HLA‐E diversity unfolded: Identification and characterization of 170 novel HLA‐E alleles

Abstract

HLA‐E is a member of the nonclassical HLA class Ib genes. Even though it is structurally highly similar to the classical HLA class Ia genes, it is less diverse and only 45 alleles and 12 proteins were known in December 2019 (IPD‐IMGT/HLA, release 3.38.0). Since 2017, we have genotyped over 3 million voluntary stem cell donors for HLA‐E by sequencing the most relevant allele‐determining bases of exons 2 and 3. As expected, most donors harbor the two predominant alleles HLA‐E*01:01 and/or HLA‐E*01:03. However, in 1666 (0.05%) of our samples we detected 345 distinct novel HLA‐E sequences. The most frequent one was identified in 162 samples and has by now been named HLA‐E*01:114. To characterize these novel alleles in full‐length, we used both short‐read Illumina and long‐read PacBio sequencing to obtain fully phased and highly accurate sequences. This resulted in 234 submissions to IPD‐IMGT/HLA comprising 170 novel HLA‐E alleles, which encode for 93 novel HLA‐E proteins, as well as 64 confirmations or sequence extensions. Consequently, the number of HLA‐E alleles in the database (release 3.42.0) has now increased to 256 HLA‐E alleles and 110 HLA‐E proteins.

Utilizing Massively Parallel Sequencing (MPS) of Human Leukocyte Antigen (HLA) Gene Polymorphism to Assess Relatedness in Deficiency Parentage Testing

“…In this report, the analysis primarily focused on classical HLA genes (HLA-A, -B, -C, -DRB1/3/4/5, -DQA1, -DQB1, -DPA1, -DPB1) and secondarily on non-classical HLA genes (HLA-F, -G, -H, -E), MICA, and MICB. Information about non-classical HLA genes allows for a more accurate description of HLA haplotype diversity but relatively few reference data exist on polymorphisms at the high-resolution level (third or fourth field) [48]. To accurately determine the relationship between individuals, it is crucial to have access to high-resolution HLA frequency data for different populations.…”

HLA Class I Molecules as Immune Checkpoints for NK Cell Alloreactivity and Anti-Viral Immunity in Kidney Transplantation

“…For HLA-E, the typing method has long been limited to resolve the dimorphic amino acid at position 107 (R or G) by either PCR-SSP (PCR with Sequence-Specific Primers (194)(195)(196)(197), PCR-SSO (PCR-Sequence Specific Oligo Probes (198), PCR-RFLP (PCR Restriction Fragment Length Polymorphism) alone (199) or in combination with ARMS (Amplification Refractory Mutation System) (200), PCR-SSCP (PCR-single strand conformation polymorphism) (201), Taqman assay (202) or sequence based typing of a limited part of the HLA-E gene either by Sanger sequencing (203)(204)(205)(206)(207) or recently also by NGS with Illumina (208). In this latter study HLA-E was typed for over 2.5 million potential stem cell donors worldwide and although only a limited 535 bp amplicon (including last part of exon 2, intron 2 and first part of exon 3) was sequenced, it has caused an explosion of new HLA-E alleles (209). Also full length sequencing of HLA-E was developed using both Sanger sequencing (210,211) and NGS (212)(213)(214)(215)(216).…”

Association of HLA‐E single nucleotide polymorphisms with human myeloid leukemia

“…HLA‐E is a nonclassical member of the major histocompatibility complex class I (MHC‐I). In recent years, many novel HLA‐E alleles have been reported, 1–3 which are composed of different single nucleotide polymorphisms (SNPs). The frequency of HLA‐E SNPs is different among Chinese and Japanese healthy individuals, 4,5 as well as patients with different diseases, 6,7 suggesting that SNPs are associated with the healthy statuses of different populations.…”