Patents Assigned to Rosetta Inpharmatics LLC
-
Patent number: 7371516Abstract: The present invention provides materials and methods which may be used to evaluate one or more different probes and select probes that are optimized for sensitivity and specificity for a particular target. In particularly preferred embodiments, the methods and compositions of the invention can be used to evaluate polynucleotide probes having different nucleotide sequences. The methods and compositions thereby allow a user to select a polynucleotide probe, e.g., having a particular nucleotide sequence, that is optimized for sensitivity and/or for specificity for a particular target polynucleotide molecule. In particularly preferred embodiments, the methods and compositions can be used to evaluate a plurality of probes simultaneously, such as on a microarray. Probes evaluated according to the methods of the invention can be selected for and used to detect a variety molecules, including a variety of polynucleotides, such as genomic polynucleotides (e.g., genomic DNA) and genomic transcripts (e.g.Type: GrantFiled: July 14, 2000Date of Patent: May 13, 2008Assignee: Rosetta Inpharmatics LLCInventor: Julja Burchard
-
Publication number: 20070292878Abstract: In one aspect, the present invention provides methods for amplifying a microRNA molecule to produce DNA molecules. The methods each include the steps of: (a) using primer extension to make a DNA molecule that is complementary to a target microRNA molecule; and (b) using a universal forward primer and a reverse primer to amplify the DNA molecule to produce amplified DNA molecules. In some embodiments of the method, at least one of the forward primer and the reverse primer comprise at least one locked nucleic acid molecule.Type: ApplicationFiled: July 18, 2007Publication date: December 20, 2007Applicant: ROSETTA INPHARMATICS LLCInventor: Christopher Raymond
-
Patent number: 7294478Abstract: An apparatus and method are provided for shipping, storing, and high-throughput processing of microarrays. An exemplary microarray cartridge according to the present invention includes a body having a cavity defined by an outer surface and two dimple features in fluid communication with the cavity. The cavity includes at least one ledge for supporting a microarray of biological probes, and a reaction chamber defined at least in part by the ledge. A plate covers the cavity and sealingly attaches to the outer surface of the body. Ports in the plate or the dimple features allow introduction of sample, reaction and wash solutions into the reaction chamber such that the solutions contacts the probes on the microarray. The disposable microarray cartridges of the present invention are used to package and store microarrays prior to use and to process microarrays in a high-throughput manner. The footprint of the cartridge is designed to be compatible with standard robotic formats or standard re-formatting approaches.Type: GrantFiled: March 5, 2002Date of Patent: November 13, 2007Assignee: Rosetta Inpharmatics LLCInventor: John Hinchcliffe
-
Publication number: 20070255053Abstract: A random-primed reverse transcriptase-in vitro transcription method of linearly amplifying RNA is provided. According to the methods of the invention, source RNA (or other single-stranded nucleic acid), preferably, mRNA, is converted to double-stranded cDNA using two random primers, one of which comprises a RNA polymerase promoter sequence (“promoter-primer”), to yield a double-stranded cDNA that comprises a RNA polymerase promoter that is recognized by a RNA polymerase. Preferably, the primer for first-strand cDNA synthesis is a promoter-primer and the primer for second-strand cDNA synthesis is not a promoter-primer. The double-stranded cDNA is then transcribed into RNA by the RNA polymerase, optimally in the presence of a reverse transcriptase that is rendered incapable of RNA-dependent DNA polymerase activity during this transcription step. The subject methods produce linearly amplified RNA with little or no 3? bias in the sequences of the nucleic acid population amplified.Type: ApplicationFiled: May 7, 2007Publication date: November 1, 2007Applicant: ROSETTA INPHARMATICS LLCInventors: Michael Ziman, Colleen Davis
-
Publication number: 20070211928Abstract: An image processing system extracts parts or characteristics of interest from prepared biological samples One suitable use of the image processing system is to find biomarkers. But many other suitable uses are possible. Some components of the system include image preprocessing (data interpolation, retention time alignment, image noise filtering, background estimation, and formation of a composite image); image feature extraction (peaks, isotope groups, and charge groups); and computation of feature characteristics and expression statistics, differential expression, and non-differential expression. Outputs of the system include a candidate list of parts or characteristic of interest for aiding further discovery.Type: ApplicationFiled: November 13, 2006Publication date: September 13, 2007Applicant: Rosetta Inpharmatics LLCInventors: Lee Weng, Andrey Bondarenko, Silvia Vega, Ernst Henle, Brandon Hunt, Alexander Spiridonov
-
Patent number: 7269517Abstract: An experiment definition system that digitally represents an experiment design. The experiment definition provides the logical structure for data analysis of scans from one or more biological experiments. The experiment definition either directly reflects the experiment design in a one-to-one relationship, or the user customizes the experiment definition. Experiment definitions are stored as a set of instructions in a database of experiment definitions. A user interface for constructing the experiment definition, and for customizing one or more automated analysis pipelines for processing the experiment definitions.Type: GrantFiled: April 18, 2003Date of Patent: September 11, 2007Assignee: Rosetta Inpharmatics LLCInventor: Andrey Bondarenko
-
Publication number: 20070185656Abstract: Methods, computer program products and systems for identifying cellular constituents in a secondary tissue that serve as surrogate markers for a target gene expressed in a primary tissue of a species are provided. A classifier is constructed using cellular constituent abundances of cellular constituents in a first plurality of cellular constituents measured in the secondary tissue in a population. This population comprises a first and second subgroup. The classifier is based on a second plurality of cellular constituents that comprises all or a portion of the first plurality of cellular constituents. Abundance levels of each cellular constituent in the second plurality of cellular constituents varies between the first and second subgroup. All or portion of the population is classified into a plurality of subtypes using the classifier. Then, one or more cellular constituents that can discriminate members of the population between a first subtype and a second subtype in the plurality of subtypes are identified.Type: ApplicationFiled: May 28, 2004Publication date: August 9, 2007Applicant: ROSETTA INPHARMATICS LLCInventor: Eric Schadt
-
Patent number: 7254487Abstract: 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.Type: GrantFiled: April 2, 2001Date of Patent: August 7, 2007Assignee: Rosetta Inpharmatics LLCInventors: Matthew Marton, Roland Stoughton
-
Publication number: 20070166707Abstract: A method for confirming the association of a query QTL or a query gene in the genome of a second species with a clinical trait T exhibited by the second species. A first QTL or a first gene in a first species that is linked to a trait T? is found. The trait T? is indicative of trait T. A region of the genome of the first species that comprises the first QTL or the first gene is mapped to a particular region of the genome of the second species. A query QTL or a query gene in the second species that is potentially associated with the trait T is found. The potential association of the query QTL or the query gene with the clinical trait T is confirmed when the query QTL or the query gene is in the particular region of the genome of the second species.Type: ApplicationFiled: December 24, 2003Publication date: July 19, 2007Applicant: ROSETTA INPHARMATICS LLCInventors: Eric Schadt, Stephanie Monks, John Lamb
-
Publication number: 20070134660Abstract: In a first aspect, the invention provides methods for screening for modulators of a target protein, comprising the steps of contacting a target protein with a candidate agent and determining whether the candidate agent modulates the activity of the target protein, wherein the target protein comprises a sequence that has more than 80% amino acid sequence identity to KIF14 (SEQ ID NO:2) or the KIF14 motor domain (SEQ ID NO:3). In a second aspect, the invention provides methods for modulating cell proliferation comprising administering to a cell an effective amount of a modulator of the activity of a target protein. Some embodiments of this aspect provide methods for treating a subject with a cellular hyperproliferation disorder, such as cancer. In a third aspect, the invention provides methods for identifying candidate subjects for treatment with an inhibitor of the activity of a target protein.Type: ApplicationFiled: May 28, 2004Publication date: June 14, 2007Applicants: ROSETTA INPHARMATICS LLC, MERCK & CO., INC.Inventors: Mao Mao, Peter Linsley, Carolyn Buser, Christopher Marshall
-
Patent number: 7229765Abstract: A random-primed reverse transcriptase-in vitro transcription method of linearly amplifying RNA is provided. According to the methods of the invention, source RNA (or other single-stranded nucleic acid), preferably, mRNA, is converted to double-stranded cDNA using two random primers, one of which comprises a RNA polymerase promoter sequence (“promoter-primer”), to yield a double-stranded cDNA that comprises a RNA polymerase promoter that is recognized by a RNA polymerase. Preferably, the primer for first-strand cDNA synthesis is a promoter-primer and the primer for second-strand cDNA synthesis is not a promoter-primer. The double-stranded cDNA is then transcribed into RNA by the RNA polymerase, optimally in the presence of a reverse transcriptase that is rendered incapable of RNA-dependent DNA polymerase activity during this transcription step. The subject methods produce linearly amplified RNA with little or no 3? bias in the sequences of the nucleic acid population amplified.Type: GrantFiled: November 28, 2001Date of Patent: June 12, 2007Assignee: Rosetta Inpharmatics LLCInventors: Michael Ziman, Colleen P. Davis
-
Publication number: 20070092913Abstract: In one aspect, the present invention provides methods for determining whether a chemical agent modulates the biological activity of a GPR105 protein. The methods of this aspect of the invention include the steps of: (a) contacting a living cell, in vitro, with a chemical agent, wherein the living cell expresses a GPR105 protein having a biological activity; (b) determining whether the chemical agent modulates the biological activity of the GPR105 protein in the living cell; and (c) validating, in vivo, the modulating effect of the chemical agent on the biological activity of the GPR105 protein.Type: ApplicationFiled: October 19, 2006Publication date: April 26, 2007Applicants: Rosetta Inpharmatics LLC, Merck and Co., Inc.Inventors: John Lamb, Joseph Mancini, Brian Kennedy
-
Patent number: 7171311Abstract: The present invention relates to genetic markers whose expression is correlated with breast cancer. Specifically, the invention provides sets of markers whose expression patterns can be used to differentiate clinical conditions associated with breast cancer, such as the presence or absence of the estrogen receptor ESR1, and BRCA1 and sporadic tumors, and to provide information on the likelihood of tumor distant metastases within five years of initial diagnosis. The invention relates to methods of using these markers to distinguish these conditions. The invention also provides methods of classifying and treating patients based on prognosis. The invention also relates to kits containing ready-to-use microarrays and computer software for data analysis using the diagnostic, prognostic and statistical methods disclosed herein.Type: GrantFiled: January 15, 2003Date of Patent: January 30, 2007Assignees: Rosetta Inpharmatics LLC, Netherlands Cancer InstituteInventors: Hongyue Dai, Yudong He, Peter S. Linsley, Mao Mao, Christopher J. Roberts, Laura Johanna Van't Veer, Marc J. Van de Vijver, Rene Bernards, A. A. M. Hart
-
Patent number: 7150969Abstract: The present invention features nucleic acids and polypeptides encoding novel splice variant isoforms of acetyl-CoA carboxylase 2 (ACC2). The polynucleotide sequence of ACC2sv1 is provided by SEQ ID NO 3. The amino acid sequence of ACC2sv1 is provided by SEQ ID NO 4. The present invention also provides methods for using ACC2sv1 polynucleotides and proteins to screen for compounds that bind to ACC2sv1.Type: GrantFiled: June 3, 2005Date of Patent: December 19, 2006Assignee: Rosetta Inpharmatics LLCInventors: Zhengyan Kan, Philip W. Garrett-Engele, Christopher D. Armour, Christopher K. Raymond, John C. Castle
-
Patent number: 7141398Abstract: In one aspect, the present invention provides methods for synthesizing multiple copies of antisense cDNA molecules from an RNA molecule, comprising using an RNA molecule as a template for synthesizing multiple copies of antisense cDNA molecules. In some embodiments of the methods, the RNA molecule is incubated with a primer and with an enzyme possessing reverse transcriptase activity under suitable conditions for synthesizing multiple copies of antisense cDNA molecules. In some embodiments, the methods produce multiple copies of double-stranded cDNA from a template RNA molecule. In further embodiments, the methods produce multiple copies of cRNA from a template RNA molecule.Type: GrantFiled: December 23, 2003Date of Patent: November 28, 2006Assignee: Rosetta Inpharmatics LLCInventors: Mingjie Zhou, Sven Duenwald, Mark Parrish
-
Patent number: 7130746Abstract: The present invention provides methods for determining the level of protein activity in a cell by: (i) measuring abundances of cellular constituents in a cell in which the activity of a specific protein is to be determined so that a diagnostic profile is thus obtained; (ii) measuring abundances of cellular constituents that occur in a cell in response to perturbations in the activity of said protein to obtain response profiles and interpolating said response profiles to generate response curves; and (iii) determining a protein activity level at which the response profile extracted from the response curves best fits the measured diagnostic profile, according to some objective measure. In alternative embodiments, the present invention also provides methods for identifying individuals having genetic mutations or polymorphisms that disrupt protein activity, and methods for identifying drug activity in vivo by determining the activity levels of proteins which interact with said drugs.Type: GrantFiled: October 12, 2001Date of Patent: October 31, 2006Assignee: Rosetta Inpharmatics LLCInventors: Stephen H. Friend, Roland Stoughton
-
Publication number: 20060240457Abstract: In one aspect, the present invention provides methods of determining whether an agent is more like a partial agonist of a target molecule than a full agonist of the same target molecule. In another aspect, the present invention provides methods to select a candidate compound that may reduce blood plasma glucose concentration in a mammal. Populations of genes are provided that are useful in the practice of the present invention.Type: ApplicationFiled: April 4, 2006Publication date: October 26, 2006Applicants: Rosetta Inpharmatics LLC, Merck & Co., Inc.Inventors: Yejun Tan, Hongyue Dai, Pek Lum, John Thompson, Joel Berger, Eric Muise, Richard Raubertas, Kenny Wong
-
Publication number: 20060166199Abstract: 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.Type: ApplicationFiled: June 27, 2003Publication date: July 27, 2006Applicant: Rosetta Inpharmatics LLC.Inventors: Matthew Marton, Michael Meyer, Allan Jones
-
Patent number: 7078169Abstract: The present invention relates to methods of identifying genes whose expression is indicative of activation of a particular biochemical or metabolic pathway or a common set of biological reactions or functions in a cell (“regulon indicator genes”) The present invention provides an example of such an indicator gene. The present invention also relates to methods of partially characterizing a gene of unknown function by determining which biological pathways, reactions or functions its expression is associated with, thereby placing the gene within a functional genetic group or “regulon”. These partially characterized genes may be used to identify desirable therapeutic targets of biological pathways of interest (“regulon target genes”) The present invention provides examples of such target genes. Methods for identifying effectors (activators and inhibitors) of regulon target genes are provided. The present invention also provides examples of regulon target gene inhibitors.Type: GrantFiled: July 26, 2002Date of Patent: July 18, 2006Assignee: Rosetta Inpharmatics LLCInventors: Matthew Ashby, Stewart Scherer, John W. Phillips, Michael Ziman, Nicholas Marini
-
Patent number: 7035739Abstract: A method for associating a gene with a trait exhibited by one or more organisms in a plurality of organisms from a species. A genetic marker map is constructed from a set of genetic markers associated with the plurality of organisms. For each gene in a plurality of genes, a quantitative trait locus analysis is performed using the genetic marker map and a quantitative trait. The quantitative trait locus analysis produces quantitative trait locus data. A quantitative trait comprises an expression statistic for a gene. The expression statistic for a gene is derived from a cellular constituent level that corresponds to the gene in each organism in the plurality of organisms. The quantitative trait locus data are clustered from each quantitative trait locus analysis to form a quantitative trait locus interaction map. Clusters of genes in the map are identified as a candidate pathway group. An expression cluster map is used to refine the candidate pathway group.Type: GrantFiled: February 3, 2003Date of Patent: April 25, 2006Assignee: Rosetta Inpharmatics LLCInventors: Eric E. Schadt, Stephanie A. Monks