Roche Nimblegen, Inc.

Ventana Medical Systems, Inc.

Roche Diagnostics Gmbh

F. Hoffmann-la Roche Ag

Nimblegen Systems Gmbh

Todd Richmond

Matthew Rodesch

Roland D Green

Thomas J Albert

Klaus-Peter Stengele

Emile Nuwaysir

Jason Norton

Tom Albert

Kate Nuwaysir

Steven W Smith

Jeffrey Jeddeloh

Thomas Albert

Jacob Kitzman

Michael Molla

Christina Middle

Mark D'Ascenzo

Jochen Bühler

Markus Ott

Jochen Buehler

Emile F Nuwaysir

Jeff Jeddeloh

Roland Green

Mark D'ASCENZO

An oligopeptide microarray and methods for the synthesis thereof are presented. Further presented is a microarray on a solid support comprising at least about 10,000 oligopeptide features per cmand preferably at least about 50,000 oligopeptide features per cm.

Methods for synthesis of an oligopeptide microarray

The present invention provides methods for optimizing oligonucleotide hybridization probes for use in basic and clinical research. Specifically, the invention involves hybridizing serially diluted genomic sample to the oligonucleotide probes on the array, such that a signal intensity is produced for each of the probes; computationally identifying optimized probes which exhibit signal intensities that correspond to the serial dilutions of genomic sample and are reproducibly strong relative to non-optimized probes.

Optimized probe selection method

The present invention relates to a microarray comprising at least 50,000 oligopeptide features per cmwhere the oligopeptide features represent at least 50%, 60%, 70%, 80%, 90%, 95%, 99%, or 100% of the proteome of a virus or an organism. The present invention further relates to methods for the synthesis of such microarrays and methods of using microarrays comprising at least 50,000 oligopeptide features per cm. In an embodiment of the invention, the oligopeptide features represent proteins expressed in the same species, wherein the oligopeptide features are presented in a tiling pattern representing at least about 5,000 to-at least about 25,000 proteins expressed in a species. In some embodiments, the oligopeptide microarray features represent proteins expressed in the same species, wherein the microarray features are present in a tiling pattern that represents at least about 5,000 to at least about 50,000 expressed proteins.

Whole proteome tiling microarrays

The present invention provides methods and compositions for the enrichment of target nucleic acids in a microarray system. In particular, the present invention provides methods and compositions for uniform enrichment of target nucleic acid molecules in a microarray format. The present invention also provides for intentionally non-uniform enrichment among target nucleic acid molecules.

Methods and systems for uniform enrichment of genomic regions

The present invention is a method to assist in the identification of single nucleotide polymorphisms (SNP) from microarray hybridization data. Data from hybridization protocols run on microarrays often have variations in the data resulting from variations in hybridization conditions and efficiencies and variations in optical intensities. An algorithm is described to screen the results to identify those data points most likely to be real SNPs as opposed to variations in the hybridization or sensing data.

Computer software to assist in identifying SNPS with microarrays

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Madison, WI, United States of America

Todd Richmond