Affymetrix, Inc.

Syntex (u.s.a.) Inc.

Dade Behring Marburg Gmbh

Behringwerke Aktiengesellschaft

Other

Charles Garrett Miyada

Maureen T Cronin

Mark S Chee

Earl A Hubbell

Robert J Lipshutz

Edward L Sheldon

Peter E Lobban

Xiaohua C Huang

Stephen P A Fodor

MacDonald S Morris

Arthur C Switchenko

Melanie W Quong

Man-Ying Laurie Wong

Glenn H McGall

John E Blume

Alan J Williams

Christopher Allen Davies

Shivani Nautiyal

Yanxiang Cao

Eric B Schell

Gangwu Mei

Thomas R Gingeras

Jennifer Dee Tan

Teresa L Born

Duc Do

Kevin L Gunderson

Stephen P Fodor

Mark O Trulson

Kai Wu

Ali Laayoun

Qing Yang

Macdonald S Morris

Carsten Rosenow

Claire Robinson

Michelle Oval

Nila Shah

Fred C Christians

Arrays for genome-wide analysis of methylation are disclosed. In a preferred aspect arrays comprising a plurality of probes complementary to a plurality of identified CpG islands in the human, mouse and rat genome are disclosed. The arrays may be used to detect methylation within CpG islands in samples from human, mouse and rat genomes.

Analysis of methylation using nucleic acid arrays

Arrays for genome-wide analysis of methylation are disclosed. IN a preferred aspect arrays comprising a plurality of probes complementary to a plurality of identified CpG islands in the human, mouse and rat genome are disclosed. The arrays may be used to detect methylation within cpG islands in samples from human, mouse and rat genomes.

The invention provides arrays of immobilized probes, and methods employing the arrays, for detecting mutations in the biotransformation genes, such as cytochromes P450. For example, one such array comprises four probe sets. A first probe set comprises a plurality of probes, each probe comprising a segment of at least three nucleotides exactly complementary to a subsequence of a reference sequence from a biotransformation gene, the segment including at least one interrogation position complementary to a corresponding nucleotide in the reference sequence. Second, third and fourth probe sets each comprise a corresponding probe for each probe in the first probe set. The probes in the second, third and fourth probe sets are identical to a sequence comprising the corresponding probe from the first probe set or a subsequence of at least three nucleotides thereof that includes the at least one interrogation position, except that the at least one interrogation position is occupied by a different nucleotide in each of the four corresponding probes from the four probe sets.

Arrays of nucleic acid probes for analyzing biotransformation genes

Oligonucleotide analogue arrays attached to solid substrates and methods related to the use thereof are provided. The oligonucleotide analogues hybridize to nucleic acids with either higher or lower specificity than corresponding unmodified oligonucleotides. Target nucleic acids which comprise nucleotide analogues are bound to oligonucleotide and oligonucleotide analogue arrays.

Modified nucleic acid probes

The invention provides methods of comparing a target nucleic acid with a reference nucleic acid using nucleic acid arrays.

Method of comparing a target nucleic acid and a reference nucleic acid

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

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

A process is provided for labeling with signal amplification a ribonucleic acid (RNA), comprising fragmenting the RNA to form RNA fragments, fixing a first ligand to a terminal phosphate located at least one of the 3&prime; end and the 5&prime; end of each of a plurality of the RNA fragments, the terminal phosphate having been released during the fragmentation, and binding a plurality of labeling agents to the first ligand on each of a plurality of the fragments.

Process for labeling a ribonucleic acid, and labeled RNA fragments which are obtained thereby

The invention provides methods for detecting variations in polymorphic sites and/or variations in gene copy number. The methods are particularly useful for analysis of biotransformation genes, such as cytochromes P450.

Analysis of genetic polymorphisms and gene copy number

A D-arabinitol dehydrogenase enzyme is disclosed. The enzyme is capable of catalyzing the oxidation of D-arabinitol and substantially incapable of catalyzing the oxidation of D-mannitol and is substantially free of other enzymes capable of oxidizing D-mannitol. Also disclosed are methods for determining D-arabinitol. In one embodiment the method comprises the steps of providing in combination (1) a medium suspected of containing D-arabinitol and (2) a D-arabinitol dehydrogenase enzyme and examining the medium for the product of the oxidation of the D-arabinitol. The enzyme utilized is capable of catalyzing the oxidation of D-arabinitol and substantially incapable of catalyzing the oxidation of D-mannitol. Kits for conducting the present method are also disclosed.

Method for detecting candida infection

The invention provides arrays of immobilized probes, and methods employing the arrays, for detecting mutations in the biotransformation genes, such as cytochromes P450. For example, one such array comprises four probe sets. A first probe set comprises a plurality of probes, each probe comprising a segment of at least three nucleotides exactly complementary to a subsequence of a reference sequence from a biotransformation gene, the segment including at least one interrogation position complementary to a corresponding nucleotide in the reference sequence. Second, third and fourth probe sets each comprise a corresponding probe for each probe in the first probe set. The probes in the second, third and fourth probe sets are identical to a sequence comprising the corresponding probe from the first probe set or a subsequece of at least three nucleotides thereof that includes the at least one interrogation position, except that the at least one interrogation position is occupied by a different nucleotide in each of the four corresponding probes from the four probe sets.

Arrays of nucleic acid probes for analyzing biotransformation genes and methods of using the same

Method for detecting Candida infection

Growing community of inventors

San Jose, CA, United States of America

Charles Garrett Miyada