Inscripta, Inc.

Akonni Biosystems, Inc.

10x Genomics, Inc.

Cepheid Corporation

Bio-rad Laboratories, Inc.

Cornell Research Foundation Inc.

Other

University of California

Microfluidic Systems, Inc.

University of Minnesota

Louisiana State University and Agricultural & Mechanical College

Phillip Belgrader

Don Masquelier

Jorge Bernate

Kevin D Ness

Andrew Garst

Richard Fox

Bruce Chabansky

Ryan T Gill

Benjamin J Hindson

Serge Saxonov

Ronald G Chang

William A McMillan

Farzad Pourahmadi

Christopher G Cooney

Michael T Taylor

Christopher Hindson

Jesus Ching

Tarjei Sigurd Mikkelsen

Brian Van Hatten

Douglas Bryan Dority

John R Stuelpnagel

Katherine Pfeiffer

Stanley H Sakai

Josephine Harada

Rajiv Bharadwaj

Michael Ybarra Lucero

Billy Wayne Colston, Jr

Eileen Spindler

Rebecca C Holmberg

Matthew David Estes

Michael Schnall-Levin

Francis Barany

Kurt Edward Petersen

Donald Masquelier

M Allen Northrup

Eric D Smith

Paul Hardenbol

Xinying Zheng

Zachary Bent

Paul Ryvkin

Matthew Lubin

Michael Graige

Jessica Michele Terry

Peter Qiang Qu

Christian Siltanen

Burak Dura

Amy Hiddessen

David Stumbo

Nathan Bade

Mirna Jarosz

Robert P Hammer

George Barany

Andrew D Price

Geoffrey McDermott

Samuel Burd

Jeffrey Mellen

Nicholas Heredia

Mohammad Rahimi Lenji

Elliott Meer

Vijay Kumar Sreenivasa Gopalan

Christopher Joachim O'Keeffe

William Watterson

Robin R Miles

Tobias Daniel Wheeler

Simant Dube

Fred Paul Milanovich

John Frederick Regan

Bob Yuan

Vincent Riot

Austin So

Indira Wu

Niranjan Srinivas

Anthony Joseph Makarewicz, Jr

Stephane Claude Boutet

Arial Bueno

Solongo B Ziraldo

Sarah Taylor

Tinsley Janna Stokes

Douglas N Modlin

Aleksandr N Perov

Steve Garber

Nitu Harshendu Thakore

Charles D Johnson

Aamir Mir

Bruce D Irvine

Robert Doebler

Anna Hickerson

Miles Gander

James D Sterling

Reza Miraghaie

Ali Nadim

Shanavaz L Nasarabadi

Clint Davis

Paul Wyatt

Billy W Colston

Isaac David Wagner

Shawn Paul Hodges

Alissa Erin Burkey

Alissa Erin Gindlesperger

David E Sipes

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

The present disclosure provides compositions, methods, systems, and devices for polynucleotide processing and analyte characterization. Such polynucleotide processing may be useful for a variety of applications, including analyte characterization by polynucleotide sequencing. The compositions, methods, systems, and devices disclosed herein generally describe barcoded oligonucleotides, which can be bound to a bead, such as a gel bead, useful for characterizing one or more analytes including, for example, protein (e.g., cell surface or intracellular proteins), genomic DNA, and RNA (e.g., mRNA or CRISPR guide RNAs). Also described herein, are barcoded labelling agents and oligonucleotide molecules useful for 'tagging' analytes for characterization.

Methods and systems for processing polynucleotides

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

The present disclosure provides modules, instruments and methods to enrich for cells edited via nucleic acid-guided nuclease editing of live cells.

Detection of nuclease edited sequences in automated modules and instruments

Nucleic acid-guided nuclease editing in mammalian cells may include passaging mammalian cells, in an automated closed cell editing instrument, into smaller aggregates when the aggregates exceed 50-300 microns in size. A library of viral particles may be delivered to the mammalian cells at a multiplicity of infection such that each mammalian cell receives one or no viral particle. The library may include viral vectors with an editing cassette including a pair of gRNA coding sequence and donor DNA. Conditions may be provided to allow a viral vector of the viral vectors to integrate into the mammalian cells. Enriching for mammalian cells may be done with an integrated viral vector. A nucleic acid-guided nuclease or nuclease fusion or a coding sequence for a nucleic acid-guided nuclease or nuclease fusion may be delivered to the enriched mammalian cells and conditions may be provided to allow editing in the mammalian cells.

Compositions, methods, modules and instruments for automated nucleic acid-guided nuclease editing in mammalian cells via viral delivery

An integrated sample purification system includes a housing, a sample container rack, a filter holder, and a cylindrical magnet. The sample container rack and the filter device holder are disposed in the housing. The sample container rack is configured to hold one or more sample containers, the filter device holder is configured to hold one or more filter devices. The cylindrical magnet is adjacent to and external to the sample container rack, and is rotated about a central, longitudinal axis of the magnet by an electric motor disposed in the housing to lyse cells. Molecules of interest in the lysed cells are purified using filters that bind specifically to the molecules of interest. The system is readily amenable to automation and rapid purification and analysis of molecules of interest, such as nucleic acids and proteins.

Integrated sample processing system

The present disclosure provides instruments, modules and methods for improved detection of edited cells following nucleic acid-guided nuclease genome editing. The disclosure provides improved automated instruments that perform methods&#x2014;including high throughput methods&#x2014;for screening cells that have been subjected to editing and identifying cells that have been properly edited.

Instruments, modules, and methods for improved detection of edited sequences in live cells

The present disclosure provides automated modules and instruments for improved detection of nuclease genome editing of live cells. The disclosure provides improved modules&#x2014;including high throughput modules&#x2014;for screening cells that have been subjected to editing and identifying and selecting cells that have been properly edited.

The disclosure provides methods for separating and/or purifying one or more molecules released from one or more fluid compartments or partitions, such as one or more droplets. Molecules can be released from a fluid compartment(s) and bound to supports that can be isolated via any suitable method, including example methods described herein. The disclosure also provides devices that can aid in isolating supports bound to molecules.

Partition processing methods and systems

In an illustrative embodiment, automated multi-module cell editing instruments are provided to automate multiple edits into nucleic acid sequences inside one or more cells.

Automated cell processing methods, modules, instruments, and systems

This invention relates to compositions of matter, methods, modules and automated, end-to-end closed instruments for automated mammalian cell growth, reagent bundle creation and mammalian cell transfection followed by nucleic acid-guided nuclease editing in live mammalian cells. The disclosed compositions and method entail making 'reagent bundles' comprising many (hundreds of thousands to millions) clonal copies of an editing cassette and delivering or co-localizing the reagent bundles with live mammalian cells such that the editing cassettes edit the cells and the edited cells continue to grow.

Compositions, methods, modules and instruments for automated nucleic acid-guided nuclease editing in mammalian cells using microcarriers

Method of haplotype analysis. In an exemplary method, an aqueous phase containing nucleic acid may be partitioned into a plurality of discrete volumes. At least one allele sequence may be amplified in the volumes from each of a first polymorphic locus and a second polymorphic locus that exhibit sequence variation in the nucleic acid. At least one measure of co-amplification of allele sequences from both loci in the same volumes may be determined. A haplotype of the first and second loci may be selected based on the at least one measure of co-amplification.

Analysis of nucleic acids

This invention relates to compositions of matter, methods, modules and instruments for automated mammalian cell growth and mammalian cell transduction followed by nucleic acid-guided nuclease editing in live mammalian cells. The present compositions and methods entail viral delivery of an editing cassette to live mammalian cells such that the editing cassettes edit the cells and the edited cells continue to grow, preferably using a fully-automated end-to-end instrument to process the cells without human intervention to enhance cell processing uniformity and to maintain the integrity of the cell culture.

Growing community of inventors

Pleasanton, CA, United States of America

Phillip Belgrader