Illumina Corporation

10x Genomics, Inc.

The Scripps Research Institute

Epic Sciences, Inc.

John R Stuelpnagel

Mark S Chee

Serge Saxonov

Katherine Pfeiffer

Jian-Bing Fan

Tarjei Sigurd Mikkelsen

Josephine Harada

Steven R Auger

Anthony W Czarnik

Phillip Belgrader

Christopher Hindson

Min-Jui Richard Shen

Michael S Graige

Jorge Velarde

Arnold Oliphant

David L Barker

Scott L Butler

Kevin L Gunderson

Steven Mark Barnard

Andrew D Price

Zachary Bent

Paul Ryvkin

Jessica Michele Terry

Elliott Meer

Christopher Joachim O'Keeffe

Solongo B Ziraldo

Geoffrey McDermott

Todd Alan Dickinson

Mohammad Rahimi Lenji

Vijay Kumar Sreenivasa Gopalan

Gan G Wang

Rajiv Bharadwaj

Robert C Kain

Michael Ybarra Lucero

Tobias Daniel Wheeler

Indira Wu

Niranjan Srinivas

Stephane Claude Boutet

Sarah Taylor

Don O'Neil

Laura S Casas

Shawn Christopher Baker

Kevin D Ness

Benjamin J Hindson

Michael Schnall-Levin

Mirna Jarosz

Xing Yang

Xinying Zheng

Patrick Marks

Dena Marrinucci

Kenneth M Kuhn

Peter Kuhn

Joshua Kunken

Anand Kolatkar

Steven M Bernard

Richard J Pytelewski

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 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

A method for detecting nucleic acids by (a) providing a sample having target nucleic acids, each nucleic acid having contiguous first, second, and third domains; (b) contacting the sample with probe sets to form hybridization complexes, wherein each probe set includes (i) a first probe having a sequence that is complementary to the first domain; and (ii) a second probe having a sequence substantially complementary to the third domain; (c) extending the first probes along the second domains of the complexes while the complexes are immobilized on a solid support; (d) ligating the extended first probes to the second probes to form templates; (e) amplifying the templates with primers that are complementary to the first and second priming sequences to produce amplicons; and (f) detecting the amplicons on the surface of a nucleic acid array.

Multiplex nucleic acid reactions

The invention provides seminal computational approaches utilizing data from non-rare cells to detect rare cells, such as circulating tumor cells (CTCs). The invention is applicable at two distinct stages of CTC detection; the first being to make decisions about data collection parameters and the second being to make decisions during data reduction and analysis. Additionally, the invention utilizes both one and multi-dimensional parameterized data in a decision making process.

Method of using non-rare cells to detect rare cells

The invention provides a method of selecting a representational sample of nucleic acid sequences from a complex mixture. The method includes: (a) contacting a complex mixture of nucleic acids under conditions sufficient for hybridization with a population of capture probes complementary to one or more nucleic acids comprising a predetermined portion of the sequence collectively present in the complex mixture to form hybridization complexes of the one or more nucleic acids with the population of probes, the population of capture probes being attached to a solid support, and (b) removing unhybridized nucleic acids to select a representational sample of nucleic acids having a complexity of less than 10% but more than 0.001% of the complex mixture, wherein the representational sample comprises a nucleic acid copy having a proportion of each sequence in the copy relative to all other sequences in the copy substantially the same as the proportions of the sequences in the predetermined portion of one or more nucleic acids within the complex mixture. A method of selecting a representational sample of genomic sequences from a complete genome also is provided. The invention further provides a nucleic acid population that includes a representational sample having a complexity of less than 10% but more than 0.001% of a complex mixture, the representational sample comprising a nucleic acid copy having a proportion of each sequence in the copy relative to all other sequences in the copy substantially the same as the proportions of sequences in a predetermined portion of a sequence collectively present in one or more nucleic acids within the complex mixture.

Compounds and method for representational selection of nucleic acids from complex mixtures using hybridization

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.

The present invention is directed to methods and compositions for generating a pool of oligonucleotides. The invention finds use in preparing a population or subpopulations of oligonucleotides in solution. The pool of oligonucleotides finds use in a variety of nucleic acid detection and/or amplification assays.

Compositions and methods for preparing oligonucleotide solutions

Growing community of inventors

Encinitas, CA, United States of America

John R Stuelpnagel