Affymetrix, Inc.

Teresa A Webster

Rui Mei

Shantanu V Kaushikkar

Linda McAllister

Earl A Hubbell

Simon Cawley

Hajime Matsuzaki

Xiaojun Di

David J Lockhart

Keith W Jones

MacDonald S Morris

Richard Chiles

Michael P Mittmann

Luis Jevons

Derek H Bernhart

Gregory Marcus

Ming-Hsiu Ho

Mei-Mei Shen

Guoying Liu

Geoffrey Yang

Eugene Wang

Ali Pirani

Methods for processing data using information gained from examining biological materials identifies and characterized probes for Single Nucleotide Polymorphisms and identifies Off Target Variants.

Systems and methods for SNP characterization and identifying off target variants

A computer program product, and related systems and methods, are described that processes emission intensity data corresponding to probes of a biological probe array. The computer program includes a genotype and statistical analysis manager that determines absolute or relative expression values based, at least in part, on a statistical measure of the emission intensity data and at least one user-selectable statistical parameter. The analysis manager may also determine genotype calls for one or more probes based, at least in part, on the emission intensity data. The analysis manager may further display the absolute or relative expression values based, at least in part, on at least one user-selectable display parameter and/or a measure of normalized change between genotype calls. The measure of normalized change may be based, at least in part, on a comparison of genotype calls and a reference value.

System, method, and computer software for the presentation and storage of analysis results

The invention relates to the selection of a collection of relevant single nucleotide polymorphisms across a genome to design a nucleic acid probe array. As such, the invention relates to diverse fields impacted by the nature of genetics, including biology, medicine, and medical diagnostics.

Methods for selecting a collection of single nucleotide polymorphisms

Methods, kits and arrays of nucleic acid probes for genotyping large numbers of human SNPs in parallel are provided. A set of more than 100,000 human SNPs, known to be biallelic in at least two populations is provided. Allele specific perfect match probes and genotyping probe sets are provided for each allele of each biallelic SNP in a set of human SNPs that is useful for genetic analysis within and across populations. Probe sets that include perfect match and mismatch probes are provided. The probe sets are suitable for inclusion in an array. The invention provides the SNP and surrounding sequence and provides the sequences in such a way as to make them available for a variety of analyses including genotyping. As such, the invention relates to diverse fields impacted by the nature of genetics, including biology, medicine, and medical diagnostics.

Methods for genotyping polymorphisms in humans

Methods, systems and computer software products are provided for determining genotype of a sample using a plurality of probes. In one preferred embodiment, a tentative genotype call is made based upon the relative allele signals. Pattern recognition is then used to validate the tentative call.

System, method, and computer software for genotyping analysis and identification of allelic imbalance

A computer program product, and related systems and methods, are described that processes emission intensity data corresponding to probes of a biological probe array. The computer program includes a genotype and statistical analysis manager that determines absolute or relative expression values based, at least in part, on a statistical measure of the emission intensity data and at least one user-selectable statistical parameter. The analysis manager may also determine genotype calls for one or more probes based, at least in part, on the emission intensity data, The analysis manager may further display the absolute or relative expression values based, at least in part, on at least one user-selectable display parameter and/or a measure of normalized change between genotype calls. The measure of normalized change may be based, at least in part, on a comparison of genotype calls and a reference value.

Method, system, and computer software for the presentation and storage of analysis results

Computer software for genotyping analysis using pattern recognition

Systems and methods for detecting monomer changes in a sample when an unknown quantity of expected monomers may also be present. Homogeneous and heterogeneous samples are exposed to polymer probes for hybridization. The hybridization affinities of the polymer probes to the samples are then compared to determine differences between the polymers in the samples. Accordingly, deletion, substitution and insertion mutations may be detected in a heterogeneous sample of nucleic acids.

Products and methods for analyzing nucleic acids including identification of substitutions, insertions and deletions

Computer-aided techniques for analyzing biological sequences like nucleic acids are provided. The computer system may analyze hybridization intensities indicating hybridization affinity between nucleic acid probes and a sample nucleic acid sequence in order to call bases in the sample sequence. Multiple base calls may be combined to form a single base call. Additionally, the computer system may analyze hybridization intensities in order to monitor gene expression or the change in gene expression as compared to a baseline.

Computer-aided techniques for analyzing biological sequences

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Loma Mar, CA, United States of America

Teresa A Webster