10x Genomics, Inc.

Bio-rad Laboratories, Inc.

Inscripta, Inc.

Lawrence Livermore National Security, LLC

Kevin D Ness

Benjamin J Hindson

Serge Saxonov

Donald Masquelier

Michael Schnall-Levin

Mirna Jarosz

Christopher Hindson

Phillip Belgrader

Paul Hardenbol

Don Masquelier

Rajiv Bharadwaj

Jorge Bernate

Billy Wayne Colston, Jr

Ryan T Gill

Xinying Zheng

Anthony Makarewicz

Debkishore Mitra

Fred Paul Milanovich

Klint Aaron Rose

Christopher F Kelly

Amy L Hiddessen

Anthony Joseph Makarewicz, Jr

Raymond P Mariella, Jr

Tobias Daniel Wheeler

Byoungsok Jung

Christopher G Bailey

Jeffrey Mellen

Nicholas Heredia

Donald A Masquelier

Dietrich A Dehlinger

Michael Ybarra Lucero

Simant Dube

Karl Albert Fisher

Samuel Burd

Maxim Shusteff

John Frederick Regan

Erin Rae Chia

Austin So

Billy W Colston

Douglas A Wajda

Douglas N Modlin

Vincent Riot

Peter A Krulevitch

Luc J Bousse

William J Benett

Mark Alan Arbore

John R Stuelpnagel

Andrew D Price

David L Klein

Patrick Marks

Thomas Henry Cauley, Iii

John Dzenitis

Jeffrey Clark Mellen

Steven R Visuri

Yuan Li

Jerry E Hurst

Phil Belgrader

Jonathan Petersen

Paul Wyatt

Shawn Paul Hodges

Camille Bodley Troup

Bill Colston

Steven Romine

Landon Merrill

Mima Jarosz

Ben Hindson

Mike Lucero

Philip Belgrader

Erin R Steenblock

Anthony J Makarewicz

Nicholas Jack Heredia

The present invention is directed to methods, compositions and systems for analyzing sequence information while retaining structural and molecular context of that sequence information.

Methods and compositions for nucleic acid analysis

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

Microfluidic channels networks and systems are provided. One network includes a first fluid channel having a first depth dimension; at least a second channel intersecting the first channel at a first intersection; at least a third channel in fluid communication with the first intersection, at least one of the first intersection and the third channel having a depth dimension that is greater than the first depth dimension. Also provided is a flow control system for directing fluids in the network. Systems are additionally provided for flowing disrupted particles into a droplet formation junction, whereby a portion of the disrupted particles or the contents thereof are encapsulated into one or more droplets. Further provided is a method for controlling filling of a microfluidic network by controlling passive valving microfluidic channel network features.

Microfluidic systems and methods of use

A system, including method and apparatus, for generating droplets suitable for droplet-based assays. The disclosed systems may include either one-piece or multi-piece droplet generation components configured to form sample-containing droplets by merging aqueous, sample-containing fluid with a background emulsion fluid such as oil, to form an emulsion of sample-containing droplets suspended in the background fluid. In some cases, the disclosed systems may include channels or other suitable mechanisms configured to transport the sample-containing droplets to an outlet region, so that subsequent assay steps may be performed.

Method of emulsion formation and modification

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

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

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.

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Mountain View, CA, United States of America

Kevin D Ness