Ddpcrquant: Threshold determination for single channel droplet digital PCR experiments

Analytical and Bioanalytical Chemistry

Volumn 407, Issue 19, 2015, Pages 5827-5834

  Trypsteen, Wim ^a   Vynck, Matthijs ^b   de Neve, Jan ^b   Bonczkowski, Pawel ^a   Kiselinova, Maja ^a   Malatinkova, Eva ^a   Vervisch, Karen ^a   Thas, Olivier ^b,c   Vandekerckhove, Linos ^a   de Spiegelaere, Ward ^a  

^a GHENT UNIVERSITY HOSPITAL   (Belgium)

^b GHENT UNIVERSITY   (Belgium)

^c UNIVERSITY OF WOLLONGONG   (Australia)

Author keywords

Automation; Data analysis; Droplet digital PCR; Extreme value distribution; R software; Rain; Threshold determination

Indexed keywords

FLUORESCENCE; POLYMERASE CHAIN REACTION; PROCEDURES;

FLUORESCENCE; POLYMERASE CHAIN REACTION;

EID: 85027917123     PISSN: 16182642     EISSN: 16182650     Source Type: Journal    
DOI: 10.1007/s00216-015-8773-4     Document Type: Article

References (22)

1. Hindson CM, Chevillet JR, Briggs HA et al (2013) Absolute quantification by droplet digital PCR versus analog real-time PCR. Nat Method 10:1003–1005
2. Sedlak RH, Jerome KR (2013) Viral diagnostics in the era of digital PCR. Diagn Microbial Infect Dis 75:1–4
3. Pinheiro LB, Coleman VA, Hindson CM et al (2012) Evaluation of a droplet digital polymerase chain reaction format for DNA copy number quantification. Anal Chem 84:1003–11
4. Hindson BJ, Ness KD, Masquelier DA et al (2011) Highthroughput droplet digital PCR system for absolute quantitation of DNA copy number. Anal Chem 83:8604–10
5. Dube S, Qin J, Ramakrishnan R (2008) Mathematical analysis of copy number variation in a DNA sample using digital PCR on a nanofluidic device. PLoS One 3, e2876
6. Kiselinova M, Pasternak AO, De Spiegelaere W et al (2014) Comparison of droplet digital PCR and seminested real-time PCR for quantification of cell-associated HIV-1 RNA. PLoS One 9, e85999
7. Strain MC, Lada SM, Luong T et al (2013) Highly precisemeasurement of HIV DNA by droplet digital PCR. PLoS One 8, e55943
8. Sedlak RH, Cook L, Huang M-L et al (2014) Identification of chromosomally integrated human herpesvirus 6 by droplet digital PCR. Clin Chem 60:765–72
9. Jones M, Williams J, Gärtner K et al (2014) Low copy target detection by Droplet Digital PCR through application of a novel open access bioinformatic pipeline, Bdefinetherain^. J Virol Methods 202:46–53
10. Dreo T, Pirc M, Ramsak Z (2014) Optimising droplet digital PCR analysis approaches for detection and quantification of bacteria : a case study of fire blight and potato brown rot. Anal Bioanal Chem 406:6513–6528
11. Buzon MJ, Massanella M, Llibre JM et al (2014) HIV-1 replication and immune dynamics are affected by raltegravir intensification of HAART-suppressed subjects. Nat Med 16:460–65
12. van der Sluis RM, van Montfort T, Centlivre M et al (2013) Quantitation of HIV-1 DNA with a sensitive Taqman assay that has broad subtype specificity. J Virol Methods 187:94–102
13. Liszewski MK, Yu JJ, O’Doherty U (2009) Detecting HIV-1 integration by repetitive-sampling Alu-gag PCR. Methods 47:254–260
14. Palmer S, Wiegand AP, Maldarelli F et al (2003) New real-time reverse transcriptase-initiated PCR assay with single-copy sensitivity for human immunodeficiency virus Type 1 RNA in Plasma. J Clin Microbiol 41:4531–4536
15. Fischer M, Joos B, Hirschel B et al (2004) Cellular viral rebound after cessation of potent antiretroviral therapy predicted by levels of multiply spliced HIV-1 RNA encoding nef. J Infect Dis 190:1979–1988
16. Lizée G, Aerts JL, Gonzales MI et al (2003) Real-time quantitative reverse transcriptase-polymerase chain reaction as a method for determining lentiviral vector titers and measuring transgene expression. Hum Gene Ther 14:497–507
17. De Spiegelaere W, Malatinkova E, Kiselinova M et al (2013) Touchdown digital polymerase chain reaction for quantification of highly conserved sequences in the HIV-1 genome. Anal Biochem 439:201–3
18. R Development Core Team (2014) R: A language and environment for statistical computing. R foundation for statistical computing, Vienna, Austria. http://www.R-project.org/ (Accessed January 2014)
19. Robertson T, Cryer JD (1974) An iterative procedure for estimating the mode. J Am Stat Assoc 69(348):1012–1016
20. Bickel DR, Fruehwirth R (2006) On a fast, robust estimator of the mode: comparisons to other robust estimators with applications. Comput Stat Data Anal 50(12):3500–3530
21. Stephenson AG (2002) evd: Extreme Value Distributions. R News, 2(2):31–32 URL: http://CRAN.R-project.org/doc/Rnews/
22. Malec P, Schienle M (2014) Nonparametric kernel density estimation near the boundary. Comput Stat Data Anal 72:57–76