Universität zu Köln

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

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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
Creators:	Creators Email ORCID ORCID Put Code Doering, Matthias UNSPECIFIED UNSPECIFIED UNSPECIFIED Kreer, Christoph UNSPECIFIED orcid.org/0000-0002-9140-9850 UNSPECIFIED Lehnen, Nathalie UNSPECIFIED UNSPECIFIED UNSPECIFIED Klein, Florian UNSPECIFIED UNSPECIFIED UNSPECIFIED Pfeifer, Nico UNSPECIFIED UNSPECIFIED UNSPECIFIED
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
Uncontrolled Keywords:	Keywords Language POLYMERASE-CHAIN-REACTION; TAQ DNA-POLYMERASE; RIBOSOMAL-RNA GENE; REVERSE-TRANSCRIPTASE; SECONDARY STRUCTURE; MISMATCH; PCR; DISCRIMINATION; ANTIBODIES; EXTENSION Multiple languages Multidisciplinary Sciences Multiple languages
Refereed:	Yes
URI:	http://kups.ub.uni-koeln.de/id/eprint/13474