A Bayesian method for calculating real-time quantitative PCR calibration curves using absolute plasmid DNA standards

BMC Bioinformatics

Volumn 9, Issue , 2008, Pages

  Sivaganesan, Mano ^a   Seifring, Shawn ^b   Varma, Manju ^b   Haugland, Richard A ^b   Shanks, Orin C ^a  

^a U S ENVIRONMENTAL PROTECTION AGENCY   (United States)

^b U S ENVIRONMENTAL PROTECTION AGENCY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BAYESIAN APPROACHES; CALIBRATION CURVES; ENVIRONMENTAL SAMPLE; MONTE CARLO MARKOV CHAIN; POSTERIOR DISTRIBUTIONS; POTENTIAL DIFFERENCE; REAL-TIME QUANTITATIVE PCR; REPLICATE MEASUREMENTS;

BAYESIAN NETWORKS; BIOMOLECULES; CALIBRATION; DNA; ESTIMATION; EXPERIMENTS; GENES; STANDARDS; UNCERTAINTY ANALYSIS;

POLYMERASE CHAIN REACTION;

GENOMIC DNA; PLASMID DNA;

ARTICLE; BACTEROIDES THETAIOTAOMICRON; BAYES THEOREM; BIOINFORMATICS; CALIBRATION; COMPARATIVE STUDY; COMPUTER PROGRAM; COMPUTER SIMULATION; ENTEROCOCCUS FAECALIS; GENE REPLICATION; GENE TARGETING; GENETIC VARIABILITY; MATHEMATICAL ANALYSIS; MONTE CARLO METHOD; NONHUMAN; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; STANDARDIZATION; ALGORITHM; AUTOMATED PATTERN RECOGNITION; DNA SEQUENCE; GENETICS; INSTRUMENTATION; METHODOLOGY; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; PLASMID; STANDARD; UNITED STATES;

ALGORITHMS; BASE SEQUENCE; BAYES THEOREM; CALIBRATION; MOLECULAR SEQUENCE DATA; PATTERN RECOGNITION, AUTOMATED; PLASMIDS; REVERSE TRANSCRIPTASE POLYMERASE CHAIN REACTION; SEQUENCE ANALYSIS, DNA; UNITED STATES;

EID: 42149119481     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-9-120     Document Type: Article

References (35)

1. Sambrook J Russell DW Molecular Cloning: A Laboratory Manual New York: Cold Spring Harbor Laboratory Press 4 2001, 1-3.
2. Higuchi R Fockler C Dollinger G Watson R Kinetic PCR analysis: Real-time monitoring of DNA amplification reactions Biotechnology 1993, 11:1026-1030. 10.1038/nbt0993-1026 7764001
3. ABI Essentials of Real Time PCR Applied Biosystems 2006.
4. Fierer N Jackson JA Vilgalys R Jackson RB Assessment of Soil Microbial Community Structure by Use of Taxon-Specific Quantitative PCR Assays Applied and Environmental Microbiology 2005, 71(7):4117-4120. 10.1128/ AEM.71.7.4117-4120.2005
5. ABI Absolute Quantitation Using Standard Curve Getting Started Guide Applied Biosystems 2006.
6. Singer VL Jones LJ Yue ST Haugland RP Characterization of PicoGreen Reagent and Development of a Fluorescence-Based Solution Assay for Double-Stranded DNA Quantitation Analytical Biochemistry 1997, 249(2):228-238. 10.1006/abio.1997.2177 9212875
7. Handlesman J Metagenomics: Application of genomics to uncultured microorganisms Microbiology and Molecular Biology Reviews 2004, 68(4):669-685. 10.1128/MMBR.68.4.669-685.2004
8. Grimes DJ Atwell RW Brayton PR Palmer LM Rollins DM Roszak DB Singleton FL Tamplin ML Colwell RR The fate of enteric pathogenic bacteria in estuarine and marine environments Microbiology Science 1986, 3:324-329.
9. Torsvik V Goksoyer J Daae FL High diversity in DNA of soil bacteria Applied and Environmental Microbiology 1990, 56:782-787.
10. Staley JT Konopka A Measurment of insitue activities of nonphotosynthetic microorganisms in aquatic and terrestrial habitats Annual Reviews in Microbiology 1985, 39:321-346. 10.1146/ annurev.mi.39.100185.001541
11. Toyota A Akiyama H Sugimura M Watanabe T Sakata K Shiramasa Y Kitta K Hino A Esaka M Maitani T Rapid Quantification Methods for Genetically Modified Maize Contents Using Genomic DNAs Pretreated by Sonication and Restriction Endonuclease Digestion for a Capillary-Type Real-Time PCR System with a Plasmid Reference Standard Bioscience, Biotechnology, and Biochemistry 2006, 70(12):2965-2973. 10.1271/bbb.60366 17151472
12. Martin B Jofre A Garriga M Pla M Aymerich T Rapid quantitative detection of Lactobacillus sakei in meat and fermented sausages by real-time PCR Applied and Environmental Microbiology 2006, 72(9):6040-6048. 10.1128/ AEM.02852-05
13. Ibekwe AW Watt PM Grieve CM Sharma VK Lyons SR Multiplex fluoregenic real-time PCR for detection and quantification of Escherichia coli O157:H7 in dairy wastewater wetlands Applied and Environmental Microbiology 2002, 68(10):4853-4862. 10.1128/AEM.68.10.4853-4862.2002
14. Rutledge RG Cote C Mathematics of quantitative kinetic PCR and the application of standard curves Nucleic Acids Research 2003 31 16 e93 169985 12907745 10.1093/nar/gng093
15. Frigessi A van de Wiel MA Holden M Svendsrud DH Glad IK Lyng H Genome-wide estimation of transcript concentrations from spotted cDNA microarry data Nucleic Acids Research 2005, 33(17):e143. 1243803 16204447 10.1093/nar/gni141
16. Conlon EM Song JJ Liu A Bayesian meta-analysis models for microarray data: A comparative study BMC Bioinformatics 2007, 8(80):1-21. 1766362 17199892
17. Lalam N Statistical Inference for Quantitative Polymerase Chain Reaction Using a Hidden Markov Model: A Bayesian Approach The Berkeley Electronic Press 2007, 6(1):1-33.
18. Lalam N Jacob C Bayesian Estimation for Quantification by Real-time Polymerase Chain Reaction Under a Branching Process Model of the DNA Molecules Amplification Process Mathematical Population Studies 2007, 14(2):111-129. 10.1080/08898480701298418
19. Brooks SP Markov chain Monte Carlo method and its application The Statistician 1998, 47:69-100.
20. Gelfand AE Smith AFM Sampling based approaches to calculating marginal densities Journal of the American Statistical Association 1990, 85:398-409. 10.2307/2289776
21. Gelman A Carlin JC Stern H Rubin DB Bayesian Data Analysis New York: Chapman & Hall 1995.
22. The BUGS Project-Bayesian inference Using Gibbs Sampling http://www.mrc-bsu.cam.ac.uk/bugs
23. Spiegelhalter DJ Abrams KR Myles JP Bayesian Approaches to Clinical Trials and Health-Care Evaluation USA: John Wiley & Sons Inc 2003.
24. Gelman A Rubin DB Inference from iterative simulation using multiple sequences Statistical Science 1992, 7:457-511. 10.1214/ss/1177011136
25. Cowles MK Carlin BP Markov Chain Monte Carlo Convergence Diagnostics: A Comparative Review Journal of the American Statistical Association 1996, 91:883-904. 10.2307/2291683
26. Shanks OC Santo Domingo JW Lamendella R Kelty CA Graham JE Competitive metagenomic DNA hybridization identifies host-specific microbial genetic markers in cow fecal samples Applied and Environmental Microbiology 2006, 72(6):4054-4060. 10.1128/AEM.00023-06
27. Haugland RA Siefring SC Wymer LJ Brenner KP Dufour AP Comparison of Enterococcus measurements in freshwater at two recreational beaches by quantitative polymerase chain reaction and membrane filter culture analysis Water Research 2005, 39:559-568. 10.1016/j.watres.2004.11.011 15707628
28. Higuchi R Krummel B Saiki RK A general method of in vitro preparation and specific mutagenesis of DNA fragments: Study of protein and DNA interactions Nucleic Acids Research 1988, 16:7351-7367. 338413 3045756 10.1093/nar/16.15.7351
29. Stocher M Leb V Berg J A convenient approach to the generation of multiple internal control DNA for a panel of real-time PCR assays Journal of Virology Methods 2003, 108:1-8. 10.1016/S0166-0934(02)00266-5
30. Blackwood AD Noble RT Development of a rapid quantitative PCR method for quantification of Bacteroides thetaiotaomicron as an alternative indicator of fecal contamination In Preparation 2007.
31. Ludwig W Schleifer KH How quantitative is quantitative PCR with respect to cell counts? Systematic and Applied Microbiology 2000, 23(4):556-562.
32. Seifring SC Varma M Atikovic E Wymer LJ Haugland RA Improved real-time PCR assays for the detection of fecal indicator bacteria in surface waters with different instrument and reagent systems Journal of Water and Health 2007.
33. Bernhard AE Field KG A PCR Assay to Discriminate Human and Ruminant Feces on the Basis of Host Differences in Bacteroides-Prevotella Genes Encoding for 16S rRNA Applied and Environmental Microbiology 2000, 66(10):4571-4574. 10.1128/AEM.66.10.4571-4574.2000
34. SAS SAS/STAT User's Guide Version 6 Cary, USA: SAS Institute Inc 4 1990
35. Zhang Y Zhang D Wenquan L Chen J Peng Y Cao W A novel real-time quantitative PCR method using attached universal template probe Nucleic Acids Research 2003, 31:e123. 219491 14530456 10.1093/nar/gng123