Affymetrix, Inc.

Cellular Research, Inc.

Becton Dickinson and Company Limited

Enumerix, Inc.

Perlegen Sciences, Inc.

Countable Labs, Inc.

Other

Affymetrix Lnc.

13.8, Inc.

Affymetrix Technologies, N.v.

Stephen P A Fodor

Glenn K Fu

Lubert Stryer

Michael C Pirrung

J Leighton Read

Geoffrey Richard Facer

Christina Fan

Julie Wilhelmy

William J Dower

Robert J Lipshutz

Hei Mun Christina Fan

Eleen Yee Lam Shum

Janice Hoiyi Lai

Dennis Solas

Richard P Rava

Xiaohua C Huang

James L Winkler

Mark S Chee

Earl A Hubbell

Douglas N Modlin

Maureen T Cronin

Charles Garrett Miyada

Edward L Sheldon

Lois Aldwin

Peter E Lobban

Christopher J Buchko

Debra A Ross

MacDonald S Morris

Rolfe C Anderson

Glenn H McGall

David Stern

Michael H Shapero

Sixing Li

Haeun Grace Lee

Martin J Goldberg

Keith W Jones

Mark O Trulson

David R Cox

Virginia W Goss

R Fabian Pease

Paul D Hoeprich, Jr

Bradley A Margus

Jung Won Keum

Roger Rudoff

George T Wu

Robert G Kuimelis

Peter J Fiekowsky

Thomas R Gingeras

Macdonald S Morris

Ian D Walton

Nila Shah

Vernon A Norviel

Luburt Stryer

Ketih W Jones

This disclosure provides for devices, methods, and systems for generating a plurality of droplets within a collecting container at an extremely high rate (e.g., of at least 1 million droplets per minute, etc.), each of the plurality of droplets comprising an aqueous mixture for a digital analysis, wherein upon generation, the plurality of droplets is stabilized in position within a region of the collecting container. The inventions enable partitioning of samples for digital analyses at unprecedented rates, where readout of signals from targets within such partitions can still be achieved in accordance with various assays.

Systems and methods for generating droplets and performing digital analyses

This disclosure provides for devices, methods, and systems for performing a non-invasive prenatal testing (NIPT) digital assay upon generating at least a large number of counts per chromosome for a set of chromosomes present in a sample, where performing the NIPT digital assay can include: distributing nucleic acids of the sample and materials for an amplification reaction across a plurality of partitions; amplifying the nucleic acids with the materials, within the plurality of partitions; and generating counts per chromosome upon detecting signals from the plurality of partitions. The inventions enable processing of samples for NIPT digital analyses and/or other digital analyses involving other loci of interest, with unprecedented partitioning, reaction, readout, and analytical performance.

Detection and digital quantitation of multiple targets

Compositions, methods and kits are disclosed for high-sensitivity single molecule digital counting by the stochastic labeling of a collection of identical molecules by attachment of a diverse set of labels. Each copy of a molecule randomly chooses from a non-depleting reservoir of diverse labels. Detection may be by a variety of methods including hybridization based or sequencing. Molecules that would otherwise be identical in information content can be labeled to create a separately detectable product that is unique or approximately unique in a collection. This stochastic transformation relaxes the problem of counting molecules from one of locating and identifying identical molecules to a series of binary digital questions detecting whether preprogrammed labels are present. The methods may be used, for example, to estimate the number of separate molecules of a given type or types within a sample.

Digital counting of individual molecules by stochastic attachment of diverse labels

The disclosure provides compositions, methods, and systems for implementation of highly multiplexed molecular diagnostic assays involving color combinatorics, stimulus-responsive probes, tandem probes, conjugated polymer probes, and other mechanisms for increasing the number of targets that can be simultaneously detected in a digital assay. Multiplexed detection of targets is achieved in a rapid manner, with respect to sample partitioning and target detection using multiple color channels for detection. Implementation of methods described also achieve detection with significantly improved signal-to-noise ratio (SNR) values.

This disclosure provides for devices, methods, and systems for generating a plurality of droplets within a collecting container at an extremely high rate (e.g., of at least 1 million droplets per minute, etc.), the plurality of droplets generated from an aqueous mixture comprising a set of single cells and a set of functionalized particles configured for a single cell assay. Upon generation, the plurality of droplets can be stabilized in position within a region of the collecting container, thereby providing a single-tube workflow for single cell analyses. Further, compositions implemented are structured to allow for overloading of partitions with functionalized particles, such that partitioned single-cells are co-localized with a subset of functionalized particles in a manner that allows for discernable tagging and downstream analyses.

Compositions, methods, and systems for single cell barcoding and sequencing

The disclosure provides for methods, compositions, and kits for multiplex nucleic acid analysis of single cells. The methods, compositions and systems may be used for massively parallel single cell sequencing. The methods, compositions and systems may be used to analyze thousands of cells concurrently. The thousands of cells may comprise a mixed population of cells (e.g., cells of different types or subtypes, different sizes).

Massively parallel single cell analysis

Methods, kits and systems are disclosed for analyzing one or more molecules in a sample. Analyzing the one or more molecules may comprise quantitation of the one or more molecules. Individual molecules may quantitated by PCR, arrays, beads, emulsions, droplets, or sequencing. Quantitation of individual molecules may further comprise stochastic labeling of the one or more molecules with a plurality of oligonucleotide tags to produce one or more stochastically labeled molecules. The methods may further comprise amplifying, sequencing, detecting, and/or quantifying the stochastically labeled molecules. The molecules may be DNA, RNA and/or proteins.

Compositions and kits for molecular counting

The invention(s) cover a composition, where units of the composition are configured to interact with each other (e.g., as neighbors) in order enable decoding of positions of captured target material relative to neighboring units of the composition. In embodiments, the composition includes: a body; and a set of molecules coupled to the body, the set of molecules comprising a first subset and a second subset, wherein the first subset is structured for target analyte capture, and wherein the second subset is structured for interactions with one or more neighboring objects. The invention(s) also cover systems incorporating one or more units of the composition and methods implementing units of the composition.

Methods, compositions, and systems for mapping locations of single molecules in multi-dimensional space

The inventions cover systems and methods for generation of emulsions having suitable clarity without requiring refractive index matching between emulsion components. Systems can include: a substrate including a set of openings; a reservoir facing the substrate at a first side and containing a sample fluid configured for droplet formation upon interacting with the set of openings of the substrate; and a collecting container facing the substrate at a second side and containing a set of fluid layers configured with a density gradient and suitable immiscibility characteristics. One or more components of the system(s) can support methods for emulsion generation, in relation to enabling interactions between multiple continuous phases and a dispersed droplet phase to generate clear emulsions. Applications of the inventions(s) can include performance of droplet-based digital PCR in an improved manner (e.g., without requiring implementation of correction factors based upon Poisson statistics).

Systems and methods for generation of emulsions with suitable clarity with applications of use

Growing community of inventors

Palo Alto, CA, United States of America

Stephen P A Fodor