Modelling the PCR amplification process by a size-dependent branching process and estimation of the efficiency
Abstract
We propose a stochastic modelling of the PCR amplification process by a size-dependent branching process starting as a supercritical Bienaymé-Galton-Watson transient phase and then having a saturation near-critical size-dependent phase. This model allows us to estimate the probability of replication of a DNA molecule at each cycle of a single PCR trajectory with a very good accuracy.
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PCR is an exponential process, so small random variations early on in amplification can have a large impact on distribution.
“PCR is an exponential process, so small random variations early on in amplification can have a large impact on distribution18–24.”
From Quantifying Molecular Bias in DNA Data Storage (2019) · cites this paper as [20]
PCR is an exponential process, so small random variations early on in amplification can have a large impact on distribution.
“PCR is an exponential process, so small random variations early on in amplification can have a large impact on distribution18–24.”
From Quantifying Molecular Bias in DNA Data Storage (2019) · cites this paper as [22]
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Quantifying Molecular Bias in DNA Data Storage
Chen, Y.-J., Takahashi, C. N., Organick, L., Stewart, K., Ang, S. D., Weiss, P., Peck, B., Seelig, G., Ceze, L., & Strauss, K. (2019) · doi:10.1101/566554 · Cited by 109 · see citing works
Combinatorial PCR Method for Efficient, Selective Oligo Retrieval from Complex Oligo Pools
Winston, C., Organick, L., Ward, D., Ceze, L., Strauss, K., & Chen, Y.-J. (2022) · ACS Synthetic Biology · doi:10.1021/acssynbio.1c00482 · Cited by 29 · see citing works
- Authors
- Lalam, N., Jacob, C., & Jagers, P.
- Affiliations
- Institut National de la Recherche Agronomique (FR)
- Chalmers University of Technology (SE)
- Corresponding author
- Lalam, N.
- Jacob, C.
- Jagers, P.
- ORCID
- Jagers, P.
- Venue
- Advances in Applied Probability
- Publisher
- Cambridge University Press (CUP)
- Published
- 2004-06
- Volume
- 36
- Issue
- 2
- Pages
- 602-615
- ISSN
- 0001-8678 (ISSN-L)
- 1475-6064
- OpenAlex
- W2158274955
- Cited by
- 46
- References
- 30
- Citations by year
- 2026: 1 · 2025: 4 · 2023: 1 · 2022: 1 · 2020: 1 · 2019: 2 · 2018: 2 · 2017: 2 · 2016: 3 · 2015: 2 · 2013: 1 · 2012: 1
- FWCI
- 5.68
- Type
- journal article
- Language
- en
- Open access
- closed
- Locations
- Advances in Applied Probability (publishedVersion)
- TU/e Research Portal (submittedVersion)
- Project Euclid (Cornell University) (submittedVersion)
- Topics
- Physical Sciences › Mathematics › Mathematical Physics › Stochastic processes and statistical mechanics
- Health Sciences › Medicine › Public Health, Environmental and Occupational Health › Mathematical and Theoretical Epidemiology and Ecology Models
- Physical Sciences › Mathematics › Statistics and Probability › Probability and Statistical Research
- Keywords
- PCR amplification, stochastic modeling, Bienaymé-Galton-Watson process, saturation
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