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

Next generation sequencing is a high throughput technology which simultaneously sequences DNA fragments within a short period. Library preparation is a critical step, as it serves the enrichment for the regions of interest from the genome. Several articles compared the performance of library preparation methods for Illumina sequencers. However, the studies comparing library preparation methods for Ion Proton are mostly missing. Here, we compared the performance of AmpliSeq and SureSelect only two whole exome sequencing library preparation methods available for Ion Proton using in-house and NA12878 reference DNAs and developed an optimised variant calling the pipeline. Our results show that both methods had a concordance rate of >97% with microarray data. Validation using NA12878 resulted in the sensitivity of >93% and positive predictive value (PPV) of >80% for both the methods. Use of our newly developed variant calling optimisation pipeline resulted into a decrease of false positive variants by 90% while increasing the sensitivity to 95% and PPV to 97% of each method.