Aim The assignment of exon novel alleles is clinically relevant in hematopoietic stem cell transplantation (HSCT), in particular for donor selection. Here we investigate the exon novelty in over 21,000 National Marrow Donor Program (NMDP) registry donors by using next generation sequencing (NGS) approach on buccal swab DNA. Methods Multiplex long-range PCR primers amplified the full-length of HLA class I genes (HLA-A, -B, -C) from promoter to 3’ UTR. Class II genes (-DQB1, -DRB1) were amplified from exon 2 through part of exon 4. PCR amplicons were pooled and sheared using Covaris fragmentation. Library preparation was performed using the Illumina TruSeq Nano kit on the Beckman FX automated platform. Each sample was tagged with a unique barcode, followed by 2 × 250 bp paired-end sequencing on the Illumina MiSeq. Exon novelty was assigned using GenDx NGSengine v2.4.0 and Omixon Twin v1.0.7 software to ensure high confidence in allele calling. Exon novelties were confirmed by Sanger sequencing and 3D protein structure was predicted using Phyre2. Results Using this automated workflow, over 21,000 NMDP registry donors were successfully typed using high-resolution by NGS. NGS-HLA typing identified 94 exon novelties (0.044%) at five loci (HLA-A = 33, -B = 16, -C = 18, -DQB1 = 12, and -DRB1 = 15). We discerned 29 synonymous and 65 non-synonymous mutations. Among them 17 novel alleles (HLA-A = 3, -B = 5, -C = 2, -DQB1 = 4, and -DRB1 = 3) were detected within key exons involved in antigen recognition (exon 2 and 3 for Class I, and exon 2 for Class II). Interestingly, there are three frameshift novelties: A∗33:01:01NEW (1598InsC), A∗66:03NEW (1598delC), and B∗38:01:01NEW (9 bp del 1705-1713). Based on the 3D protein structure, these three proteins are truncated on α 3. Future experiments will determine if these proteins lose function or have lower cell surface expression. Conclusion Long-range, unambiguous HLA genotyping is achievable on clinical buccal swab-extracted DNA. High resolution HLA typing provides more accurate matching of the HLA-A, -B, -C, -DQB1, and -DRB1 alleles to improve patient survival. This work is the first step to define permissive mismatches in the context of HSCT, and it emphasize the need to improve our knowledge on donor selection.
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