Affymetrix, Inc.

The Salk Institute Biotechnology Industrial Associates, Inc.

Affymetric, Inc.

Thomas R Gingeras

Mark S Chee

Robert J Lipshutz

Ronald J Sapolsky

David J Lockhart

Gordon G Wong

Macdonald S Morris

Eugene L Brown

Lubert Stryer

Maureen T Cronin

Charles Garrett Miyada

David H Mack

Anthony J Berno

Ghassan Ghandour

Ching Wang

Glenn H McGall

Mark O Trulson

MacDonald S Morris

Claire Robinson

Kevin L Gunderson

Stephen P A Fodor

Earl A Hubbell

Stephen P Fodor

Thomas E Shenk

Edward L Sheldon

Kai Wu

Peter E Lobban

Qing Yang

Xiaohua C Huang

Duc Do

Hua Zhu

Carsten Rosenow

Deborah Y Kwoh

Michelle Oval

Earl A Hubble

Nila Shah

Jorg Drenkow

Garry Miyada

Michelle Smedsrud-Oval

Fred C Christians

The present invention relates to novel methods for sequencing and mapping genetic markers in polynucleotide sequences using Type-IIs restriction endonucleases. The methods herein described result in the 'capturing' and determination of specific oligonucleotide sequences located adjacent to Type-IIs restriction sites. The resulting sequences are useful as effective markers for use in genetic mapping, screening and manipulation.

Capturing sequences adjacent to type-IIs restriction sites for genomic library mapping

Capturing sequences adjacent to type-IIS restriction sites for genomic library mapping

This invention provides oligonucleotide based arrays and methods for speciating and phenotyping organisms, for example, using oligonucleotide sequences based on therpoB gene. The groups or species to which an organism belongs may be determined by comparing hybridization patterns of target nucleic acid from the organism to hybridization patterns in a database.

Chip-based speciation and phenotypic characterization of microorganisms

The invention provides chips of immobilized probes, and methods employing the chips, for comparing a reference polynucleotide sequence of known sequence with a target sequence showing substantial similarity with the reference sequence, but differing in the presence of e.g., mutations.

Arrays of nucleic acid probes on biological chips

This invention provides polynucleotide probes, sequences and methods for speciating and phenotyping organisms, for example, using probes based on therpoB gene. The groups or species to which an organism belongs may be determined by comparing hybridization patterns of target nucleic acid from the organism to hybridization patterns in a database.

Mycobacterial rpoB sequences

Certain human genes have been found to be induced or repressed in host cells infected with HCMV. A large set of such genes has been identified. These have diagnostic use in determining the extent of tissue damage caused by the infection as well as in determining the stage of disease progression of the HCMV infection. Such genes are likely those involved in mediating the pathology of the infected tissues. Thus by identifying agents which are able to reverse the induction or repression of such genes, one can find candidate therapeutic agents for use in treating and or preventing HCMV-caused disease pathologies.

Expression monitoring for human cytomegalovirus (HCMV) infection

This invention provides methods of monitoring the expression levels of a multiplicity of genes. The methods involve hybridizing a nucleic acid sample to a high density array of oligonucleotide probes where the high density array contains oligonucleotide probes complementary to subsequences of target nucleic acids in the nucleic acid sample. In one embodiment, the method involves providing a pool of target nucleic acids comprising RNA transcripts of one or more target genes, or nucleic acids derived from the RNA transcripts, hybridizing said pool of nucleic acids to an array of oligonucleotide probes immobilized on surface, where the array comprising more than 100 different oligonucleotides and each different oligonucleotide is localized in a predetermined region of the surface, the density of the different oligonucleotides is greater than about 60 different oligonucleotides per 1 cm, and the olignucleotide probes are complementary to the RNA transcripts or nucleic acids derived from the RNA transcripts; and quantifying the hybridized nucleic acids in the array.

Expression monitoring by hybridization to high density oligonucleotide arrays

This invention provides oligonucleotide based arrays and methods for speciating and phenotyping organisms, for example, using oligonucleotide sequences based on thegene. The groups or species to which an organism belongs may be determined by comparing hybridization patterns of target nucleic acid from the organism to hybridization patterns in a database.

Chip-based species identification and phenotypic characterization of microorganisms

This invention provides nucleic acid affinity matrices that bear a large number of different nucleic acid affinity ligands allowing the simultaneous selection and removal of a large number of preselected nucleic acids from the sample. Methods of producing such affinity matrices are also provided. In general the methods involve the steps of a) providing a nucleic acid amplification template array comprising a surface to which are attached at least 50 oligonucleotides having different nucleic acid sequences, and wherein each different oligonucleotide is localized in a predetermined region of said surface, the density of said oligonucleotides is greater than about 60 different oligonucleotides per 1 cm , and all of said different oligonucleotides have an identical terminal 3&prime; nucleic acid sequence and an identical terminal 5&prime; nucleic acid sequence. b) amplifying said multiplicity of oligonucleotides to provide a pool of amplified nucleic acids; and c) attaching the pool of nucleic acids to a solid support.

Nucleic acid affinity columns

This invention provides methods of performing nucleic acid hybridization assays on high-density substrate-bound oligonucleotide arrays involving including in the hybridization mixture an isostabilizing agent, a denaturing agent or a renaturation accelerant.

Hybridization assays on oligonucleotide arrays

The presently claimed invention provides methods, compositions, and apparatus for studying nucleic acids. Specifically, the present invention provides a novel enrichment and labeling strategy for ribonucleic acids. In one embodiment, the invention provides enriching for a population of interest in a complex population by diminishing the presence of a target sequence. In a further embodiment, the invention can be used to reproducibly label and detect extremely small amounts of nucleic acids.

Preparation of nucleic acid samples

This invention provides methods of monitoring the expression levels of a multiplicity of genes. The methods involve hybridizing a nucleic acid sample to a high density array of oligonucleotide probes where the high density array contains oligonucleotide probes complementary to subsequences of target nucleic acids in the nucleic acid sample. In one embodiment, the method involves providing a pool of target nucleic acids comprising RNA transcripts of one or more target genes, or nucleic acids derived from the RNA transcripts, hybridizing said pool of nucleic acids to an array of oligonucleotide probes immobilized on surface, where the array comprising more than 100 different oligonucleotides and each different oligonucleotide is localized in a predetermined region of the surface, the density of the different oligonucleotides is greater than about 60 different oligonucleotides per 1 cm , and the olignucleotide probes are complementary to the RNA transcripts or nucleic acids derived from the RNA transcripts; and quantifying the hybridized nucleic acids in the array.

Methods of identifying nucleic acid probes to quantify the expression of a target nucleic acid

The present invention relates to novel methods for sequencing and mapping genetic markers in polynucleotide sequences using Type-IIs restriction endonucleases. The methods herein described result in the &ldquo;capturing&rdquo; and determination of specific oligonucleotide sequences located adjacent to Type-IIs restriction sites. The resulting sequences are useful as effective markers for use in genetic mapping, screening and manipulation.

Methods for analyzing nucleic acids using a type IIs restriction endonuclease

Nucleic acid affinity matrices that bear a large number of different nucleic acid affinity ligands allowing the simultaneous selection and removal of a large number of preselected nucleic acids from the sample. Methods of producing such affinity matrices are also provided. In general the methods involve the steps of a) providing a nucleic acid amplification template array comprising a surface to which are attached at least 50 oligonucleotides having different nucleic acid sequences, and wherein each different oligonucleotide is localized in a predetermined region of the surface, the density of the oligonucleotides is greater than about 60 different oligonucleotides per 1 cm , and all of the different oligonucleotides have an identical terminal 3&prime; nucleic acid sequence and an identical terminal 5&prime; nucleic acid sequence. b) amplifying the multiplicity of oligonucleotides to provide a pool of amplified nucleic acids; and c) attaching the pool of nucleic acids to a solid support.

Expression monitoring by hybridization to high density nucleic acid arrays

Growing community of inventors

Santa Clara, CA, United States of America

Thomas R Gingeras