Rosetta Inpharmatics, Inc.

Microsoft Technology Licensing, LLC

Agilent Technologies, Inc.

Matthew Marton

Roland Stoughton

Carol T Schembri

Mel N Kronick

John S Hinchcliffe

Barnett E Saunders

Allan Jones

Dianne Rees

Michael Meyer

This invention provides methods for determining drug specificity, therapeutic index and effective doses for individual patients. According to the methods of the invention, graded levels of drug are applied to a biological sample or a patient. A plurality of cellular constituents are measured to determine the activity of the drug on a target pathway and at least one off-target pathway. A drug specificity is determined by comparing the target and off target activities of the drug. A therapeutic concentration (or dose) is defined as a concentration (or dose) of the drug that induces certain response in the target pathway. A toxic concentration (or dose) is defined as a concentration (or dose) of the drug that induces certain response in the off target pathway. Therapeutic index is the ratio of the toxic concentration over therapeutic concentration. Methods are also provided to determine an effective dose of a drug for a patient by measuring the activity of the drug on the particular patient.

Methods for determining therapeutic index from gene expression profiles

Methods and devices are disclosed for microarray analysis. In one embodiment a method is disclosed for processing a non-standard size slide having an array of chemical compounds attached to a surface of the slide. A sample is exposed to the surface of the non-standard size slide wherein components in the sample bind to the chemical compounds on the surface of the slide. The sample and the slide are incubated under conditions for carrying out the binding reactions, and the surface of the non-standard size slide is examined for the results of the binding reactions. Prior to the exposing step or the incubating step or the examining step, the non-standard size slide is placed into a slide holder comprising a slide-holding section a slide-holding section adapted to dispose the non-standard size slide to a processing instrument in a manner similar to that for a standard size slide. The non-standard size slide may also include an identifier such as a bar code.

Manufacture and use of non-standard size microarray slides

The present invention relates to methods and compositions for assessing the quality of microarrays. In particular, the invention relates to the use of quality control probes that are synthesized on the microarray monomer by monomer in a step-by-step synthesis. By assessing the degree of signal from the quality control probes and determining their deviation from expected signal intensities, the quality of microarray synthesis can be ascertained. The invention further relates to a method of detecting defects occurring during storage or processing of the microarray. The invention further relates to a method of using a computer to identify microarrays that have had a defect or defects during synthesis, storage, or processing.

Methods to assess quality of microarrays

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Matthew Marton