Automatic threshold setting and baseline determination for...

Details Automatic threshold setting and baseline determination for... Automatic threshold setting and baseline determination for...

2006-12-27

2011-10-11

Lin, Jerry (Department: 1631)

Data processing: measuring, calibrating, or testing

Measurement system in a specific environment

Biological or biochemical

Reexamination Certificate

active

08036832

ABSTRACT:
The invention discloses a system and methods for quantitating the presence of nucleic acid sequences by evaluation of amplification data generated using real-time PCR. In one aspect, the methods may be adapted to identify a threshold and threshold cycle for one or more reactions based upon evaluation of exponential and baseline regions for each amplification reaction. The methodology used in the analysis may be readily automated such that subjective user interpretation of the data is substantially reduced or eliminated.

REFERENCES:
patent: 6174670 (2001-01-01), Wittwer et al.
patent: 6303305 (2001-10-01), Wittwer et al.
patent: 6783934 (2004-08-01), McMillan et al.
patent: 2003/0148332 (2003-08-01), Taylor et al.
patent: 1 041 158 (2000-10-01), None
patent: 1 138 783 (2001-10-01), None
U.S. Appl. No. 11/645,863, Non-Final Office Action mailed Nov. 13, 2009.
U.S. Appl. No. 11/646,089, Final Office Action mailed Jan. 7, 2010.
U.S. Appl. No. 11/810,337, Final Office Action mailed Jan. 7, 2010.
Roche Molecular Biochemicals:“LightCyder Operator's manual,” http://biochem.roche.com./lightcycler. 2000, version 3.5, pp. 1-189.
Haake et al. “Label-Free Biochemical Detection Coupled On-Line to Liquid Chromatography,”Analytical Chemistry.2000, vol. 72, pp. 3635-3641.
“LightCycler Relative Quanitification Software”, Roche Molecular Biochemicals, Version 1.0, Mar. 2001.
“LightCycler Absolute Quanitification with External Standards”, Roche Molecular Biochemicals, Technical Note No. LC Nov. 2000.
Woudenberg et al.,Quantitative PCR by Real Time Detection,SPIE vol. 2680, pp. 306-315 (1996).
Lie et al.,Advances in Quantitative PCR Technology: 5′Nuclease Assays, Analytical Biotechnology,pp. 43-48 (1998).
Peccoud et al.,Statistical Estimations of PCR Amplification Rates,pp. 1-17, (1998).
Rasmussen et al.,Quantitative PCR by Continuous Fluorescence Monitoring of a Double Strand DNA Specific Binding Dye,Biochemica, No. 2, pp. 8-11, (1998).
Nitsche et al.,Different Real-Time PCR Formats Compared for the Quantitative Detection of Human Cytomegalovirus DNA,Clinical Chemistry, 45:11, (1932-1937, 1999).
Grove,Quantitative Real-Time Polymerase Chain Reaction for the Core Facility Using TaqMan and the Perkin-Elmer/Applied Biosystems Division 7700 Sequence Detector,ABRF, pp. 1-11, (1999).
Roche Molecular Biochemicals Technical Note No. LC 11/2000.Absolute Quantification with External Standards,Roche, pp. 1-20, (2000).
Giulietti et al.,An Overview of Real-Time Quantitative PCR: Applications to Quantify Cytokine Gene Expression,Methods, vol. 25, pp. 386-401, Elsevier Science (USA) (2001).
Applied Biosystems,User Bulletin #2, ABI Prism 7700 Sequence Detection System,pp. 1-36, (Dec. 11, 1997).
Yajima et al.,Quantitative Reverse Transcription-PCR Assay of the RNA Component of Human Telomerase Using the TaqMan Fluorogenic Detection System,Clinical Chemistry 44:12, pp. 2441-2445, (1998).
Winer et al.,Development and Validation of Real-Time Quantitative Reverse Transcriptase-Polymerase Chain Reaction for Monitoring Gene Expression in Cardiac Myocytes in Vitro,Analytical Biochemistry, vol. 270, No. 1, pp. 41-49(9), (May 1999).
Freeman et al.,Quantitative RT-PCR: Pitfalls and Potential,BioTechniques, vol. 26, No. 1, pp. 112-125, (1999).
Bustin,Absolute Quantification of mRNA Using Real-Time Reverse Transcription Polymerase Chain Reaction Assays,Journal of Molecular Endocrinology, vol. 25, pp. 169-193, (2000).
Saraswathy et al.,Human Immunodeficiency Virus Type 1 Subtypes Among Malaysian Intravenous Drug Users,Southeast Asian J. Trop Med. Public Health, (Abstract), vol. 31, No. 2, pp. 283-286, (2000).
Rostaing et al.,Changes in Hepatitis C Virus RNA Viremia Concentrations in Long-Term Renal Transplant Patients after Introduction of Mycophenolate Mofetil,Transplantation, vol. 15, No. 69(5), pp. 991-994, (Abstract), (Mar. 15, 2000).
Roche Applied Science Technical Note No. LC 13/2001,Relative Quantification,pp. 1-28.
Morin et al.,Laboratory for Conservation Genetics, Leipzig,Molecular Ecology, vol. 10, pp. 1835-1844, as reproduced at www.rareDNA.com, (2001).
Alexandersen et al.,The Early Pathogenesis of Foot-and-Mouth Disease in Pigs Infected by Contact: A Quantitative Time-Course Study Using TaqMan RT-PCR,Gen Virol, vol. 82, (pt 4), pp. 747-755, (Abstract), (2001).
Levis et al.,Strategy for the Maximization of Clinically Relevant Information from Hepatitis C Virus,RT-PCT Quantification, J. Clin. Virol, vol. 20, No. 3, pp. 163-171 (2001).
Pfaffl,A New Mathematical Model for Relative Quantification in Real-Time RT-PCR,Nucleic Acids Research, vol. 29, No. 9, p. e45 (2001).
Livak et al.,Analysis of Relative Gene Expression Data Using Real-Time Quantitative PCR and the2-ΔΔCTMethod,Methods, vol. 25, pp. 402-408, (2001).
Bustin,Quantification of mRNA Using Real-Time Reverse Transcription PCR(RT-PCR):Trends and Problems,Journal of Molecular Endocrinology, vol. 29, pp. 23-39, (2002).
Ginzinger,Gene Quantification Using Real-Time Quantitative PCR: An Emerging Technology Hits the Mainstream,Elsevier Science Inc., Experimental Hematology, vol. 30, pp. 503-512, (2002).
Morrison et al.,Nanoliter High Throughput Quantitative PCR,Nucleic Acids Research, vol. 34, No. 18, pp. 1-9 and e 123 (2006).
Applied Biosystems,Data Analysis on the ABI PRISM™7700 Sequence Detection System: Setting Baseline and Thresholds,pp. 1-12, (2002).
Communication dated Aug. 1, 2007, from European Patent Application No. 03737616.7.
Supplementary Partial European Search Report dated Jul. 25, 2007, from European Patent Application No. 03737616.7.
Annex dated Jul. 25, 2007, from European Patent Application No. 03737616.7.
Heid et al., “Real Time Quantitative PCR” Genome Research, Cold Spring Harbor Press, Woodbury, NY, US, vol. 6, No. 10, pp. 986-994, XP000642795, ISSN: 1088-9051, (Oct. 1996).
Higuchi et al. “Kinetic PCR Analysis Real-Time Monitoring of DNA Amplification Reactions”, BIO/Technology, Nature Publishing Co., NY, US, vol. 11, No. 9, pp. 1026-1030, XP000197685, ISSN: 0733-222X, (Sep. 1993).

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