments provided herein relate to methods and compositions for next generation sequencing. Some embodiments include the preparation of a template library from a target nucleic acid using one-sided transposition, sequencing the template library, and capturing the contiguity information.

Methods and compositions using one-sided transposition

Compositions, systems, and methods for detecting events are provided. A composition can include a nanopore including a first side, a second side, and an aperture extending through the first and second sides; and a permanent tether including head and tail regions and an elongated body disposed there between. The head region can be anchored to or adjacent to the first or second side of the nanopore. The elongated body including a reporter region can be movable within the aperture responsive to a first event occurring adjacent to the first side of the nanopore. For example, the reporter region is translationally movable toward the first side responsive to the first event, then toward the second side, then toward the first side responsive to a second event. The first event can include adding a first nucleotide to a polynucleotide. The second event can include adding a second nucleotide to the polynucleotide.

Compositions, systems, and methods for detecting events using tethers anchored to or adjacent to nanopores

The current document discusses a detection system comprising a mechanical-change sensor that exhibits one or more mechanical changes when specifically interacting with entities within a target, each entity having a type, a mechanical-change-to-signal transducer that transduces the one or more mechanical changes into a signal, and an analysis subsystem that determines the types of entities within the target using the signal.

Sequence-detection system

A method for analyzing macromolecules, including peptides, polypeptides, and proteins, employing nucleic acid encoding is disclosed.

Macromolecule analysis employing nucleic acid encoding

Embodiments of the present disclosure include methods and compositions for functionalizing molecules, such as oligonucleotides, with functional groups, including polyhistidine tags useful in affinity methods. Some embodiments include methods for modifying and purifying complex mixtures of molecules by exchange of functional tags.

Functionalization and purification of molecules by reversible group exchange

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

The present disclosure relates to systems and methods for the amplification of nucleic acids, including, but not limited to, the amplification of nucleic acid libraries and whole genome amplification.

Compositions and methods for the amplification of nucleic acids

Presented herein are methods and compositions for tagmentation of nucleic acids. The methods are useful for generating tagged DNA fragments that are qualitatively and quantitatively representative of the target nucleic acids in the sample from which they are generated.

Transposase compositions for reduction of insertion bias

Growing community of inventors

Encinitas, CA, United States of America

Kevin L Gunderson