Patents Represented by Attorney Michael J. Gilly
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Patent number: 8318432Abstract: Cross-reacting hybridization probe for detecting HIV-1 and HIV-2 nucleic acids. The probe advantageously exhibited uniformly high signal-to-noise ratios when hybridized to HIV-1 and HIV-2 target nucleic acids. The probe can be used, for example, in screening applications for detecting donated blood contaminated with either of the two analytes.Type: GrantFiled: January 21, 2010Date of Patent: November 27, 2012Assignee: Gen-Probe IncorporatedInventors: Jeffrey M. Linnen, Wen Wu
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Patent number: 8275556Abstract: Method for quantifying analyte polynucleotide in a test sample using real-time amplification and adjustment of a stored calibration curve. The method may be practiced using as few as a single adjustment calibrator to adjust the stored curve. This simplifies the quantitative analysis procedure, while still providing the advantages of internal calibration adjustment to account for variation in amplification reaction efficiency.Type: GrantFiled: March 24, 2011Date of Patent: September 25, 2012Assignee: Gen-Probe IncorporatedInventor: James M. Carrick
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Patent number: 8224584Abstract: System for quantifying analyte polynucleotides employs computer-implemented analysis of real-time amplification data using a calibration curve defined by parametric equations.Type: GrantFiled: October 27, 2010Date of Patent: July 17, 2012Assignee: Gen-Probe IncorporatedInventors: James M. Carrick, Mark R. Kennedy, Jeffrey D. Chismar
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Patent number: 8145435Abstract: System for analyzing a polynucleotide-containing sample using real-time amplification and monitoring. The system includes a computer or processing device with software for performing a vector analysis of growth curves. The vector analysis advantageously simplifies polynucleotide quantitation by circumventing the need to establish thresholds used for calculating initiation of the growth phase, or to calculate derivatives.Type: GrantFiled: May 27, 2010Date of Patent: March 27, 2012Assignee: Gen-Probe IncorporatedInventors: James M. Carrick, Jeffrey D. Chismar, Michael J. Gilly
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Patent number: 8071301Abstract: Method of preparing a biological sample appropriate for use in a subsequent in vitro nucleic acid amplification reaction. The method involves a rapid, transient exposure to alkaline conditions which can be achieved by mixing an alkaline solution with a pH-buffered solution that includes a detergent and the biological sample to be tested for the presence of particular nucleic acid species using in vitro amplification. The invented method advantageously can improve detection of some target nucleic acids without substantially compromising detectability of others. The method is particularly useful for simultaneously preparing RNA and DNA templates that can be used in multiplex amplification reactions.Type: GrantFiled: June 30, 2010Date of Patent: December 6, 2011Assignee: Gen-Probe IncorporatedInventors: Kui Gao, Michael M. Becker, Wen Wu, Jeffrey M. Linnen
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Patent number: 7930106Abstract: Methods and kits for preparing and adjusting pre-defined master calibration curves of the type used for quantifying analyte polynucleotides by real-time nucleic acid amplification. Particularly disclosed are methods of preparing one or more master calibration curves on one instrument, and then using those master calibration curves on a different instrument.Type: GrantFiled: November 30, 2007Date of Patent: April 19, 2011Assignee: Gen-Probe IncorporatedInventor: James M. Carrick
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Patent number: 7927840Abstract: Compositions, methods and kits for detecting flavivirus nucleic acids. Particularly described are methods for detecting West Nile virus nucleic acids in the 3? non-coding region.Type: GrantFiled: October 31, 2007Date of Patent: April 19, 2011Assignee: Gen Probe IncorporatedInventors: Jeffrey M. Linnen, Reinhold B. Pollner
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Patent number: 7831417Abstract: Method of preparing a calibration curve and determining the amount of an analyte polynucleotide present in a test sample, particularly using real-time amplification data. The method involves determining indicia of amplification for both the internal calibrator and analyte polynucleotide standards, each as a function of the amount of analyte polynucleotide standard input into the amplification reaction.Type: GrantFiled: November 14, 2006Date of Patent: November 9, 2010Assignee: Gen-Probe IncorporatedInventors: James M. Carrick, Mark R. Kennedy, Jeffrey D. Chismar
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Patent number: 7803581Abstract: Method of preparing a biological sample appropriate for use in a subsequent in vitro nucleic acid amplification reaction. The method involves a rapid, transient exposure to alkaline conditions which can be achieved by mixing an alkaline solution with a pH-buffered solution that includes a detergent and the biological sample to be tested for the presence of particular nucleic acid species using in vitro amplification. The invented method advantageously can improve detection of some target nucleic acids without substantially compromising detectability of others. The method is particularly useful for simultaneously preparing RNA and DNA templates that can be used in multiplex amplification reactions.Type: GrantFiled: March 24, 2009Date of Patent: September 28, 2010Assignee: Gen-Probe IncorporatedInventors: Kui Gao, Michael M. Becker, Wen Wu, Jeffrey M. Linnen
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Patent number: 7785844Abstract: Compositions, methods and kits for detecting viral nucleic acids. Targets that can be detected in accordance with the invention include HBV and/or HIV-1 and/or HCV nucleic acids. Particularly described are oligonucleotides that are useful as hybridization probes and amplification primers that facilitate detection of very low levels of HBV nucleic acids.Type: GrantFiled: October 15, 2007Date of Patent: August 31, 2010Assignee: Gen-Probe IncorporatedInventors: Jeffrey M. Linnen, Daniel P. Kolk, Janel M. Dockter, Damon K. Getman, Tadashi Yoshimura, Martha K. Ho-Sing-Loy, Reinhold B. Pollner, Leslie A. Stringfellow
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Patent number: 7739054Abstract: Machine executable method of analyzing growth curve data to identify the transition from a baseline phase into a growth phase. Applications of the method include analysis of results from time-dependent monitoring of amplicon synthesis in a nucleic acid amplification reaction to quantify a starting amount of a nucleic acid template in a test sample. The method advantageously simplifies the quantitation by circumventing the need to establish thresholds used for calculating initiation of the growth phase, to calculate derivatives, or to perform linear regression analysis.Type: GrantFiled: June 22, 2006Date of Patent: June 15, 2010Assignee: Gen-Probe IncorporatedInventors: James M. Carrick, Jeffrey D. Chismar, Michael J. Gilly
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Patent number: 7732169Abstract: Methods for detecting flavivirus nucleic acids. Particularly described are methods for detecting very low levels of West Nile virus nucleic acids in the 5? non-coding/capsid region.Type: GrantFiled: September 11, 2006Date of Patent: June 8, 2010Assignee: Gen-Probe IncorporatedInventors: Jeffrey M. Linnen, Reinhold P. Pollner, Wen Wu, Geoffrey G. Dennis
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Patent number: 7666600Abstract: Compositions, methods and kits for detecting the nucleic acids of HIV-1, HIV-2, or the combination of HIV-1 and HIV-2. Particularly described are oligonucleotides that are useful as hybridization probes and amplification primers, including cross-reacting hybridization probes and cross-reacting amplification primers, for detecting very low levels of viral nucleic acids.Type: GrantFiled: August 13, 2007Date of Patent: February 23, 2010Assignee: Gen-Probe IncorporatedInventors: Jeffrey M. Linnen, Wen Wu
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Patent number: 7582470Abstract: Compositions, methods and devices for detecting nucleic acids. The invention particularly regards composite arrays of immobilized amplification primers and hybridization probes. Also disclosed are compositions and methods for covalently immobilizing oligonucleotides and other biological molecules to glass and plastic surfaces.Type: GrantFiled: July 17, 2003Date of Patent: September 1, 2009Assignee: Gen-Probe IncorporatedInventor: Kenneth A. Browne
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Patent number: 7510837Abstract: Method of preparing a biological sample appropriate for use in a subsequent in vitro nucleic acid amplification reaction. The method involves a rapid, transient exposure to alkaline conditions which can be achieved by mixing an alkaline solution with a pH-buffered solution that includes a detergent and the biological sample to be tested for the presence of particular nucleic acid species using in vitro amplification. The invented method advantageously can improve detection of some target nucleic acids without substantially compromising detectability of others. The method is particularly useful for simultaneously preparing RNA and DNA templates that can be used in multiplex amplification reactions.Type: GrantFiled: February 17, 2006Date of Patent: March 31, 2009Assignee: Gen-Probe IncorporatedInventors: Kui Gao, Michael M. Becker, Wen Wu, Jeffrey M. Linnen
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Patent number: 7449328Abstract: Device for identifying microbial organisms using a collection of polynucleotide probes, each probe having binding specificity for the ribosomal nucleic acids of at least one microbe. The collection of probes is organized into a series of “addresses” that provide information about the presence or absence of one or more polynucleotide sequences in the biological sample. The system is particularly suited to automated analysis.Type: GrantFiled: August 30, 2004Date of Patent: November 11, 2008Assignee: Gen-Probe IncorporatedInventor: James J. Hogan
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Patent number: 7255996Abstract: Compositions, methods and kits for detecting the nucleic acids of HIV-1, HIV-2, or the combination of HIV-1 and HIV-2. Particularly described are oligonucleotides that are useful as hybridization probes and amplification primers, including cross-reacting hybridization probes and cross-reacting amplification primers, for detecting very low levels of viral nucleic acids.Type: GrantFiled: December 16, 2004Date of Patent: August 14, 2007Assignee: Gen-Probe IncorporatedInventors: Jeffrey M. Linnen, Wen Wu
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Patent number: 7115374Abstract: Compositions, methods and kits for detecting flavivirus nucleic acids. Particularly described are oligonucleotides that are useful as hybridization probes and amplification primers for detecting very low levels of West Nile virus nucleic acids.Type: GrantFiled: October 16, 2003Date of Patent: October 3, 2006Assignee: Gen-Probe IncorporatedInventor: Jeffrey M. Linnen
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Patent number: 7070933Abstract: Unitary hybridization probes having stem-and-loop structures, wherein the stem portion of the structure comprises a pair of interactive arms that are substantially prevented from interacting with target polynucleotides. One arm of the invented parallel-stem hybridization probe has a backbone polarity opposite that of the target-complementary loop sequence of the probe. Rather than interacting in an antiparallel fashion, the arms of parallel-stem hybridization probes interact in a parallel fashion. The arms of the invented dual inversion probes interact in a conventional antiparallel fashion, but have backbone polarities opposite that of the target-complementary loop portion of the probe. Arm portions of the inversion probes do not substantially contribute to sequence-dependent stabilization of probe:target hybrids. Incorporating inversion linkages into the structures of these probes dramatically simplifies the process of designing stem-and-loop hybridization probes.Type: GrantFiled: March 14, 2003Date of Patent: July 4, 2006Assignee: Gen-Probe IncorporatedInventor: Kenneth A. Browne
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Patent number: 6908735Abstract: Methods useful for improving results obtained with enzyme-based polynucleotide amplification reactions. More particularly, the invented methods are useful for: (1) promoting amplification of template-specific products such that the amount of amplicon produced reflects the pre-amplification amount of analyte, even in reactions primed with low levels of analyte polynucleotide; (2) facilitating biological specimen processing such that the amount of amplicon produced in subsequent amplification reactions will be substantially independent of the efficiency of analyte polynucleotide isolation from the specimen; and (3) controlling the amount of analyte amplicon produced in the amplification reaction.Type: GrantFiled: August 30, 2001Date of Patent: June 21, 2005Assignee: Gen-Probe IncorporatedInventor: Kiyotada Nunomura