Affymetrix, Inc.

Perlegen Sciences, Inc.

Genetic Technologies Limited

Anthony J Berno

Mark S Chee

Ghassan Ghandour

Lubert Stryer

Thomas R Gingeras

David H Mack

Ching Wang

David R Cox

Nila Patil

David A Hinds

David J Balaban

Huu Minh Tran

Thomas B Ryder

Vincent E Phillips

Robert Yang

Joyti Baid

The present invention relates to methods for identifying variations that occur in the human genome and relating these variations to the genetic basis of disease and drug response. In particular, the present invention relates to identifying individual SNPs, determining SNP haplotype blocks and patterns, and, further, using the SNP haplotype blocks and patterns to dissect the genetic bases of disease and drug response. The methods of the present invention are useful in whole genome analysis.

Computer systems and methods for genomic analysis

The invention provides novel human mitochondrial polymorphisms, and probes and primers for detecting the same. Detection of such polymorphisms is useful in a variety of fields such as forensic analysis, epidemiology and preventive medicine.

Polymorphisms in human mitochondrial DNA

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

An interactive and dynamic data analysis tool that helps interactive analysis in real time on medium size datasets having complex structure is described. In one aspect, the data analysis tool is capable of being configured to act as a data producer tool arranged to provide a data source. The data analysis tool can also be configured as a data consumer tool capable of receiving and processing a particular data source. The data source tool and the data consumer tool are connected together to form a framework that takes the form of a data mapping context that mediates the data provided by the data source and a particular data role.

Architecture for developing and reusing analytic and visualization components and methods of use thereof

Methods for genomic analysis

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

A schema-isolated system is disclosed for developing, modifying, or maintaining client applications that accesses target databases. The system includes a middleware-table inserter that inserts middleware tables into the target database. The middleware tables include a set of compatibility data relating one or more client-application data requests with one or more corresponding target-database data capabilities. The middleware tables also include a data communication component. This component receives a client-application data request from the client application, and, based on at least a first datum of the set of compatibility data, provides to the client application the one or more target-database data capabilities corresponding to the client-application data request. The first compatibility datum relates the one or more client-application data requests with the one or more corresponding target-database data capabilities based, at least in part, on an application-usage-independent criterion. An application-usage-independent criterion may be a syntax criterion, a configuration criterion, or a component-usage criterion. The first compatibility datum may include at least one SQL query. The at least one target database may be a relational database.

System, method, and product for development and maintenance of database-related software applications

Systems and methods for detecting differences in sample polymers, such as nucleic acid sequences, are provided. Hybridization affinity information for the sample polymers is clustered so that the differences, if any, between or among the sample polymers can be readily identified. By clustering the hybridization affinity information of the sample polymers, differences in the sample polymers can be accurately achieved even in the presence of random and systematic errors.

Polymorphism detection utilizing clustering analysis

Systems and methods for organizing information relating to study of polymorphisms. A database model is provided which interrelates information about one or more of, e.g, subjects from whom samples are extracted, primers used in extracting the DNA from the subjects, about the samples themselves, about experiments done on samples, about particular oligonucleotide probe arrays used to perform experiments, about analysis procedures performed on the samples, and about analysis results. The model is readily translatable into database languages such as SQL. The database model scales to permit storage of information about large numbers of subjects, samples, experiments, chips, etc.

Method and system for providing a polymorphism database

This invention provides oligonucleotide based arrays and methods for speciating and phenotyping organisms, for example, using oligonucleotide sequences based on the,rpoB 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.

A genetic sample is analyzed by providing a gene probe array including a plurality of genetic probes having different receptors. The sample is processed to include at least one fluorescently tagged ligand. The array is hybridized by exposing the probes to the processed sample such that ligands can bind to complementary receptors. Composite data having a data dynamic range is obtained from the array using an optical scanner which has a scanner dynamic range that is smaller than the data dynamic range. The scanner optically irradiates and scans the probes and detects fluorescent emissions at a first wavelength which is selected such that the scanner produces valid first data in a low intensity portion of the data dynamic range and is in saturation in at least part of a high intensity portion of the data dynamic range. The scanner then optically irradiates and scans the probes with light and detects fluorescent emissions at a second wavelength which is selected such that the scanner produces valid second data in a high intensity portion of the data dynamic range and is in cutoff in at least part of a low intensity portion of the data dynamic range. A scale factor correlation function is calculated between the first data and the second data, and is applied to convert the second data to have a same scale factor as the first data. The first data for the first portion of the data dynamic range is combined with the converted second data for the second portion of the data dynamic range to obtain the composite data.

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San Jose, CA, United States of America

Anthony J Berno