Evaluation of the Performance of AmpliSeq and SureSelect Exome Sequencing Libraries for Ion Proton

Piyush Gampawar; Yasaman Saba; Ulrike Werner; Reinhold Schmidt; Bertram Müller-Myhsok; Helena Schmidt

doi:10.3389/fgene.2019.00856

Evaluation of the Performance of AmpliSeq and SureSelect Exome Sequencing Libraries for Ion Proton

Front Genet. 2019 Sep 25:10:856. doi: 10.3389/fgene.2019.00856. eCollection 2019.

Authors

Piyush Gampawar¹, Yasaman Saba¹, Ulrike Werner¹, Reinhold Schmidt², Bertram Müller-Myhsok^{3

4

5}, Helena Schmidt¹

Affiliations

¹ Research Unit-Genetic Epidemiology, Gottfried Schatz Research Centre for Cell Signaling, Metabolism and Aging, Molecular Biology and Biochemistry, Medical University Graz, Graz, Austria.
² Department of Neurology, Clinical Division of Neurogeriatrics, Medical University Graz, Graz, Austria.
³ Max Planck Institute of Psychiatry, Munich, Germany.
⁴ Munich Cluster for Systems Neurology (SyNergy), Munich, Germany.
⁵ Institute of Translational Medicine, University of Liverpool, Liverpool, United Kingdom.

Abstract

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 values of >93% and >80%, respectively. Application of our variant calling pipeline decreased the number of false positive variants dramatically by 90% and resulted in positive predictive value of 97%. This improvement is highly relevant in research as well as clinical setting.

Keywords: AmpliSeq; SureSelect; exome sequencing; ion proton sequencer; library preparation; validation.