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qPCR


References 1 Kubista, M, Andrade, JM, Bengtsson, M, Forootan, A, Jonák, J, Lind, K, Sindelka, R, Sjöback, R, Sjögreen, B, Strömbom, L, Ståhlberg, A, Zoric, N. The real-time polymerase chain reaction. Mol Aspects Med. 2006 Apr-Jun;27(2-3):95-125. Epub 2006 Feb 3. 2 http://www.appliedbiosystems.com/ absite/us/en/home/applications- technologies/real-time-pcr/real-time-pcr- instruments/openarray-real-time-pcr- system.html. 3 http://www.fluidigm.com/. 4 http://www.roche.com/products/product- details.htm?type=product&id=134. 5 http://www.wafergen.com/. 6 Letertre, C, Perelle, S, Dilasser, F, Arar, K, Fach, P. Evaluation of the performance of LNA and MGB probes in 5’-nuclease PCR assays. Mol Cell Probes. 2003 Dec;17(6):307-11. 7 http://www.lifetechnologies.com/news- gallery/press-releases/2011/oe-i-1-millio-o-loger- a-log-shot.html. 8 http://www.swiftbiosci.com/technology/ my-t-primers. 9 Rådström, P, Knutsson, R, Wolffs, P, Lövenklev, M, Löfström, C. Pre-PCR processing: strategies to generate PCR-compatible samples. Mol Biotechnol. 2004 Feb;26(2):133-46. 10 Kermekchiev, MB, Kirilova, LI, Vail, EE, Barnes, WM. Mutants of Taq DNA polymerase resistant to PCR inhibitors allow DNA amplification from whole blood and crude soil samples. Nucleic Acids Res. 2009 Apr;37(5):e40. Epub 2009 Feb 10. 11 Higuchi, Russell, Fockler, Carita, Dollinger, Gavin and Watson, Robert. Kinetic PCR Analysis: Real-time Monitoring of DNA Amplification Reactions. Nature Biotechnology 11, 1026 – 1030 (1993). doi:10.1038/ nbt0993-1026. 12 Sykes, PJ, Neoh, SH, Brisco, MJ, Hughes, E, Condon, J, Morley, AA. Quantitation of targets for PCR by use of limiting dilution. Biotechniques. 1992 Sep;13(3):444-9. 13 Kalinina, O, Lebedeva, I, Brown, J, Silver, J. Nanoliter scale PCR with TaqMan detection. Nucleic Acids Res. 1997 May 15;25(10): 1999-2004. 14Vogelstein, B, Kinzler, KW. Digital PCR. Proc Natl Acad Sci U S A. 1999 Aug 3;96(16):9236-41. 15 http://www.tataa.com/Services/Projects. html#Digital. 16 Sanders, R, Huggett, JF, Bushell, CA, Cowen, S, Scott, DJ, Foy, CA. Evaluation of digital PCR for absolute DNA quantification. Anal Chem. 2011 Sep 1;83(17):6474-84. Epub 2011 Aug 1. 17 http://www.tataa.com/products/ValidPrime- Control-of-Genomic-Background/View-all- products.html. 18 Dube, Simant, Qin, Jian, Ramakrishnan, Ramesh. Mathematical Analysis of Copy Number Variation in a DNA Sample Using Digital PCR on a Nanofluidic Device. PLoS ONE 3 (2008), pp. e2876–e2883.


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19Weaver, Suzanne, Dube, Simant, Mir, Alain, Qin, Jian Gang, Sun, Ramakrishnan, Ramesh, Jones, Robert C and Livak, Kenneth J. Taking qPCR to a higher level: Analysis of CNV reveals the power of high throughput qPCR to enhance quantitative resolution. Methods Volume 50, Issue 4, April 2010, Pages 271-276. The ongoing Evolution of qPCR. 20 http://www.tataa.com/Courses/Course- Modules.html#2daysbiostatistics. 21 Laurell, Henrik. ValidPrime for accurate real time qPCR quantification of RNA without DNase treatment. Presentation at the 2011 years qPCR Symposium in Prague (www.qpcrsymposium.eu). 22 Liu, YJ, Zheng, D, Balasubramanian, S, Carriero, N, Khurana, E, Robilotto, R, Gerstein, MB. Comprehensive analysis of the pseudogenes of glycolytic enzymes in vertebrates: the anomalously high number of GAPDH pseudogenes highlights a recent burst of retrotrans-positional activity. BMC Genomics. 2009 Oct 16;10:480. 23 http://www.pseudogene.org/. 24Wang, J, Ramakrishnan, R, Tang, Z, Fan, W, Kluge, A, Dowlati, A, Jones, RC, Ma, PC. Quantifying EGFR alterations in the lung cancer genome with nanofluidic digital PCR arrays. Clin Chem. 2010 Apr;56(4):623-32. Epub 2010 Mar 5. 25 Ottesen, EA, Hong, JW, Quake, SR, Leadbetter, JR. Microfluidic digital PCR enables multigene analysis of individual environmental bacteria. Science. 2006 Dec 1;314(5804):1464-7. 26Tadmor, AD, Ottesen, EA, Leadbetter, JR, Phillips, R. Probing individual environmental bacteria for viruses by using microfluidic digital PCR. Science. 2011 Jul 1;333(6038):58-62. 27 Lun, Fiona MF, Chiu, Rossa, WK. Chan, KC Allen, Leung, Tak Yeung, Lau, Tze Kin and Lo, YM Dennis. Microfluidics Digital PCR Reveals a Higher than Expected Fraction of Fetal DNA in Maternal Plasma. Clinical Chemistry. 2008;54:1664-1672. 28 Goh, HG, Lin, M, Fukushima, T, Saglio, G, Kim, D, Choi, SY, Kim, SH, Lee, J, Lee, YS, Oh, SM, Kim, DW. Sensitive quantitation of minimal residual disease in chronic myeloid leukemia using nanofluidic digital polymerase chain reaction assay. Leuk Lymphoma. 2011 May;52(5):896-904. Epub 2011 Feb 21. 29 Sindelka, R, Sidova, M, Svec, D, Kubista, M. Spatial expression profiles in the Xenopus laevis oocytes measured with qPCR tomography. Methods. 2010 Jan 4.


doi:10.1016/j.ymeth.2009.12.011. 30 Huang, Q, Zheng, L, Zhu, Y, Zhang, J, Wen, H, Huang, J, Niu, J, Zhao, X, Li, Q. Multicolor combinatorial probe coding for real-time PCR. PLoS One. 2011 Jan 14;6(1):e16033. 31 Zhong, Q, Bhattacharya, S, Kotsopoulos, S, Olson, J, Taly, V, Griffiths, AD, Link, DR, Larson, JW. Multiplex digital PCR: breaking the one target per color barrier of quantitative PCR. Lab Chip. 2011 Jul 7;11(13):2167-74. Epub 2011 May 17.


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32 Sundberg, SO, Wittwer, CT, Gao, C, Gale, BK. Spinning disk platform for microfluidic digital polymerase chain reaction. Anal Chem. 2010 Feb 15;82(4):1546-50. 33 Shen, F, Du, W, Kreutz, JE, Fok, A, Ismagilov, RF. Digital PCR on a SlipChip. Lab Chip. 2010 Oct 21;10(20):2666-72. Epub 2010 Jul 1. 34 Heyries, Kevin A, Tropini, Carolina, VanInsberghe, Michael, Doolin, Callum, Petriv, Oleh I, Singhal, Anupam, Leung, Kaston, Hughesman, Curtis B and Hansen, Carl L. Megapixel digital PCR. Nature methods VOL.8 NO.8, AUGUST 2011, 649. 35Tawfik, DS, Griffiths, AD. Man-made cell-like compartments for molecular evolution. Nat Biotechnol. 1998 Jul;16(7):652-6. 36 Nakano, Michihiko, Komatsu, Jun, Matsuura, Shun-ichi, Takashima, Kazunori, Katsura, Shinji, Mizuno, Akira. Single-molecule PCR using water- in-oil emulsion. Journal of Biotechnology, Volume 102, Issue 2, 24 April 2003, Pages 117-124. 37 Kiss, MM, Ortoleva-Donnelly, L, Beer, NR, Warner, J, Bailey, CG, Colston, BW, Rothberg, JM, Link, DR, Leamon, JH. High-throughput quantitative polymerase chain reaction in picoliter droplets. Anal Chem. 2008 Dec 1;80(23):8975-81. 38 http://www.quantalife.com. 39 http://www.raindancetech.com. 40 http://www.genomeweb.com/pcrsample- prep/raindance-eyes-early-2012-digital-pcr- launch-preps-new-sequence-enrichment-platf. 41 http://www.stokesbio.com/. 42 Schütze, Tatjana and Glökler, Jörn. Idiot-proof emulsion PCR. LabTimes. 2010; 2010(1):50. 43 http://www.img.cas.cz/ge/.

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