High-resolution characterization of allelic and haplotypic HLA frequency distribution in a Spanish population using high-throughput next-generation sequencing

Next-generation sequencing (NGS) at the HLA-A, -B, -C, -DPA1, -DPB1, -DQA1, -DQB1, -DRB1 and -DRB3/4/5 loci was performed on 282 healthy unrelated individuals from different major regions of Spain. High-resolution HLA genotypes defined by full sequencing of class I loci and extended coverage of class II loci were obtained to determine allele frequencies and also to estimate extended haplotype frequencies. HLA alleles were typed at the highest resolution level (4-field level, 4FL); with exception of a minor deviation in HLA-DPA1, no statistically significant deviations from expected Hardy Weinberg Equilibrium (HWE) proportions were observed for all other HLA loci. This study provides new 4FL-allele and -haplotype frequencies estimated for the first time in the Spanish population. Furthermore, our results describe extended haplotypes (including the less frequently typed HLA-DPA1 and HLA-DQA1 loci) and show distinctive haplotype associations found at 4FL-allele definition in this Spanish population study. The distinctive allelic and haplotypic diversity found at the 4FL reveals the high level of heterozygosity and specific haplotypic associations displayed that were not apparent at 2-field level (2FL). Overall, these results may contribute as a useful reference source for future population studies, for HLA-disease association studies as a healthy control group dataset and for improving donor recruitment strategies of bone marrow registries. HLA genotyping data of this Spanish population cohort was also included in the 17th International Histocompatibility and Immunogenetics Workshop (IHIW) as part of the study of HLA diversity in unrelated worldwide populations using NGS.

Report from the Killer-cell Immunoglobulin-like Receptors (KIR) component of the 17th International HLA and Immunogenetics Workshop

The goals of the KIR component of the 17th International HLA and Immunogenetics Workshop (IHIW) were to encourage and educate researchers to begin analyzing KIR at allelic resolution, and to survey the nature and extent of KIR allelic diversity across human populations. To represent worldwide diversity, we analyzed 1269 individuals from ten populations, focusing on the most polymorphic KIR genes, which express receptors having three immunoglobulin (Ig)-like domains (KIR3DL1/S1, KIR3DL2 and KIR3DL3). We identified 13 novel alleles of KIR3DL1/S1, 13 of KIR3DL2 and 18 of KIR3DL3. Previously identified alleles, corresponding to 33 alleles of KIR3DL1/S1, 38 of KIR3DL2, and 43 of KIR3DL3, represented over 90% of the observed allele frequencies for these genes. In total we observed 37 KIR3DL1/S1 allotypes, 40 for KIR3DL2 and 44 for KIR3DL3. As KIR allotype diversity can affect NK cell function, this demonstrates potential for high functional diversity worldwide. Allelic variation further diversifies KIR haplotypes. We determined KIR3DL3 ∼ KIR3DL1/S1 ∼ KIR3DL2 haplotypes from five of the studied populations, and observed multiple population-specific haplotypes in each. This included 234 distinct haplotypes in European Americans, 191 in Ugandans, 35 in Papuans, 95 in Egyptians and 86 in Spanish populations. For another 35 populations, encompassing 642,105 individuals we focused on KIR3DL2 and identified another 375 novel alleles, with approximately half of them observed in more than one individual. The KIR allelic level data gathered from this project represents the most comprehensive summary of global KIR allelic diversity to date, and continued analysis will improve understanding of KIR allelic polymorphism in global populations. Further, the wealth of new data gathered in the course of this workshop component highlights the value of collaborative, community-based efforts in immunogenetics research, exemplified by the IHIW.

Four new HLA class I alleles, HLA-A*02:681, HLA-A*30:111, HLA-A*68:164 and HLA-B*35:01:46

Four new HLA class I alleles, HLA-A*02:681, HLA-A*30:111, HLA-A*68:164 and HLA-B*35:01:46 were described in Spaniards.

HLA-A*30:99 shows a new amino acid position 156 within HLA-A*30 subtypes

A novel HLA-A*30:99 allele was characterized in a Spanish individual.

Two new HLA-B35 subtypes characterized in Spaniards: HLA-B*35:270 and HLA-B*35:273

Two new HLA-B*35 alleles, B*35:270 and B*35:273, were characterized in the Spanish population.

Characterization of two novel HLA-A null alleles: A*11:210N and A*26:107N

Two new HLA-A null alleles were characterized, A*11:210N and A*26:107N.

A new HLA-B allele, B*44:203, sequenced in a Spanish Caucasian cord blood unit

HLA-B*44:203 shows one nucleotide difference to B*44:03:01 at codon 171 (TAC>CAC, Y171>H171).

A new HLA allele, HLA-B*08:108, described in two unrelated Spanish individuals

HLA-B*08:108 shows one nucleotide difference regarding B*08:01:01 at codon 109 (CTC>TTC, L109>F109).

Description of two novel HLA-B alleles, B*37:34 and B*44:152

Two novel HLA-B alleles were characterized. HLA-B*37:34 shows two nucleotide differences regarding B*37:10 at codons 79 (CGC>CGG) and 80 (ACC>ATC), resulting in one amino acid replacement at position 80 (T>I). HLA-B*44:152 differs from B*44:02:01 in one nucleotide at codon 81 (GCG>ACG) giving rise to a leucine to threonine substitution at position 81.

Description of HLA-A*33:49 in a Spanish cord blood unit

A*33:49 has one nucleotide change regarding A*33:01:01 at exon 3, producing an amino acid replacement at codon 97, M97 to I97.

Sequencing of a new HLA-DRB1*04:98 allele in a Spanish donor

DRB1*04:98 shows four nucleotide changes regarding DRB1*04:01:01, resulting in two amino acids replacement at positions A73G and A74R.

Characterization of the novel HLA-A*3217 allele in two Caucasian Spanish donors

A novel human leukocyte antigen-A allele, officially named A*3217, was found in two unrelated Spanish donors. A*3217 differs from A*320101 in a point mutation at codon 70 (CAC-->CAG), generating an amino acid substitution of His to Gln.

Sequencing of new HLA-A*3025 and HLA-Cw*0221 alleles found in Caucasian donors

Two new human leukocyte antigen (HLA) class I alleles, A*3025 and Cw*0221, were identified in Spanish Caucasian donors by polymerase chain reaction-sequence-specific oligonucleotide and subsequently characterized by full coding region sequencing. HLA-A*3025 shows a single amino acid replacement at residue 70 (H>Q) compared with A*300201. HLA-Cw*0221 differs from Cw*020202 by a change at position 14 (H>Q).

Description of a new HLA-B allele: HLA-B*4077

HLA-B*4077 differs from B*400101, B*4036, and B*401401 in five, four, and three nucleotides, respectively. However, amino acid alignment would indicate a closer relationship with B*4036 allele, showing a single amino acid replacement at codon 131 (R>S).

Report of a novel B*3579 allele in an Ecuadorian family: confirmation and extension of A*6836 and B*3922 sequences

Human leukocyte antigen (HLA) class I sequencing typing of a cord blood unit obtained from an Ecuadorian family showed the presence of the recently described A*6836 and B*3922 alleles. Sequences of these two antigens were confirmed and completed. Additionally, a new HLA-B allele, B*3579, was found in the same family, showing a difference of one amino acid residue at position 211 (Ala > Glu) compared with B*3543.

Description of three new HLA-A*02 subtypes in Caucasians: A*0281, A*0289 and A*9224

Three new HLA-A*02 alleles were completely characterized by sequencing-based typing (SBT). A*0281 and A*9224 showed eight clustered amino acid differences into the Bw4/Bw6 epitope at positions 74-83, regarding A*02010101. Both disclosed the same Bw4 motif described for A*25 and A*32 alleles. A*9224 has an additional mismatch at residue 265 (G>V) in the alpha3 domain, which has not been reported for any other human leukocyte antigen (HLA) class I molecule. HLA-A*0289 differed from A*02010101 in the conserved amino acid residue 192 (H>Q).

HLA-B*9523 increases the extremely high B*15-group polymorphism

HLA-B*9523 differs from B*1591 and B*1503 in point nucleotide mutations at codon 167 (TCG --> TGG) and 152 (GAG --> GTG), respectively.

A new human leukocyte antigen DRB1 allele, HLA-DRB1*1375

DRB1*1375 differs from DRB1*1304 allele in a point nucleotide mutation at codon 67 (ATC-->TTC), which produces an amino acid residue change from I to F.