Lynx Therapeutics, Inc.

Population Genetics Technologies Ltd.

10x Genomics, Inc.

The Scripps Research Institute

Spectragen, Inc.

Illumina Corporation

Solexa, Inc.

Compass Genetics, LLC

E.i. Dupont De Nemours and Company

Medical Research Council

Combichem, Inc.

The Molecular Sciences Institute, Inc.

Campass Genetics LLC

Population Genetics Technologies Litd.

Sydney Brenner

Robert Osborne

Gi Mikawa

Andrew Slatter

Michael C Pallas

George Stefan Golda

John Bridgham

Glenn Albrecht

Kevin P Corcoran

Robert B Dubridge

James Casbon

Andreas Claas

Conrad Lichtenstein

Stephen C Macevicz

Richard A Lerner

Kim D Janda

Hiroko Maruyama

Ichiro Maruyama

Sergei M Gryaznov

Sarah N McCurdy

David H Lloyd

Rongdian Fu

Kenneth J Livak

Andre Rosenthal

Aspects of the present invention include analyzing nucleic acids from single cells using methods that include using tagged polynucleotides containing multiplex identifier sequences.

Methods for analyzing nucleic acids

Methods for analyzing nucleic acids from single cells

Aspects of the present invention include methods and compositions for determining the number of individual polynucleotide molecules originating from the same genomic region of the same original sample that have been sequenced in a particular sequence analysis configuration or process. In these aspects of the invention, a degenerate base region (DBR) is attached to the starting polynucleotide molecules that are subsequently sequenced (e.g., after certain process steps are performed, e.g., amplification and/or enrichment). The number of different DBR sequences present in a sequencing run can be used to determine/estimate the number of different starting polynucleotides that have been sequenced. DBRs can be used to enhance numerous different nucleic acid sequence analysis applications, including allowing higher confidence allele call determinations in genotyping applications.

Increased confidence of allele calls with molecular counting

Aspects of the present invention are drawn to processes for moving a region of interest in a polynucleotide from a first position to a second position with regard to a domain within the polynucleotide, also referred to as a 'reflex method'. In certain embodiments, the reflex method results in moving a region of interest into functional proximity to specific domain elements present in the polynucleotide (e.g., primer sites and/or multiplex identifier). Compositions, kits and systems that find use in carrying out the reflex processes described herein are also provided.

Compositions and methods for intramolecular nucleic acid rearrangement

An apparatus and system are provided for simultaneously analyzing a plurality of analytes anchored to microparticles. Microparticles each having a uniform population of a single kind of analyte attached are disposed as a substantially immobilized planar array inside of a flow chamber where steps of an analytical process are carried out by delivering a sequence of processing reagents to the microparticles by a fluidic system under microprocessor control. In response to such process steps, an optical signal is generated at the surface of each microparticle which is characteristic of the interaction between the analyte carried by the microparticle and the delivered processing reagent. The plurality of analytes are simultaneously analyzed by collecting and recording images of the optical signals generated by all the microparticles in the planar array. A key feature of the invention is the correlation of the sequence of optical signals generated by each microparticle in the planar array during the analytical process.

System and apparatus for sequential processing of analytes

The invention provides methods and compositions for attaching oligonucleotide tags to polynucleotides for the purpose of carrying out analytical assays in parallel and for decoding the oligonucleotide tags of polynucleotides selected in such assays. Words, or subunits, of oligonucleotide tags index submixtures in successively more complex sets of submixtures (referred to herein as 'tiers' of submixtures) that a polynucleotide goes through while successive words are added to a growing tag. By identifying each word of an oligonucleotide tag, a series of submixtures is identified including the first submixture that contains only a single polynucleotide, thereby providing the identity of the selected polynucleotide. The analysis of the words of an oligonucleotide tag can be carried out in parallel, e.g. by specific hybridization of the oligonucleotide tag to its tag complement on an addressable array; or such analysis can be carried out serially by successive specific hybridizations of labeled word complements, or the like.

Methods and compositions for tagging and identifying polynucleotides

Aspects of the present invention are drawn to processes for moving a region of interest in a polynucleotide from a first position to a second position with regard to a domain within the polynucleotide, also referred to as a 'reflex method'. In certain embodiments, the reflex method results in moving a region of interest into functional proximity to specific domain elements present in the polynucleotide (e.g., primer sites and/or multiplex indentifier). Compositions, kits and systems that find use in carrying out the reflex processes described herein are also provided.

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Ely, United Kingdom

Sydney Brenner