A new method for robust quantitative and qualitative analysis of real-time PCR

Shain, Eric B.; Clemens, John M.

doi:10.1093/nar/gkn408

Cited by 58 publications

(39 citation statements)

References 10 publications

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“…Additional safeguard features include an internal control based on a house keeping gene and a proprietary algorithm for amplification curve validation. 23 The assay has shown clinical sensitivity and specificity comparable with HC2 and INNO-LiPA in our referral population, and the results compare well with those observed in referral populations by other groups. 15,16 The typing agreement with INNO-LiPA was excellent and ART is reliably distinguishing infections by HPV16 and HPV18 from infections caused by other HR-HPV genotypes.…”

Section: Discussionsupporting

confidence: 84%

Comparison of Abbott RealTime High Risk HPV and Hybrid Capture 2 for the detection of high-risk HPV DNA in a referral population setting

Venturoli

Leo

Nocera

et al. 2012

Journal of Clinical Virology

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Section: Discussionsupporting

confidence: 84%

Comparison of Abbott RealTime High Risk HPV and Hybrid Capture 2 for the detection of high-risk HPV DNA in a referral population setting

Venturoli

Leo

Nocera

et al. 2012

Journal of Clinical Virology

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“…The analysis of discrepant results also made use of quantitative data available for the Abbott assay. As described previously (16), the Abbott software calculates a measure called the FCN, the cycle number at which the change in signal from one amplification cycle to the next is greatest. The FCN is used as an alternative to the cycle threshold.…”

Section: Methodsmentioning

confidence: 99%

Evaluation of the Abbott RealTi m e CT/NG Assay in Comparison to the Roche Cobas Amplicor CT/NG Assay

2011

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Several commercial methods exist for the molecular detection of Chlamydia trachomatis and Neisseria gonorrhoeae in clinical samples. Here we evaluated the performance characteristics of the newly FDAcleared Abbott RealTime CT/NG assay (where "CT" stands for Chlamydia trachomatis and "NG" stands for Neisseria gonorrhoeae) that uses the automated m2000 molecular platform. Results were compared to those of the Roche Cobas Amplicor CT/NG assay. A total of 926 cervical swab, 45 female urine, 6 male urethral swab, and 407 male urine specimens from 1,384 patients were examined. After resolving all Roche N. gonorrhoeae-positive results with two additional real-time PCR assays, we found that the agreement between the assays was excellent. For urine samples, there was 99.6% positive agreement and 97.7% negative agreement for C. trachomatis, and for male urine samples, there was 100% positive agreement and 99.7% negative agreement for N. gonorrhoeae. For cervical swab samples, there was 98.8% positive agreement and 98.5% negative agreement for C. trachomatis, and there was 96.6% positive agreement and 99.8% negative agreement for N. gonorrhoeae. In limiting dilution analyses, we found that the Abbot assay was more sensitive than the Roche assay for both C. trachomatis and N. gonorrhoeae. In addition, there appeared to be an enhanced ability of the Abbott assay to detect dual infections, especially in the presence of large amounts of N. gonorrhoeae and small amounts of C. trachomatis organisms. In summary, we conclude that the Abbott RealTime CT/NG assay is an accurate and automated new addition to the available testing options for C. trachomatis and N. gonorrhoeae.The incidences of Chlamydia trachomatis and Neisseria gonorrhoeae infection continue to increase globally. A more intensive screening effort has been advocated by the U.S. Preventive Services Task Force (18), the Centers for Disease Control and Prevention (24), other public health agencies, and medical societies to bring this emerging epidemic under control. This includes the yearly screening of sexually active women under the age of 25 years for C. trachomatis. The goal of screening is to prevent transmission and the severe sequelae of unrecognized infection, such as pelvic inflammatory disease and associated infertility.Rapid, automated, and sensitive nucleic acid amplification testing methods are needed to respond optimally to this public health mandate. In this regard, there have been limited published evaluations of the recently FDA-cleared Abbott RealTime CT/NG assay (where "CT" stands for Chlamydia trachomatis and "NG" stands for Neisseria gonorrhoeae) (9). There was a recent report of clinical trial data comparing the Abbott assay to Gen-Probe Aptima Combo 2 (AC2), BD ProbeTec ET CT/GC, and GC culture (where "GC" represents N. gonorrhoeae) (6). There was also one prior study from Canada using a CE-marked Abbott kit with different cutoff and interpretation algorithms (8) and a U.S. study performed by Abbott Laboratories (Des Plaines, IL) using a prototype ...

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“…Every data point is treated as exact (i.e., the fitted curve intersects with it) by use of piecewise polynomial regression. This is the approach of efficiency estimation in Shain and Clemens (37 ). We conducted a simulation as in Fig.…”

Section: Resultsmentioning

confidence: 99%

Impact of Smoothing on Parameter Estimation in Quantitative DNA Amplification Experiments

et al. 2015

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BACKGROUND: Quantification cycle (Cq) and amplification efficiency (AE) are parameters mathematically extracted from raw data to characterize quantitative PCR (qPCR) reactions and quantify the copy number in a sample. Little attention has been paid to the effects of preprocessing and the use of smoothing or filtering approaches to compensate for noisy data. Existing algorithms largely are taken for granted, and it is unclear which of the various methods is most informative. We investigated the effect of smoothing and filtering algorithms on amplification curve data.

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A new method for robust quantitative and qualitative analysis of real-time PCR

Cited by 58 publications

References 10 publications

Comparison of Abbott RealTime High Risk HPV and Hybrid Capture 2 for the detection of high-risk HPV DNA in a referral population setting

Comparison of Abbott RealTime High Risk HPV and Hybrid Capture 2 for the detection of high-risk HPV DNA in a referral population setting

Evaluation of the Abbott RealTi m e CT/NG Assay in Comparison to the Roche Cobas Amplicor CT/NG Assay

Impact of Smoothing on Parameter Estimation in Quantitative DNA Amplification Experiments

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