Bio-rad Laboratories, Inc.

Nicholas Heredia

Kevin D Ness

Serge Saxonov

Ronald Lebofsky

Jeffrey Mellen

Phillip Belgrader

Benjamin J Hindson

Michael Ybarra Lucero

Simant Dube

John Frederick Regan

Dianna Maar

Austin So

Billy Wayne Colston, Jr

Anthony Makarewicz

Phil Belgrader

Billy W Colston

Paul Wyatt

Shawn Paul Hodges

Camille Bodley Troup

Bill Colston

Mike Lucero

Ben Hindson

Methods of generating a nucleic acid signature for identifying particles associated in a partition are provided. In one aspect, the method comprises: partitioning a sample into a plurality of partitions comprising a particle comprising a solid support surface, the solid support surface having a plurality of oligonucleotide primers conjugated thereon, wherein the oligonucleotide primers comprise a barcode sequence, and wherein the partitions have 0, 1, or more than 1 particles per partition; providing in a partition a substrate comprising a barcode sequence or repeating clonal barcode sequences; and in the partition, associating a first particle conjugated to oligonucleotide primers comprising a first barcode sequence and a second particle conjugated to oligonucleotide primers comprising a second barcode sequence to a barcode sequence from the substrate, thereby generating a nucleic acid signature for the particles in the partition.

Multiple beads per droplet resolution

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

Methods and compositions are provided for improved nucleic acid amplification assays. In some embodiments, the nucleic acid amplification assay is a tagged amplicon primer extension (TAPE) nucleic acid amplification reaction.

Split-cycle and tape amplification

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

Methods and compositions are provided for improved nucleic acid amplification assays.

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.

Oil compositions and methods for use in droplet formation or in spacing of droplets are disclosed. The oil compositions may include a combination, such as a silicone oil and a fluorine-containing compound. The droplets can contain analytes (e.g., nucleic acids) and may be used for molecular reactions (e.g., digital PCR) and detection.

Methods and compositions for using oils for analysis and detection of molecules

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.

Growing community of inventors

Mountain House, CA, United States of America

Nicholas Heredia