Predicting the sensitivity and specificity of published real-time PCR assays

Annals of Clinical Microbiology and Antimicrobials

Volumn 7, Issue , 2008, Pages

  Lemmon, Gordon H ^a   Gardner, Shea N ^b  

^a VANDERBILT UNIVERSITY SCHOOL OF MEDICINE   (United States)

^b LAWRENCE LIVERMORE NATIONAL LABORATORY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; BACTERIUM DETECTION; BIOINFORMATICS; CONTROLLED STUDY; FALSE NEGATIVE RESULT; FALSE POSITIVE RESULT; GENE SEQUENCE; INFORMATION RETRIEVAL; METHODOLOGY; NONHUMAN; PREDICTION; PROTEIN DATABASE; QUALITY CONTROL; REAL TIME POLYMERASE CHAIN REACTION; SENSITIVITY AND SPECIFICITY; STRAIN DIFFERENCE; TAXONOMY; VIRUS DETECTION; DIAGNOSTIC PROCEDURE; GENETICS; HUMAN; OLIGONUCLEOTIDE PROBE; POLYMERASE CHAIN REACTION; STANDARD;

PRIMER DNA;

DNA PRIMERS; HUMANS; MOLECULAR DIAGNOSTIC TECHNIQUES; OLIGONUCLEOTIDE PROBES; POLYMERASE CHAIN REACTION; SENSITIVITY AND SPECIFICITY;

EID: 54049155739     PISSN: None     EISSN: 14760711     Source Type: Journal    
DOI: 10.1186/1476-0711-7-18     Document Type: Article

References (36)

1. Espy MJ Uhl JR Sloan LM Buckwalter SP Jones MF Vetter EA Yao JDC Wengenack NL Rosenblatt JE Cockerill FR III Smith TF Real-time PCR in clinical microbiology: Applications for routine laboratory testing Clinical Microbiology Reviews 2006, 19(1):165-256 1360278 16418529 10.1128/CMR.19.1.165-256.2006
2. Altschul SF Gish W Miller W Myers EW Lipman DJ Basic local alignment search tool J Mol Biol 1990, 215:403-410. 2231712
3. Phillipy AM Mason JA Ayanbule K Sommer DD Taviani E Huq A Colwell RR Knight IT Salzberg SL Comprehensive DNA signature discovery and validation PLoS Computational Biology 2007, 18(3):e98. 10.1371/ journal.pcbi.0030098
4. TaqSim: TaqMan PCR Simulator http://staff.vbi.vt.edu/dyermd/publications/ taqsim.html
5. The Perl Directory http://www.perl.org/
6. van Elden L van Loon AM van Alphen F Hendriksen K Hoepelman A van Kraaij M Oosterheert J Schipper P Schuurman R Nijhuis M Frequent Detection of Human Coronaviruses in Clinical Specimens from Patients with Respiratory Tract Infection by Use of a Novel Real-Time Reverse-Transcriptase Polymerase Chain Reaction The Journal of Infectious Diseases 2004, 189:x652-657. 10.1086/381207
7. Padalko E Nuyens D De Palma A Verbeken E Aerts JL De Clercq E Carmeliet P Neyts J The Interferon Inducer Ampligen Markedly Protects Mice against Coxsackie B3 Virus-Induced Myocarditis Antimicrobial Agents and Chemotherapy 2004, 48(1):267-274. 10.1128/AAC.48.1.267-274.2004
8. Brilot F Geenen V Hober D Stoddart CA Coxsackievirus B4 Infection of Human Fetal Thymus Cells Journal of Virology 2004, 78(18):9854-9861. 514990 15331720 10.1128/JVI.78.18.9854-9861.2004
9. Weidmann M Muhlberger E Hufert FT Rapid detection protocol for filoviruses Journal of Clinical Virology 2004, 30(1):94-99. 10.1016/ j.jcv.2003.09.004 15072761
10. Drosten C Gottig S Schilling S Asper M Panning M Schmitz H Gunther S Rapid Detection and Quantification of RNA of Ebola and Marburg Viruses, Lassa Virus, Crimean-Congo Hemorrhagic Fever Virus, Rift Valley Fever Virus, Dengue Virus, and Yellow Fever Virus by Real-Time Reverse Transcription-PCR Journal of Clinical Microbiology 2002, 40(7):2323-2330. 120575 12089242 10.1128/JCM.40.7.2323-2330.2002
11. Killgore GE Holloway B Tenover FC A 5′ Nuclease PCR (TaqMan) High-Throughput Assay for Detection of the mecA Gene in Staphylococci Journal of Clinical Microbiology 2000, 38(7):2516-2519. 86956 10878035
12. Wellinghausen N Wirths B Franz AR Karolyi L Marre R Reischl U Algorithm for the identification of bacterial pathogens in positive blood cultures by real-time LightCycler polymerase chain reaction (PCR) with sequence-specific probes Diagnostic Microbiology and Infectious Disease 2004, 48(4):229-241. 10.1016/j.diagmicrobio.2003.11.005
13. Hummel KB Lowe L Bellini WJ Rota PA Development of quantitative gene-specific real-time RT-PCR assays for the detection of measles virus in clinical specimens Journal of Virological Methods 2006, 132(1-2):166-173. 10.1016/j.jviromet.2005.10.006 16274752
14. Gardner SN Kuczmarski TA Vitalis EA Slezak TR Limitations of TaqMan PCR for detecting divergent viral pathogens illustrated by hepatitis A, B, C, and E viruses and human immunodeficiency virus Journal of Clinical Microbiology 2003, 41:2417-2427. 156483 12791858 10.1128/ JCM.41.6.2417-2427.2003
15. Chao D Davis BS Chang GJ Development of Mulitplex Real-Time Reverse Transcriptase PCR Assays for Detecting Eight Medically Important Flaviviruses in Mosquitoes Journal of Clinical Microbiology 2007, 45(2):584-589. 1829073 17108075 10.1128/JCM.00842-06
16. Chien L Liao T Shu P Huang J Gubler DJ Chang GJ Development of Real-Time Reverse Transcriptase PCR Assays To Detect and Serotype Dengue Viruses Journal of Clinical Microbiology 2006, 44(4):1295-1304. 1448645 16597854 10.1128/JCM.44.4.1295-1304.2006
17. Slezak TR Kuczmarski T Ott L Torres C Medeiros D Smith J Truitt B Mulakken N Lam M Vitalis E Zemla A Zhou C Gardner SN Comparative genomics tools applied to bioterrorism defense Briefings in Bioinformatics 2003, 4:133-149. 10.1093/bib/4.2.133 12846395
18. Fitch JP Gardner SN Kuczmarski TA Kurtz So Myers R Ott LL Slezak TR Vitalis EA Zemla AT McCready PM Rapid Development of Nucleic Acid Diagnostics Proceedings of the IEEE 2002, 90(11):1708-1721. 10.1109/ JPROC.2002.804680
19. Gardner SN Lam MW Mulakken NJ Torres CL Smith JR Slezak TR Sequencing needs for viral diagnostics Journal of Clinical Microbiology 2004, 42:5472-5476. 535215 15583268 10.1128/JCM.42.12.5472-5476.2004
20. Ellis JS Smith JW Braham S Lock M Barlow K Zambon MC Design and Validation of an H5 TaqMan Real-Time One-Step Reverse Transcription-PCR and Confirmatory Assays for Diagnosis and Verification of Influenza A Virus H5 Infections in Humans Journal of Clinical Microbiology 2007, 45(5):1535-1543. 1865909 17473050 10.1128/JCM.02007-06
21. Watzinger F Suda M Preuner S Baumgartinger R Ebner K Baskova L Niesters HGM Lawitschka A Lion T Real-Time Quantitative PCR Assays for Detection and Monitoring of Pathogenic Human Viruses in Immunosuppressed Pediatric Patients Journal of Clinical Microbiology 2004, 42(11):5189-5198. 525141 15528714 10.1128/JCM.42.11.5189-5198.2004
22. Morris T Robertson B Gallagher M Rapid reverse transcription-PCR detection of hepatitis C virus RNA in serum by using the TaqMan fluorogenic detection system Journal of Clinical Microbiology 1996, 34(12):2933-2936. 229436 8940425
23. Lanciotti RS Kerst AJ Nasci RS Godsey MS Mitchell CJ Savage HM Komar N Panella NA Allen BC Volpe KE Davis BS Roehrig JT Rapid Detection of West Nile Virus from Human Clinical Specimens, Field-Collected Mosquitoes, and Avian Samples by a TaqMan Reverse Transcriptase-PCR Assay Journal of Clinical Microbiology 2000, 38(11):4066-4071. 87542 11060069
24. Pas SD Fries E De Man RA Osterhaus A Niesters H Development of a Quantitative Real-Time Detection Assay for Hepatitis B Virus DNA and Comparison with Two Commercial Assays Journal of Clinical Microbiology 2000, 38(8):2897-2901. 87141 10921947
25. Weinberger KM Wiedenmann E Bohm S Jilg W Sensitive and accurate quantitation of hepatitis B virus DNA using a kinetic fluorescence detection system (TagMan PCR) Journal of Virological Methods 2000, 85(1-2):75-82. 10.1016/S0166-0934(99)00154-8 10716340
26. Piiparinen H Hockerstedt K Gronhagen-Riska C Lautenschlager I Comparison of two quantitative CMV PCR tests, Cobas Amplicor CMV Monitor and TaqMan assay, and pp65-antigenemia assay in the determination of viral loads from peripheral blood of organ transplant patients Journal of Clinical Virology 2004, 30(3):258-266. 15135746
27. Corey L Huang M Selke S Wald A Differentiation of herpes simplex virus types 1 and 2 in clinical samples by a real-time taqman PCR assay Journal of Medical Virology 2005, 76(3):350-355. 10.1002/jmv.20365 15902702
28. Hawrami K Breuer J Development of a flurogenic polymerase chain reaction assay (TaqMan) for the detection and quantitation of varicella zoster virus Journal of Virological Methods 1999, 79(1):33-40. 10.1016/ S0166-0934(98)00176-1 10328533
29. Uchida K Shinohara M Shimada S Segawa Y Doi R Gotoh A Hondo R Rapid and sensitive detection of mumps virus RNA directly from clinical samples by real-time PCR Journal of Medical Virology 2005, 75(3):470-474. 10.1002/ jmv.20291 15648065
30. Wise MG Suarez DL Seal BS Pedersen JC Senne DA King DJ Kapczynski DR Spackman E Development of a Real-Time Reverse-Transcription PCR for Detection of Newcastle Disease Virus RNA in Clinical Samples Journal of Clinical Microbiology 2004, 42(1):329-338. 321685 14715773 10.1128/ JCM.42.1.329-338.2004
31. Rouet F Ekouevi DK Chaix M Burgard M Inwoley A D'Aquin Tony T Danel C Anglaret X Leroy V Msellati P Dabis F Rouzioux C Transfer and Evaluation of an Automated, Low-Cost Real-Time Reverse Transcription-PCR Test for Diagnosis and Monitoring of Human Immunodeficiency Virus Type 1 Infection in a West African Resource-Limited Setting Journal of Clinical Microbiology 2005, 43(6):2709-2717. 1151915 15956387 10.1128/ JCM.43.6.2709-2717.2005
32. Verstrepen WA Kuhn S Kockx MM Vyvere Van De ME Mertens AH Rapid Detection of Enterovirus RNA in Cerebrospinal Fluid Specimens with a Novel Single-Tube Real-Time Reverse Transcription-PCR Assay Journal of Clinical Microbiology 2001, 39(11):4093-4096. 88492 11682535 10.1128/ JCM.39.11.4093-4096.2001
33. Giles J Hardick J Yuenger J Dan M Reich K Zenilman J Use of Applied Biosystems 7900HT Sequence Detection System and Taqman Assay for Detection of Quinolone-Resistant Neisseria gonorrhoeae Journal of Clinical Microbiology 2004, 42(7):3281-3283. 446300 15243093 10.1128/ JCM.42.7.3281-3283.2004
34. Apfalter P Barousch W Nehr M Makristathis A Willinger B Rotter M Hirschl AM Comparison of a New Quantitative ompA-Based Real-time PCR TaqMan Assay for Detection of Chlamydia pneumoniae DNA in Respiratory Specimens with Four Conventional PCR Assays Journal of Clinical Microbiology 2003, 41(2):592-600. 149699 12574252 10.1128/JCM.41.2.592-600.2003
35. Ivacic L Reed KD Mitchell PD Ghebranious N A LightCycler TaqMan assay for detection of Borrelia burgdorferi sensu lato in clinical samples ScienceDirect - Diagnostic Microbiology and Infectious Disease 2007, 57(2):137-143. 10.1016/j.diagmicrobio.2006.08.005
36. Doyle CK Labruna MB Breitschwerdt EB Tang Y Corstvet RE Hegarty BC Bloch KC Li P Walker DH McBride JW Detection of Medically Important Ehrlichia by Quantitative Multicolor TaqMan Real-Time Polymerase Chain Reaction of the dsb Gene Journal of Molecular Diagnostics 2005, 7(4):504-514. 1888493 16237220