Improving statistical inference on pathogen densities estimated by quantitative molecular methods: Malaria gametocytaemia as a case study

BMC Bioinformatics

Volumn 16, Issue 1, 2015, Pages

  Walker, Martin ^a   Basáñez, María Gloria ^a   Ouédraogo, André Lin ^b   Hermsen, Cornelus ^c   Bousema, Teun ^c,d   Churcher, Thomas S ^a  

^a IMPERIAL COLLEGE LONDON   (United Kingdom)

^b Burkina Faso   (Burkina Faso)

^c RADBOUD UNIVERSITY MEDICAL CENTER   (Netherlands)

^d LONDON SCHOOL OF HYGIENE AND TROPICAL MEDICINE   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

ASSAYS; BAYESIAN NETWORKS; CALIBRATION; NUCLEIC ACIDS; POLYMERASE CHAIN REACTION; RELIABILITY; STATISTICS; UNCERTAINTY ANALYSIS;

DIAGNOSTIC PERFORMANCE; INTER-ASSAY VARIABILITY; NUCLEIC ACID SEQUENCE BASED AMPLIFICATION; QUANTITATIVE REAL-TIME POLYMERASE CHAIN REACTION; REVERSE TRANSCRIPTASES; STATISTICAL CALIBRATION; TRADITIONAL CALIBRATION; TRADITIONAL TECHNIQUES;

PATHOGENS;

PROTOZOAL DNA;

BAYES THEOREM; BLOOD; GENETICS; HUMAN; ISOLATION AND PURIFICATION; MALARIA, FALCIPARUM; NUCLEIC ACID SEQUENCE BASED AMPLIFICATION; PARASITOLOGY; PLASMODIUM FALCIPARUM; PROCEDURES; REAL TIME POLYMERASE CHAIN REACTION; REPRODUCIBILITY; SENSITIVITY AND SPECIFICITY; STATISTICAL ANALYSIS;

BAYES THEOREM; DATA INTERPRETATION, STATISTICAL; DNA, PROTOZOAN; HUMANS; MALARIA, FALCIPARUM; PLASMODIUM FALCIPARUM; REAL-TIME POLYMERASE CHAIN REACTION; REPRODUCIBILITY OF RESULTS; SELF-SUSTAINED SEQUENCE REPLICATION; SENSITIVITY AND SPECIFICITY;

EID: 84923865771     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/s12859-014-0402-2     Document Type: Article

References (51)

1. Tang YW, Procop GW, Persing DH. Molecular diagnostics of infectious diseases. Clin Chem. 1997;43:2021-38.
2. Ferguson NM, Cummings DA, Cauchemez S, Fraser C, Riley S, Meeyai A, et al. Strategies for containing an emerging influenza pandemic in Southeast Asia. Nature. 2005;437:209-14.
3. Fraser C, Hollingsworth TD, Chapman R, de Wolf F, Hanage WP. Variation in HIV-1 set-point viral load: epidemiological analysis and an evolutionary hypothesis. Proc Natl Acad Sci U S A. 2007;104:17441-6.
4. Wain J, Diep TS, Ho VA, Walsh AM, Nguyen TT, Parry CM, et al. Quantitation of bacteria in blood of typhoid fever patients and relationship between counts and clinical features, transmissibility, and antibiotic resistance. J Clin Microbiol. 1998;36:1683-7.
5. World Health Organization. Consolidated guidelines on the use of antiretroviral drugs for treating and preventing HIV infection: recommendations for a public health approach. In: Book Consolidated guidelines on the use of antiretroviral drugs for treating and preventing HIV infection: recommendations for a public health approach. Geneva: World Health Organization; 2013.
6. Woodhead M, Blasi F, Ewig S, Garau J, Huchon G, Ieven M, et al. Guidelines for the management of adult lower respiratory tract infections-full version. Clin Microbiol Infect. 2011;17 Suppl 6:E1-E59.
7. Murray JS, Elashoff MR, Iacono-Connors LC, Cvetkovich TA, Struble KA. The use of plasma HIV RNA as a study endpoint in efficacy trials of antiretroviral drugs. AIDS. 1999;13:797-804.
8. Mens PF, Sawa P, van Amsterdam SM, Versteeg I, Omar SA, Schallig HD, et al. A randomized trial to monitor the efficacy and effectiveness by QT-NASBA of artemether-lumefantrine versus dihydroartemisinin-piperaquine for treatment and transmission control of uncomplicated Plasmodium falciparum malaria in western Kenya. Malar J. 2008;7:237.
9. Bustin SA. Absolute quantification of mRNA using real-time reverse transcription polymerase chain reaction assays. J Mol Endocrinol. 2000;25:169-93.
10. Schmittgen TD, Livak KJ. Analyzing real-time PCR data by the comparative C(T) method. Nat Protoc. 2008;3:1101-8.
11. Osborne C. Statistical calibration: a review. Int Stat Rev. 1991;59:309-36.
12. Ferre F. Quantitative or semi-quantitative PCR: reality versus myth. PCR Methods Appl. 1992;2:1-9.
13. Nolan T, Hands RE, Bustin SA. Quantification of mRNA using real-time RT-PCR. Nat Protoc. 2006;1:1559-82.
14. Khairnar K, Martin D, Lau R, Ralevski F, Pillai DR. Multiplex real-time quantitative PCR, microscopy and rapid diagnostic immuno-chromatographic tests for the detection of Plasmodium spp: performance, limit of detection analysis and quality assurance. Malar J. 2009;8:284.
15. El Mubarak HS, De Swart RL, Osterhaus AD, Schutten M. Development of a semi-quantitative real-time RT-PCR for the detection of measles virus. J Clin Virol. 2005;32:313-7.
16. Bustin SA, Benes V, Garson JA, Hellemans J, Huggett J, Kubista M, et al. The MIQE guidelines: minimum information for publication of quantitative real-time PCR experiments. Clin Chem. 2009;55:611-22.
17. Miller JN. Basic statistical methods for analytical chemistry part 2. Calibration and regression methods* A review. Analyst. 1991;116:3-14.
18. Schneider P, Schoone G, Schallig H, Verhage D, Telgt D, Eling W, et al. Quantification of Plasmodium falciparum gametocytes in differential stages of development by quantitative nucleic acid sequence-based amplification. Mol Biochem Parasitol. 2004;137:35-41.
19. Churcher TS, Bousema T, Walker M, Drakeley C, Schneider P, Ouedraogo AL, et al. Predicting mosquito infection from Plasmodium falciparum gametocyte density and estimating the reservoir of infection. Elife. 2013;2:e00626.
20. Ponnudurai T, Lensen AH, Meis JF, Meuwissen JH. Synchronization of Plasmodium falciparum gametocytes using an automated suspension culture system. Parasitology. 1986;93(Pt 2):263-74.
21. Jiang J. Linear and Generalized Linear Mixed Models and Their Appications. New York: Springer; 2007.
22. McCulloch CE, Searle SR. Generalized, Linear and Mixed Models. New York: John Wiley & Sons; 2001.
23. Eisenhart C. The interpretation of certain regression methods and their use in biological and industrial research. Ann Math Stat. 1939;10:162-86.
24. Nadarajah S. On the ratio X/Y for some elliptically symmetric distributions. J Multivar Anal. 2006;97:342-58.
25. Marsaglia G. Ratios of normal variables. J Stat Softw. 2006;16:1-10.
26. McCulloch JH. Posterior Confidence Intervals in Linear Calibration Problems: Calibrating the Thompson Ice Core Index. Cleveland: Ohio State University; 2010.
27. Naszódi LJ. Elimination of the bias in the course of calibration. Technometrics. 1978;20:201-5.
28. Shulka GK. On the problem of calibration. Technometrics. 1972;14:547-53.
29. Danzer K, Currie LA, Chem CGAA. Guidelines for calibration in analytical chemistry - Part 1. Fundamentals and single component calibration (IUPAC recommendations 1998). Pure Appl Chem. 1998;70:993-1014.
30. Massart DL, Vandeginste BGM, Deming SN, Michotte Y, Kaufman L. Chemometrics: a textbook. Amsterdam: Elsevier; 1988.
31. Fieller EC. Some problems in interval estimation. J R Stat Soc Series B Stat Methodol. 1954;16:175-85.
32. Graybill FA. Theory and Application of the Linear Model. North Scituate, MA: Duxbury Press; 1976.
33. De Beer JO, De Beer TR, Goeyens L. Assessment of quality performance parameters for straight line calibration curves related to the spread of the abscissa values around their mean. Anal Chim Acta. 2007;584:57-65.
34. Lai KK, Cook L, Krantz EM, Corey L, Jerome KR. Calibration curves for real-time PCR. Clin Chem. 2005;51:1132-6.
35. Vankeerberghen P, Smeyers-Verbeke J. The quality coefficient as a tool in decisions about the quality of calibration in graphite furnace atomic absorption spectrometry. Chemom Intell Lab Syst. 1992;15:195-202.
36. Hoadley B. A Bayesian look at inverse regression. J Am Stat Assoc. 1970;65:356-69.
37. Gelman A, Carlin JB, Stern HS, Rubin DB. Bayesian Data Analysis. London: Chpaman & Hall; 2004.
38. Lunn D, Spiegelhalter D, Thomas A, Best N. The BUGS project: Evolution, critique and future directions. Stat Med. 2009;28:3049-67.
39. Lunn DJ, Thomas A, Best NG, Spiegelhalter DJ. WinBUGS - a Bayesian modelling framework: concepts, structure and extensibility. Stat Comput. 2000;10:325-37.
40. Spiegelhalter DJ, Best NG, Carlin BR, van der Linde A. Bayesian measures of model complexity and fit. J Roy Stat Soc B Stat Meth. 2002;64:583-616.
41. Karlen Y, McNair A, Perseguers S, Mazza C, Mermod N. Statistical significance of quantitative PCR. BMC Bioinformatics. 2007;8:131.
42. Yuan JS, Reed A, Chen F, Stewart Jr CN. Statistical analysis of real-time PCR data. BMC Bioinformatics. 2006;7:85.
43. Ruijter JM, Ramakers C, Hoogaars WM, Karlen Y, Bakker O, van den Hoff MJ, et al. Amplification efficiency: linking baseline and bias in the analysis of quantitative PCR data. Nucleic Acids Res. 2009;37:e45.
44. Niesters HG. Quantitation of viral load using real-time amplification techniques. Methods. 2001;25:419-29.
45. Cohen JF, Chalumeau M, Levy C, Bidet P, Thollot F, Wollner A, et al. Spectrum and inoculum size effect of a rapid antigen detection test for group A streptococcus in children with pharyngitis. PloS One. 2012;7:e39085.
46. Wampfler R, Mwingira F, Javati S, Robinson L, Betuela I, Siba P, et al. Strategies for Detection of Plasmodium species Gametocytes. PLoS One. 2013;8:e76316.
47. Fiscus SA, Cheng B, Crowe SM, Demeter L, Jennings C, Miller V, et al. HIV-1 viral load assays for resource-limited settings. PLoS Med. 2006;3:e417.
48. Schneider P, Wolters L, Schoone G, Schallig H, Sillekens P, Hermsen R, et al. Real-time nucleic acid sequence-based amplification is more convenient than real-time PCR for quantification of Plasmodium falciparum. J Clin Microbiol. 2005;43:402-5.
49. Okell LC, Bousema T, Griffin JT, Ouedraogo AL, Ghani AC, Drakeley CJ. Factors determining the occurrence of submicroscopic malaria infections and their relevance for control. Nat Commun. 2012;3:1237.
50. Sivaganesan M, Seifring S, Varma M, Haugland RA, Shanks OC. A Bayesian method for calculating real-time quantitative PCR calibration curves using absolute plasmid DNA standards. BMC Bioinformatics. 2008;9:120.
51. Plummer M. JAGS: A program for analysis of Bayesian graphical models using Gibbs sampling. In: Hornik K, Leisch F, Zeileis A, editors. Proceedings of the 3rd International Workshop on Distributed Statistical Computing; Vienna, Austria. 2003.