Exons 4, 5 and 7 are amplified in three PCR reactions using primer mixes targeting all KIR genes. The PCR products contain sample specific identification sequences and can therefore be combined for joint sequencing on Illumina MiSeq or HiSeq instruments. Up to 4800 samples are sequenced on one 2 × 250 rapid run HiSeq flowcell yielding on average about 60,000 reads per sample evenly split between HLA and KIR. Sequencing data is analyzed by neXtype, an inhouse software, and currently yields presence/absence calls for the KIR genes with KIR2DS4 and KIR2DS4N being distinguished and KIR2DL5A and KIR2DL5B being combined into KIR2DL5.
Validation yielded 100% concordance with the pretypings for all 109 samples passing the predefined internal quality criteria. Within the first 4 months in 2015 we performed successful KIR typing for more than 100.000 samples. Initial analysis indicates that haplotypes lacking the KIR core genes 3DP1 and 2DL4 are more common than previously anticipated.
Our amplicon-based NGS typing approach enables us to type up to 5000 samples/day for KIR. Typing costs including KIR increased only moderately compared to the former profile including 6 HLA loci (A, B, C, DRB1, DQB1 and DPB1), CCR5, and blood groups ABO and Rh. This facilitated DKMS to expand the profile for all newly registered donors to include KIR typing.