Whole-Gene Next-Generation Sequencing of HLA Genes Reveals Hidden Diversity of Intronic Regions

Authors: György Horváth, Krisztina Rigó, Tim Hague, Szilveszter Juhos

Intronic regions of HLA alleles are less studied, but with the help of modern NGS kits covering whole genes it is easier to investigate this relatively unknown domain of sequences. To reveal the diversity of these regions we are presenting the comparison of intronic consensus sequences obtained from hundreds of samples with a special attention
to conserved and polymorphic regions.

Methods and Materials:
399 clinical samples from diverse population was sequenced to obtain whole-gene consensus sequences of Class-I and some Class-II (HLA-DQB1, HLA-DRB1) loci on an Illumina MiSeq instrument producing 2×250 bps long pairs. The consensus sequences were built by the Omixon TWIN software, and the intronic consensuses were extraced for multiple sequence alignement. Intron 1 for Class-II genes were not included in
the study, as these were not covered completely for all samples.

Many of the consensus sequences revealed novelties in intronic sequences that were not present in the IMGT/HLA database. Besides these, the sequencing methodology and the consensus building made it possible to build the intronic part of references that are represented by coding sequences only in the database.

The whole-gene NGS approach of HLA genes can reveal us polymorphism and conservation in intronic parts and by obtaining fully phased consensuses it is possible to fill the gaps in reference sequences containing only exons.

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