Affymetrix, Inc.

Xiaohua C Huang

Robert J Lipshutz

Stephen P A Fodor

Mark S Chee

Earl A Hubbell

Maureen T Cronin

Charles Garrett Miyada

Edward L Sheldon

Peter E Lobban

MacDonald S Morris

Stephen P Fodor

Paul Kaplan

William J Dower

Dennis Solas

Thomas R Gingeras

Macdonald S Morris

Thomas B Ryder

Stephen Pa Fodor

Tom Ryder

Nila Shah

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

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

Devices and techniques for hybridization of nucleic acids and for determining the sequence of nucleic acids. Arrays of nucleic acids are formed by techniques, preferably high resolution, light-directed techniques. Positions of hybridization of a target nucleic acid are determined by, e.g., epifluorescence microscopy. Devices and techniques are proposed to determine the sequence of a target nucleic acid more efficiently and more quickly through such synthesis and detection techniques.

Identifying a base in a nucleic acid

A method for determining the genotype of one or more individuals at a polymorphic locus employs amplification of a region of DNA using primers containing tags and hybridization of the products to one or more probes on a solid support. The genotype or ratio of alleles is identified from the pattern of hybridization. The method can also be used to determine the frequency of different alleles in a population.

Identification of alleles

The present invention provides a number of oligonucleotide sequences which can be used for a wide variety of analyses applicable to the diverse fields impacted by the nature of molecular interaction, including chemistry, biology, medicine, and medical diagnostics. In certain embodiments these oligonucleotides may be used as probes to be used in, for example, gene expression analysis.

Oligonucleotides

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

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

A method for determining the genotype of one or more individuals at a polymorphic locus employs amplification of a region of DNA, labeling of allele-specific extension primers containing tags, and hybridization of the products to an array of probes. The genotype is identified from the pattern of hybridization. The method can also be used to determine the frequency of different alleles in a population.

Allele detection using primer extension with sequence-coded identity tags

Hybridization and sequencing of nucleic acids using base pair mismatches

Probe kit for identifying a base in a nucleic acid

The invention provides arrays of immobilized probes, and methods employing the arrays, for detecting mutations in the CFTR gene.

Growing community of inventors

Mountain View, CA, United States of America

Xiaohua C Huang