Digital polymerase chain reaction

Digital polymerase chain reaction (digital PCR, DigitalPCR, dPCR, or dePCR) is a biotechnology refinement of conventional polymerase chain reaction methods that can be used to directly quantify and clonally amplify nucleic acids including DNA, cDNA or RNA. The key difference between dPCR and traditional PCR lies in the method of measuring nucleic acids amounts, with the former being a more precise method than PCR, though also more prone to error in the hands of inexperienced users.[1]:217 PCR carries out one reaction per single sample. dPCR also carries out a single reaction within a sample, however the sample is separated into a large number of partitions and the reaction is carried out in each partition individually. This separation allows a more reliable collection and sensitive measurement of nucleic acid amounts. The method has been demonstrated as useful for studying variations in gene sequences — such as copy number variants and point mutations — and it is routinely used for clonal amplification of samples for "next-generation sequencing."

PCR basics

The polymerase chain reaction method is used to quantify nucleic acids by amplifying a nucleic acid molecule with the enzyme DNA polymerase. Conventional PCR is based on the theory that amplification is exponential. Therefore, nucleic acids may be quantified by comparing the number of amplification cycles and amount of PCR end-product to those of a reference sample. However, many factors complicate this calculation, creating uncertainties and inaccuracies. These factors include the following: initial amplification cycles may not be exponential; PCR amplification eventually plateaus after an uncertain number of cycles; and low initial concentrations of target nucleic acid molecules may not amplify to detectable levels. However, the most significant limitation of PCR is that PCR amplification efficiency in a sample of interest may be different from that of reference samples. Since PCR is an exponential process, only twofold differences in amplification can be observed, greatly impacting the validity and precision of the results.

dPCR working principle

A sample is partitioned so that individual nucleic acid molecules within the sample are localized and concentrated within many separate regions. (The capture or isolation of individual nucleic acid molecules has been effected in micro well plates, capillaries, the dispersed phase of an emulsion, and arrays of miniaturized chambers, as well as on nucleic acid binding surfaces.) The partitioning of the sample allows one to estimate the number of different molecules by assuming that the molecule population follows the Poisson distribution. As a result, each part will contain "0" or "1" molecules, or a negative or positive reaction, respectively. After PCR amplification, nucleic acids may be quantified by counting the regions that contain PCR end-product, positive reactions. In conventional PCR, the number of PCR amplification cycles is proportional to the starting copy number. dPCR, however, is not dependent on the number of amplification cycles to determine the initial sample amount, eliminating the reliance on uncertain exponential data to quantify target nucleic acids and therefore provides absolute quantification.

Development

The original dPCR paper was published by Dr Alec Morley and Pamela Sykes in 1992. The purpose was to quantify PCR targets, rather than the PCR amplified products in an attempt to track and measure the absolute lowest number of leukemic cells in a patient with leukemia. The purpose was to monitor residual disease in leukemia patients, and thereby treat the patients at the earliest possible moment of detection of disease recurrence. Further evolutions of the technology allowed for more practical use of this method with a wider audience, with small partitions created by emulsion droplets and/or microfluidics.[2]

A development occurred in 1995 with co-inventions by Brown at Cytonix and Silver at the National Institutes of Health of single-step quantitization and sequencing methods employing nano-scale physical containment arrays (Brown, Silver),[3] and open chambers (Brown) using localized clonal colonies in 1D and 2D capillaries, macro volumes, gels, free chambers, and affinity surfaces/particles. resulting in a 1997 U. S. Patent,[4] and subsequent divisional and continuation patents. The concepts of electrowetting and digital microfluidics were further introduced (Brown) as one means of manipulating nano fluid volumes.

Digital PCR has been shown to be a promising surveillance tool for illnesses such as cancer, and as a vital front end to determining genomic content, including sequencing the human genome.

Based on the concept Vogelstein and Kinzler developed a technology called BEAMing (Beads, Emulsion, Amplification, Magnetics) and quantified KRAS mutations in stool DNA from colorectal cancer patients.[5][6]

Significant additional developments have included using emulsion beads for digital PCR by Dressman and colleagues.[7]

It has also proved useful for the analysis of heterogeneous methylation.[8]

In 2006 Fluidigm introduced the first commercial system for digital PCR based on integrated fluidic circuits (chips) having integrated chambers and valves for partitioning samples.

In 2008, Inostics started to provide BEAMing digital PCR services for the detection of mutations in plasma/serum and tissue.

QuantaLife developed a fundamentally distinct method of partitioning, the Droplet Digital PCR (ddPCR) technology, which partitions a sample into 20,000 droplets and provides digital counting of nucleic acid targets. In 2011, Quantalife was acquired by Bio-Rad Laboratories.[9]

In 2013, RainDance Technologies launched a digital PCR platform based on its picoliter-scale droplet technology, which generates up to 10 million picoliter-sized droplets per lane.[10][11] The technology was first demonstrated in a paper published in Lab on a Chip by scientists from Université de Strasbourg and Université Paris Descartes.[11][12] Later that year, RainDance Technologies announced a partnership with Integrated DNA Technologies to develop reagents for the digital PCR platform.[13]

Digital PCR has many applications, including the detection and quantification of low-level pathogens, rare genetic sequences, copy number variations, and relative gene expression in single cells. This method provides the information with accuracy and precision. Clonal amplification enabled by single-step digital PCR is a key factor in reducing the time and cost of many of the "next-generation sequencing" methods and hence enabling personal genomics.

MIQE

The "Minimum Information for Publication of Quantitative Digital PCR Experiments" or "digital MIQE" guidelines are a comprehensive set of best practices which aim to increase the validity and comparability of digital PCR experiments reported in published literature.[1]:217 The guide was published in 2013 and followed publication in 2009 of "MIQE", a comparable guide for quantitative real-time PCR.[14][15] In the two years following publication of the "digital MIQE", less than 20% of published digital PCR papers have cited the guideline.[1]:217

References

  1. 1 2 3 Perkel, Jeffrey (May 2015). "Guiding our PCR Experiments". Tech News. BioTechniques 58 (5): 217–21.
  2. ↑ Sykes PJ, Neoh SH, Morley AA; et al. (September 1992). "Quantitation of targets for PCR by use of limiting dilution.". BioTechniques 13 (3): 444–9. PMID 1389177.
  3. ↑ Kalinina, O; Brown J; Silver J (1997). "Nanoliter scale PCR with TaqMan detection". Nucleic Acids Research 25 (10): 1999–2004. doi:10.1093/nar/25.10.1999. PMC 146692. PMID 9115368.
  4. ↑ US patent 6143496, Brown, JF; Silver, JE & Kalinina, OV, "Method of sampling, amplifying and quantifying segment of nucleic acid, polymerase chain reaction assembly having nanoliter-sized sample chambers, and method of filling assembly", issued 2000-11-07, assigned to Cytonix and US Department of Health and Human Services
  5. ↑ Vogelstein, B; Kinzler KW (1999). "Digital PCR". Proceedings of the National Academy of Sciences of the United States of America 96 (16): 9236–41. doi:10.1073/pnas.96.16.9236. PMC 17763. PMID 10430926.
  6. ↑ Pohl, G; Shih, I-M (2004). "Principle and applications of digital PCR". Expert Review of Molecular Diagnostics (Informa) 4 (1): 41–7. doi:10.1586/14737159.4.1.41. PMID 14711348.
  7. ↑ Dressman, D; Yan H; Traverso G; Kinzler KW; Vogelstein B (2003). "Transforming single DNA molecules into fluorescent magnetic particles for detection and enumeration of genetic variations". Proceedings of the National Academy of Sciences of the United States of America 100 (15): 8817–22. doi:10.1073/pnas.1133470100. PMC 166396. PMID 12857956.
  8. ↑ Mikeska, T; Candiloro IL; Dobrovic A (2010). "The implications of heterogeneous DNA methylation for the accurate quantification of methylation". Epigenomics 2 (4): 561–73. doi:10.2217/epi.10.32. PMID 22121974.
  9. ↑ "Bio-Rad Acquires QuantaLife and Digital PCR Technology" (Press release). Bio-Rad. 5 October 2011.
  10. ↑ "RainDance Launches Digital PCR Platform; Claims Sensitivity, Operating Cost Superiority". PCR Insider. Genomeweb. 29 March 2012.(subscription required)
  11. 1 2 Kubista, M. (1 May 2012). "Drivers and Hurdles for qPCR". Feature Article. Genetic Engineering & Biotechnology News 32 (9).
  12. ↑ Pekin D, Skhiri Y, Baret JC; et al. (July 2011). "Quantitative and sensitive detection of rare mutations using droplet-based microfluidics". Lab on a Chip 11 (13): 2156–66. doi:10.1039/c1lc20128j. PMID 21594292.
  13. ↑ "RainDance, IDT Partner on Consumables for Digital PCR Platform". GenomeWeb Daily News (Genomeweb). 15 October 2012.(registration required)
  14. ↑ Huggett JF; Foy CA; Benes V; et al. (June 2013). "The digital MIQE guidelines: Minimum Information for Publication of Quantitative Digital PCR Experiments". Clinical Chemistry 59 (6): 892–902. doi:10.1373/clinchem.2013.206375.
  15. ↑ Bustin SA; Benes V; Garson JA; et al. (April 2009). "The MIQE Guidelines: Minimum Information for Publication of Quantitative Real-Time PCR Experiments". Clinical Chemistry 55 (4): 611–22. doi:10.1373/clinchem.2008.112797. PMID 19246619.

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