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

Full text not available from this repository.

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:
CreatorsEmailORCIDORCID Put Code
Doering, MatthiasUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Kreer, ChristophUNSPECIFIEDorcid.org/0000-0002-9140-9850UNSPECIFIED
Lehnen, NathalieUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Klein, FlorianUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Pfeifer, NicoUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
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:
KeywordsLanguage
POLYMERASE-CHAIN-REACTION; TAQ DNA-POLYMERASE; RIBOSOMAL-RNA GENE; REVERSE-TRANSCRIPTASE; SECONDARY STRUCTURE; MISMATCH; PCR; DISCRIMINATION; ANTIBODIES; EXTENSIONMultiple languages
Multidisciplinary SciencesMultiple languages
Refereed: Yes
URI: http://kups.ub.uni-koeln.de/id/eprint/13474

Downloads

Downloads per month over past year

Altmetric

Export

Actions (login required)

View Item View Item