10x Genomics, Inc.

Bio-rad Laboratories, Inc.

Lawrence Livermore National Security, LLC

Akonni Biosystems, Inc.

Quantilife, Inc.

Benjamin J Hindson

Kevin D Ness

Serge Saxonov

Michael Schnall-Levin

Donald Masquelier

Mirna Jarosz

Christopher Hindson

Paul Hardenbol

Billy Wayne Colston, Jr

Rajiv Bharadwaj

Amy L Hiddessen

Phillip Belgrader

Anthony Makarewicz

Xinying Zheng

Erin Rae Chia

Debkishore Mitra

Fred Paul Milanovich

Donald A Masquelier

Anthony Joseph Makarewicz, Jr

Michael Ybarra Lucero

Chunxiao Han

Adam Lowe

Pranav Patel

Keith P Bjornson

Simant Dube

Samuel Burd

Nicholas Heredia

Jeffrey Mellen

Indira Wu

Paul William Wyatt

Billy W Colston

Anthony J Makarewicz

Erin R Steenblock

Tarjei Sigurd Mikkelsen

Neil Reginald Beer

Tobias Daniel Wheeler

Kamila Belhocine

Paul Ryvkin

John Frederick Regan

Vincent Riot

John Dzenitis

Joseph P Fitch

Austin So

Geoff McDermott

Douglas N Modlin

Jason Underwood

Yaqi Wang

Lance F Bentley Tammero

John R Stuelpnagel

Andrew D Price

Patrick Marks

Zahra Kamila Belhocine

Adam McCoy

Svilen Tzonev

Yuan Li

Paul Wyatt

J Chance Carter

Ryan T Koehler

Shawn Paul Hodges

Philip Belgrader

Mima Jarosz

Landon Merrill

Billy W Colson, Jr

Camille Bodley Troup

Adam M Mccoy

The present disclosure relates to methods, compositions and systems for haplotype phasing and copy number variation assays. Included within this disclosure are methods and systems for combining the barcode comprising beads with samples in multiple separate partitions, as well as methods of processing, sequencing and analyzing barcoded samples.

Analysis of nucleic acid sequences

The invention described herein solves challenges in providing a proficient, rapid and meaningful analysis of sequencing data. Methods and computer program products of the invention allow for a system to receive, analyze, and display sequencing data in real-time. The invention provides solutions to several difficulties encountered in assembling short sequencing-reads, and by doing so the invention improves the worth and significance of sequencing data.

Sequencing methods

Method of analysis. In the method, a microfluidic device defining a flow path extending from an inlet to an outlet may be selected. A sample-containing fluid may be introduced into the flow path via the inlet. Volumes of the sample-containing fluid may be isolated from one another on the flow path. A two-dimensional monolayer of the volumes may be imaged. The two-dimensional monolayer may be formed along the flow path between the inlet and the outlet.

Method of analysis

Methods of partition-based analysis. In an exemplary method, a device having a port fluidically connected to a chamber may be selected. A sample-containing fluid may be placed into the port. The sample-containing fluid may be moved from the port to the chamber. Partitions of the sample-containing fluid may be formed. A monolayer of the partitions in the chamber may be created. At least a portion of the monolayer may be imaged.

Partition-based method of analysis

Provided herein are compositions, systems and methods for tagging molecular events, reactions, species, etc., but without the need for complex, highly diverse libraries of tagging molecules. Provided are tagging moieties that can have a smaller number, a few, or even a single original 'tagging' structure that may be transformed or transformable, in situ, into a collection of larger numbers of unique tagging or “barcode” moieties.

Systems and methods for differentially tagging nucleic acid molecules

The present disclosure provides methods and compositions for detecting polynucleotides in a sample and for quantifying polynucleotide load in a sample. The polynucleotides can be associated with a disease, disorder, or condition. In some applications, methylated DNA is quantified, e.g., in order to determine the load of polynucleotides in a sample. The present disclosure also provides methods and compositions for determining the load of fetal polynucleotides in a biological sample, e.g., the load of fetal polynucleotides (e.g., DNA, RNA) in maternal plasma. The present disclosure provides methods and compositions for detecting cellular processes such as cellular viability, growth rates, and infection rates. This disclosure also provides compositions and methods for detecting differences in copy number of a target polynucleotide. In some embodiments, the methods and compositions provided herein are useful for diagnosis of fetal genetic abnormalities, when the starting sample is maternal tissue (e.g., blood, plasma). The methods and materials described apply techniques for allowing detection of small, but statistically significant, differences in polynucleotide copy number.

Methods and compositions for detecting genetic material

This disclosure provides methods and compositions for sample processing, particularly for sequencing applications. Included within this disclosure are bead compositions, such as diverse libraries of beads attached to large numbers of oligonucleotides containing barcodes. Often, the beads provides herein are degradable. For example, they may contain disulfide bonds that are susceptible to reducing agents. The methods provided herein include methods of making libraries of barcoded beads as well as methods of combining the beads with a sample, such as by using a microfluidic device.

Methods and systems for processing polynucleotides

This disclosure provides microwell capsule array devices. The microwell capsule array devices are generally capable of performing one or more sample preparation operations. Such sample preparation operations may be used as a prelude to one more or more analysis operations. For example, a device of this disclosure can achieve physical partitioning and discrete mixing of samples with unique molecular identifiers within a single unit in preparation for various analysis operations. The device may be useful in a variety of applications and most notably nucleic-acid-based sequencing, detection and quantification of gene expression and single-cell analysis.

Capsule array devices and methods of use

The disclosure provides devices, systems and methods for the generation of encapsulated reagents and the partitioning of encapsulated reagents for use in subsequent analyses and/or processing, such as in the field of biological analyses and characterization.

Fluidic devices, systems, and methods for encapsulating and partitioning reagents, and applications of same

System, including methods, apparatus, compositions, and kits, for making and using a stabilized emulsion. A method of generating a stabilized emulsion is provided. In the method, an aqueous phase may be provided. The aqueous phase may include an effective concentration of one or more skin-forming proteins. An emulsion may be formed. The emulsion may include droplets of a dispersed phase disposed in a continuous phase, with the aqueous phase being the continuous phase or the dispersed phase. The emulsion may be heated to create an interfacial skin between each droplet and the continuous phase, to transform the droplets into capsules.

Emulsion chemistry for encapsulated droplets

The present invention is directed to methods, compositions and systems for capturing and analyzing sequence information contained in targeted regions of a genome. Such targeted regions may include exomes, partial exomes, introns, combinations of exonic and intronic regions, genes, panels of genes, and any other subsets of a whole genome that may be of interest.

Methods and compositions for targeted nucleic acid sequencing

The present disclosure provides compositions, methods, systems, and devices for polynucleotide processing. Such polynucleotide processing may be useful for a variety of applications, including polynucleotide sequencing.

Growing community of inventors

Livermore, CA, United States of America

Benjamin J Hindson