Gampawar, Piyush, Saba, Yasaman, Werner, Ulrike, Schmidt, Reinhold, Mueller-Myhsok, Bertram 
ORCID: 0000-0002-0719-101X and Schmidt, Helena
(2019)
Evaluation of the Performance of AmpliSeq and SureSelect Exome Sequencing Libraries for Ion Proton.
FRONTIERS IN GENETICS, 10 (SEP).
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Evaluation of the Performance of AmpliSeq and SureSelect Exome Sequencing Libraries for Ion Proton.pdf - Published version Download (2MB) | Preview |
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 <i>hitherto</i> 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.
| Item Type: | Article |
|---|---|
| Uncontrolled Keywords: | exome sequencing, ion proton sequencer, AmpliSeq, SureSelect, library preparation, validation |
| Depositing User: | Symplectic Admin |
| Date Deposited: | 18 Nov 2019 09:33 |
| Last Modified: | 19 Jan 2023 00:20 |
| DOI: | 10.3389/fgene.2019.00856 |
| Related URLs: | |
| URI: | https://livrepository.liverpool.ac.uk/id/eprint/3062019 |
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