Doering, Matthias, Kreer, Christoph ORCID: 0000-0002-9140-9850, Lehnen, Nathalie, Klein, Florian and Pfeifer, Nico
(2019).
Modeling the Amplification of Immunoglobulins through Machine Learning on Sequence-Specific Features.
Sci Rep, 9.
LONDON:
NATURE PUBLISHING GROUP.
ISSN 2045-2322
Abstract
Successful primer design for polymerase chain reaction (PCR) hinges on the ability to identify primers that efficiently amplify template sequences. Here, we generated a novel Taq PCR data set that reports the amplification status for pairs of primers and templates from a reference set of 47 immunoglobulin heavy chain variable sequences and 20 primers. Using logistic regression, we developed TMM, a model for predicting whether a primer amplifies a template given their nucleotide sequences. The model suggests that the free energy of annealing, Delta G, is the key driver of amplification (p = 7.35e-12) and that 3' mismatches should be considered in dependence on Delta G and the mismatch closest to the 3' terminus (p = 1.67e-05). We validated TMM by comparing its estimates with those from the thermodynamic model of DECIPHER (DE) and a model based solely on the free energy of annealing (FE). TMM outperformed the other approaches in terms of the area under the receiver operating characteristic curve (TMM: 0.953, FE: 0.941, DE: 0.896). TMM can improve primer design and is freely available via openPrimeR (http://openPrimeR.mpi-inf.mpg.de).
Item Type: | Journal Article | ||||||||||||||||||||||||
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URN: | urn:nbn:de:hbz:38-134741 | ||||||||||||||||||||||||
DOI: | 10.1038/s41598-019-47173-w | ||||||||||||||||||||||||
Journal or Publication Title: | Sci Rep | ||||||||||||||||||||||||
Volume: | 9 | ||||||||||||||||||||||||
Date: | 2019 | ||||||||||||||||||||||||
Publisher: | NATURE PUBLISHING GROUP | ||||||||||||||||||||||||
Place of Publication: | LONDON | ||||||||||||||||||||||||
ISSN: | 2045-2322 | ||||||||||||||||||||||||
Language: | English | ||||||||||||||||||||||||
Faculty: | Unspecified | ||||||||||||||||||||||||
Divisions: | Unspecified | ||||||||||||||||||||||||
Subjects: | no entry | ||||||||||||||||||||||||
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Refereed: | Yes | ||||||||||||||||||||||||
URI: | http://kups.ub.uni-koeln.de/id/eprint/13474 |
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