Fluidigm Corporation

10x Genomics, Inc.

Bio-rad Laboratories, Inc.

University of California

Applera Corporation

Fluidign Corporation

Michael Ybarra Lucero

Marc Alexander Unger

Geoffrey Richard Facer

Hany Ramez Nassef

Tarjei Sigurd Mikkelsen

Lincoln McBride

Serge Saxonov

Phillip Belgrader

Katherine Pfeiffer

Ian D Manger

Benjamin J Hindson

Michael Schnall-Levin

Jonas Frisen

Patrik Stahl

Kevin D Ness

Nicholas Heredia

Jeffrey Mellen

Rajiv Bharadwaj

Christopher Hindson

John R Stuelpnagel

Andrew D Price

Billy Wayne Colston, Jr

Geoffrey McDermott

Tobias Daniel Wheeler

Simant Dube

Zachary Bent

Paul Ryvkin

Jessica Michele Terry

Andrew Paul May

Hou-Pu Chou

Kenneth J Livak

Augusto Manuel Tentori

Yifeng Yin

Eswar Prasad Ramachandran Iyer

Yong Yi

Stephane Claude Boutet

Emily Miyashita-Lin

Anja Wienecke

Enric Llorens Bobadilla

Mohammad Rahimi Lenji

Austin So

Jennifer Chew

Maja Marklund

John Frederick Regan

Josephine Harada

Vijay Kumar Sreenivasa Gopalan

Elliott Meer

Solongo B Ziraldo

Indira Wu

Niranjan Srinivas

Sarah Taylor

Christopher Joachim O'Keeffe

Muhammad A Sharaf

Svilen Tzonev

Geoff Facer

Paul Wyatt

Billy W Colston

Linda Kvastad

Ryan T Koehler

Shawn Paul Hodges

Kathy Yokobata

Anja Weinecke

Camille Bodley Troup

Lincoln Mcbride

Eva Gracia Villacampa

Joakim Lundeberg

Meghan L F Frey

The present disclosure relates to materials and methods for spatially analyzing nucleic acids that have been fragmented with a transposase enzyme, alone or in combination with other types of analytes.

Method for transposase-mediated spatial tagging and analyzing genomic DNA in a biological sample

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

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

Provided herein are improved methods, compositions, and kits for analysis of nucleic acids. The improved methods, compositions, and kits can enable copy number estimation of a nucleic acid in a sample. Also provided herein are methods, compositions, and kits for determining the linkage of two or more copies of a target nucleic acid in a sample (e.g. whether the two or more copies are on the same chromosome or different chromosomes) or for phasing alleles.

A method for carrying out nucleic acid amplification reactions using a microfluidic device is described. Amplification primers and other amplification reagents are deposited at a plurality of reaction sites in the device, a sample solution containing amplifiable polynucleotides is introduced into the reaction sites, and amplification is carried out.

Thermal reaction device and method for using the same

The invention provides an assay method for detection and/or quantification of a plurality of nucleic acid or protein targets in a sample. In the method probes are used to associate a detectable tag sequence with each of the selected targets present in the sample. Probes or primers sufficient to identify at least 25, and preferably at least 500, different targets are used. The method involves segregating aliquots of the sample from each other and detecting the tag sequences in each aliquot.

Methods for detection and quantification of nucleic acid or protein targets in a sample

A variety of elastomeric-based microfluidic devices and methods for using and manufacturing such devices are provided. Certain of the devices have arrays of reaction sites to facilitate high throughput analyzes. Some devices also include reaction sites located at the end of blind channels at which reagents have been previously deposited during manufacture. The reagents become suspended once sample is introduced into the reaction site. The devices can be utilized with a variety of heating devices and thus can be used in a variety of analyzes requiring temperature control, including thermocycling applications such as nucleic acid amplification reactions, genotyping and gene expression analyzes.

Microfluidic device with reaction sites configured for blind filling

Growing community of inventors

South San Francisco, CA, United States of America

Michael Ybarra Lucero