Medizinische Universität Graz Austria/Österreich - Forschungsportal - Medical University of Graz
Gewählte Publikation:
SHR Neuro Krebs Kardio Lipid Stoffw Microb
Gampawar, P; Saba, Y; Werner, U; Schmidt, R; Müller-Myhsok, B; Schmidt, H.
Evaluation of the Performance of AmpliSeq and SureSelect Exome Sequencing Libraries for Ion Proton.
Front Genet. 2019; 10: 856-856.
Doi: 10.3389/fgene.2019.00856
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- Führende Autor*innen der Med Uni Graz
- Gampawar Piyush Gajananrao
- Schmidt Helena
- Co-Autor*innen der Med Uni Graz
- Saba Yasaman
- Schmidt Reinhold
- Werner Ulrike
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- 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. Copyright © 2019 Gampawar, Saba, Werner, Schmidt, Müller-Myhsok and Schmidt.
- Find related publications in this database (Keywords)
- exome sequencing
- ion proton sequencer
- AmpliSeq
- SureSelect
- library preparation
- validation