P076 KIR allele level typing by a novel neXtype algorithm

KIR genes are recognized to play an important role for stem cell transplantation. The high polymorphism of these genes makes it difficult to achieve high resolution typing results.Based on paired-end short amplicon next generation sequencing (NGS) data from the Ilumina Miseq and HiSeq systems, neXtype was adapted to type KIR on allelic level. neXtype reports KIR allele typing results in the genotype list (GL) string format and implicitly provides gene copy numbers.neXtype copes with KIR typing challenges in several consecutive steps:In a first step based on the IPD-KIR library, each read is assigned the best matching known exon sequence using the tree-concept of neXtype. In a second step, the copy numbers of the identified allelic variants per exon are determined for a given primer batch. This estimated exon copy number is subsequently required for the scoring system. As a third step, combination of exon-specific results determines KIR alleles present in the sample. The number of valid exon combinations per gene yields the gene copy number. Currently, neXtype uses exons 3, 4, 5, 7, 8, and 9. The assignment of reads to a specific gene is a priori not possible as some alleles of different genes share identical exon DNA sequences. Therefore, valid combinations for those gene-bridging exons must be analyzed simultaneously. neXtype uses a scoring system based on the difference between the copy number as given by valid exon combinations from step three and the estimated exon copy number from step two. The exon combination with the lowest score is taken as the typing result and presented as a GL string.With this algorithm, samples with pre-known typing results were confirmed. In summary, we show that cost efficient high-throughput NGS data can be used for allele level KIR typing. As a consequence, allele level KIR typing could be included into the standard typing profile of newly registered stem cell donors, thus allowing for refined donor selection algorithms.