Abstract
Nucleic acids are the ultimate biomarker and real-time PCR (qPCR) is firmly established as the method of choice for nucleic acid detection. Together, they allow the accurate, sensitive and specific identification of pathogens, and the use of qPCR has become routine in diagnostic laboratories. The reliability of qPCR-based assays relies on a combination of optimal sample selection, assay design and validation as well as appropriate data analysis and the “Minimal Information for the Publication of real-time PCR” (MIQE) guidelines aim to improve both the reliability of assay design as well as the transparency of reporting, essential conditions if qPCR is to remain the benchmark technology for molecular diagnosis.
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References
Bustin SA, Benes V, Nolan T, Pfaffl MW (2005) Quantitative real-time RT-PCR—a perspective. J Mol Endocrinol 34:597–601
Morrison T, Hurley J, Garcia J, Yoder K, Katz A, Roberts D, Cho J, Kanigan T, Ilyin SE, Horowitz D, Dixon JM, Brenan CJ (2006) Nanoliter high throughput quantitative PCR. Nucleic Acids Res 34:e123
Zhang C, Xing D (2007) Miniaturized PCR chips for nucleic acid amplification and analysis: latest advances and future trends. Nucleic Acids Res 35:4223–4237
Cho YK, Kim J, Lee Y, Kim YA, Namkoong K, Lim H, Oh KW, Kim S, Han J, Park C, Pak YE, Ki CS, Choi JR, Myeong HK, Ko C (2006) Clinical evaluation of micro-scale chip-based PCR system for rapid detection of hepatitis B virus. Biosens Bioelectron 21: 2161–2169
Kaigala GV, Huskins RJ, Preiksaitis J, Pang XL, Pilarski LM, Backhouse CJ (2006) Automated screening using microfluidic chip-based PCR and product detection to assess risk of BK virus-associated nephropathy in renal transplant recipients. Electrophoresis 27:3753–3763
Ascioglu S, Rex JH, de Pauw B, Bennett JE, Bille J, Crokaert F, Denning DW, Donnelly JP, Edwards JE, Erjavec Z, Fiere D, Lortholary O, Maertens J, Meis JF, Patterson TF, Ritter J, Selleslag D, Shah PM, Stevens DA, Walsh TJ (2002) Defining opportunistic invasive fungal infections in immunocompromised patients with cancer and hematopoietic stem cell transplants: an international consensus. Clin Infect Dis 34:7–14
Klingspor L, Loeffler J (2009) Aspergillus PCR formidable challenges and progress. Med Mycol 47(Suppl 1):S241–S247
Duval SM, Donnelly JP, Barnes R, Löffler J (2008) PCR-based methods with aspergillosis as a model. J Invasive Fungal Infect 2:46–51
Perlin DS, Zhao Y (2009) Molecular diagnostic platforms for detecting Aspergillus. Med Mycol 47(Suppl 1):S223–S232
White PL, Bretagne S, Klingspor L, Melchers WJ, McCulloch E, Schulz B, Finnstrom N, Mengoli C, Barnes RA, Donnelly JP, Loeffler J (2010) Aspergillus PCR: one step closer to standardization. J Clin Microbiol 48:1231–1240
Mengoli C, Cruciani M, Barnes RA, Loeffler J, Donnelly JP (2009) Use of PCR for diagnosis of invasive aspergillosis: systematic review and meta-analysis. Lancet Infect Dis 9:89–96
Khot PD, Fredricks DN (2009) PCR-based diagnosis of human fungal infections. Expert Rev Anti Infect Ther 7:1201–1221
Garson JA, Huggett JF, Bustin SA, Pfaffl MW, Benes V, Vandesompele J, Shipley GL (2009) Unreliable real-time PCR analysis of human endogenous retrovirus-W (HERV-W) RNA expression and DNA copy number in multiple sclerosis. AIDS Res Hum Retroviruses 25:377–378
de Vries TJ, Fourkour A, Punt CJ, van de Locht LT, Wobbes T, van den BS, de Rooji MJ, Mensink EJ, Ruiter DJ, van Muijen GN (1999) Reproducibility of detection of tyrosinase and MART-1 transcripts in the peripheral blood of melanoma patients: a quality control study using real-time quantitative RT-PCR. Br J Cancer 80:883–891
Peccoud J, Jacob C (1996) Theoretical uncertainty of measurements using quantitative polymerase chain reaction. Biophys J 71:101–108
Afzal MA, Osterhaus AD, Cosby SL, Jin L, Beeler J, Takeuchi K, Kawashima H (2003) Comparative evaluation of measles virus-specific RT-PCR methods through an international collaborative study. J Med Virol 70:171–176
Niesters HG (2001) Quantitation of viral load using real-time amplification techniques. Methods 25:419–429
Niesters HG (2004) Molecular and diagnostic clinical virology in real time. Clin Microbiol Infect 10:5–11
Gabert J, Beillard E, van der Velden VH, Bi W, Grimwade D, Pallisgaard N, Barbany G, Cazzaniga G, Cayuela JM, Cave H, Pane F, Aerts JL, De Micheli D, Thirion X, Pradel V, Gonzalez M, Viehmann S, Malec M, Saglio G, van Dongen JJ (2003) Standardization and quality control studies of ‘real-time’ quantitative reverse transcriptase polymerase chain reaction of fusion gene transcripts for residual disease detection in leukemia - a Europe Against Cancer program. Leukemia 17:2318–2357
Muller MC, Hordt T, Paschka P, Merx K, La Rosee P, Hehlmann R, Hochhaus A (2004) Standardization of preanalytical factors for minimal residual disease analysis in chronic myelogenous leukemia. Acta Haematol 112:30–33
Griffiths LJ, Anyim M, Doffman SR, Wilks M, Millar MR, Agrawal SG (2006) Comparison of DNA extraction methods for Aspergillus fumigatus using real-time PCR. J Med Microbiol 55:1187–1191
Fredricks DN, Smith C, Meier A (2005) Comparison of six DNA extraction methods for recovery of fungal DNA as assessed by quantitative PCR. J Clin Microbiol 43:5122–5128
Bustin SA, Nolan T (2004) Pitfalls of quantitative real-time reverse-transcription polymerase chain reaction. J Biomol Tech 15:155–166
Kwok S, Higuchi R (1989) Avoiding false positives with PCR. Nature 339:237–238
Millon L, Grenouillet F, Crouzet J, Larosa F, Loewert S, Bellanger AP, Deconinck E, Legrand F (2010) False-positive Aspergillus real-time PCR assay due to a nutritional supplement in a bone marrow transplant recipient with GVH disease. Med Mycol 48:661–664
Monpoeho S, Coste-Burel M, Costa-Mattioli M, Besse B, Chomel JJ, Billaudel S, Ferre V (2002) Application of a real-time polymerase chain reaction with internal positive control for detection and quantification of enterovirus in cerebrospinal fluid. Eur J Clin Microbiol Infect Dis 21:532–536
Nolan T, Hands RE, Ogunkolade BW, Bustin SA (2006) SPUD: a qPCR assay for the detection of inhibitors in nucleic acid preparations. Anal Biochem 351:308–310
Bustin SA, Benes V, Garson JA, Hellemans J, Huggett J, Kubista M, Mueller R, Nolan T, Pfaffl MW, Shipley GL, Vandesompele J, Wittwer CT (2009) The MIQE guidelines: minimum information for publication of quantitative real-time PCR experiments. Clin Chem 55:611–622
Taylor CF, Field D, Sansone SA, Aerts J, Apweiler R, Ashburner M, Ball CA, Binz PA, Bogue M, Booth T, Brazma A, Brinkman RR, Michael Clark A, Deutsch EW, Fiehn O, Fostel J, Ghazal P, Gibson F, Gray T, Grimes G, Hancock JM, Hardy NW, Hermjakob H, Julian RK Jr, Kane M, Kettner C, Kinsinger C, Kolker E, Kuiper M, Novere NL, Leebens-Mack J, Lewis SE, Lord P, Mallon AM, Marthandan N, Masuya H, McNally R, Mehrle A, Morrison N, Orchard S, Quackenbush J, Reecy JM, Robertson DG, Rocca-Serra P, Rodriguez H, Rosenfelder H, Santoyo-Lopez J, Scheuermann RH, Schober D, Smith B, Snape J, Stoeckert CJ Jr, Tipton K, Sterk P, Untergasser A, Vandesompele J, Wiemann S (2008) Promoting coherent minimum reporting guidelines for biological and biomedical investigations: the MIBBI project. Nat Biotechnol 26:889–896
Brazma A, Hingamp P, Quackenbush J, Sherlock G, Spellman P, Stoeckert C, Aach J, Ansorge W, Ball CA, Causton HC, Gaasterland T, Glenisson P, Holstege FC, Kim IF, Markowitz V, Matese JC, Parkinson H, Robinson A, Sarkans U, Schulze-Kremer S, Stewart J, Taylor R, Vilo J, Vingron M (2001) Minimum information about a microarray experiment (MIAME)-toward standards for microarray data. Nat Genet 29:365–371
Taylor CF, Paton NW, Lilley KS, Binz PA, Julian RK Jr, Jones AR, Zhu W, Apweiler R, Aebersold R, Deutsch EW, Dunn MJ, Heck AJ, Leitner A, Macht M, Mann M, Martens L, Neubert TA, Patterson SD, Ping P, Seymour SL, Souda P, Tsugita A, Vandekerckhove J, Vondriska TM, Whitelegge JP, Wilkins MR, Xenarios I, Yates JR III, Hermjakob H (2007) The minimum information about a proteomics experiment (MIAPE). Nat Biotechnol 25:887–893
Lefever S, Hellemans J, Pattyn F, Przybylski DR, Taylor C, Geurts R, Untergasser A, Vandesompele J (2009) RDML: structured language and reporting guidelines for real-time quantitative PCR data. Nucleic Acids Res 37:2066–2069
Hammerle-Fickinger A, Riedmaier I, Becker C, Meyer HH, Pfaffl MW, Ulbrich SE (2010) Validation of extraction methods for total RNA and miRNA from bovine blood prior to quantitative gene expression analyses. Biotechnol Lett 32(1):35–44
Tichopad A, Kitchen R, Riedmaier I, Becker C, Stahlberg A, Kubista M (2009) Design and optimization of reverse-transcription quantitative PCR experiments. Clin Chem 55:1816–1823
Livak KJ, Schmittgen TD (2001) Analysis of relative gene expression data using real-time quantitative PCR and the 2(-Delta Delta C(T)) Method. Methods 25:402–408
Pfaffl MW (2001) A new mathematical model for relative quantification in real-time RT-PCR. Nucleic Acids Res 29:E45
Schmittgen TD, Livak KJ (2008) Analyzing real-time PCR data by the comparative C(T) method. Nat Protoc 3:1101–1108
Yuan JS, Wang D, Stewart CN Jr (2008) Statistical methods for efficiency adjusted real-time PCR quantification. Biotechnol J 3:112–123
Yuan JS, Reed A, Chen F, Stewart CN Jr (2006) Statistical analysis of real-time PCR data. BMC Bioinformatics 7:85
Ramirez M, Castro C, Palomares JC, Torres MJ, Aller AI, Ruiz M, Aznar J, Martin-Mazuelos E (2009) Molecular detection and identification of Aspergillus spp. from clinical samples using real-time PCR. Mycoses 52:129–134
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Johnson, G., Nolan, T., Bustin, S.A. (2013). Real-Time Quantitative PCR, Pathogen Detection and MIQE. In: Wilks, M. (eds) PCR Detection of Microbial Pathogens. Methods in Molecular Biology, vol 943. Humana Press, Totowa, NJ. https://doi.org/10.1007/978-1-60327-353-4_1
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DOI: https://doi.org/10.1007/978-1-60327-353-4_1
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