Affymetrix, Inc.

Xiaojun Di

Earl A Hubbell

Rui Mei

Simon Cawley

Hajime Matsuzaki

Teresa A Webster

Keith W Jones

Richard Chiles

Gregory Marcus

Guoying Liu

Geoffrey Yang

Wei-min Liu

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 and computer software products are provided for analyzing gene expression data. In one embodiment, methods, systems and computer software are provided for comparative gene expression analysis using intensity dependent normalization factors.

System and computer software products for comparative gene expression analysis

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Cupertino, CA, United States of America

Xiaojun Di