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Methods ARTICLE Provisionally accepted The full-text will be published soon. Notify me

Front. Genet. | doi: 10.3389/fgene.2019.00856

Evaluation of the performance of AmpliSeq and SureSelect exome sequencing libraries for Ion Proton

  • 1Institute of Molecular Biology and Biochemistry, Medical University of Graz, Austria
  • 2Department of Neurology, Medical University of Graz, Austria
  • 3Max Planck Institute of Psychiatry (MPI), Germany

Library preparation for whole exome sequencing is a critical step serving the enrichment of the regions of interest. For Ion Proton, there are only two exome library preparation methods available, AmpliSeq and SureSelect. Although of major interest, a comparison of the two methods is hitherto missing in the literature. Here we systematically evaluate the performance of AmpliSeq and SureSelect and present an improved variant calling pipeline. We used 12 in-house DNA samples with genome-wide and exome microarray data and a commercially available reference DNA (NA12878) for evaluation. Both methods had a high concordance (>97%) with microarray genotypes and when validating against NA12878 a sensitivity and positive predictive value (PPV) of >93% and >80%, respectively. Application of our variant calling pipeline decreased the number of false positive variants dramatically by 90% and resulted in PPV of 97%. This improvement is highly relevant in research as well as clinical setting.

Keywords: Exome Sequencing (ES), Ion Proton sequencer, Ampliseq™, SureSelect, Library preparation protocol, Validation

Received: 11 Jun 2019; Accepted: 16 Aug 2019.

Copyright: © 2019 Gampawar, Saba, Werner, Schmidt, Müller-Myhsok and Schmidt. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

* Correspondence: Mx. Helena Schmidt, Institute of Molecular Biology and Biochemistry, Medical University of Graz, Graz, Austria, helena.schmidt@medunigraz.at