**4.2. NGS step**

Although the 454 GS FLX was used often in the early stages of development of NGS-based HLA genotyping, the benchtop next-generation sequencers such as the GS Junior system, Ion Torrent PGM system, and the MiSeq system have been used more recently for the development and application of the HLA genotyping methods (Table 2). At the moment, complicated operations such as the preparation of NGS libraries are necessary for each of the different second generation sequencing platforms. However, the NGS companies are attempting to overcome these procedural bottlenecks by simplifying, automating, and speeding-up of the preparatory steps for NGS. For example, a new protocol using Ion Isothermal Amplification Chemistry that enables sequence reads of up to and beyond 500 bp, and Ion Hi-Q™ Sequencing Chemistry that reduces consensus insertion and deletion (indel) errors, including homopoly‐ mer errors, might lead to further simplification and cost reduction with higher data quality.
