Revealing complete complex KIR haplotypes phased by long-read sequencing technology.

The killer cell immunoglobulin-like receptor (KIR) region of human chromosome 19 contains up to 16 genes for natural killer (NK) cell receptors that recognize human leukocyte antigen (HLA)/peptide complexes and other ligands. The KIR proteins fulfill functional roles in infections, pregnancy, autoimmune diseases and transplantation. However, their characterization remains a constant challenge. Not only are the genes highly homologous due to their recent evolution by tandem duplications, but the region is structurally dynamic due to frequent transposon-mediated recombination. A sequencing approach that precisely captures the complexity of KIR haplotypes for functional annotation is desirable. We present a unique approach to haplotype the KIR loci using single-molecule, real-time (SMRT) sequencing. Using this method, we have-for the first time-comprehensively sequenced and phased sixteen KIR haplotypes from eight individuals without imputation. The information revealed four novel haplotype structures, a novel gene-fusion allele, novel and confirmed insertion/deletion events, a homozygous individual, and overall diversity for the structural haplotypes and their alleles. These KIR haplotypes augment our existing knowledge by providing high-quality references, evolutionary informers, and source material for imputation. The haplotype sequences and gene annotations provide alternative loci for the KIR region in the human genome reference GrCh38.p8.

Maternal and fetal human leukocyte antigen class Ia and II alleles in severe preeclampsia and eclampsia.

A line of investigations indicate that genes in the human leukocyte antigen (HLA) complex are involved in a successful acceptance of the semiallogeneic fetus during pregnancy. In this study, associations between specific HLA class Ia (HLA-A and -B) and class II (HLA-DRB1, -DQA1, -DQB1, -DPA1 and -DPB1) alleles and the risk of developing severe preeclampsia/eclampsia were investigated in a detailed and large-scale study. In total, 259 women diagnosed with severe preeclampsia or eclampsia and 260 matched control women with no preeclampsia, together with their neonates, were included in the study. HLA genotyping for mothers and neonates was performed using next-generation sequencing. The HLA-DPB1*04:01:01G allele was significantly more frequent (Pc=0.044) among women diagnosed with severe preeclampsia/eclampsia compared with controls, and the DQA1*01:02:01G allele frequency was significantly lower (Pc=0.042) among newborns born by women with severe preeclampsia/eclampsia compared with controls. In mothers with severe preeclampsia/eclampsia, homozygosity was significantly more common compared with controls at the HLA-DPB1 locus (Pc=0.0028). Although the current large study shows some positive results, more studies, also with a functional focus, are needed to further clarify a possible role of the classical HLA genes in preeclampsia.

Identification of HLA-B*56 variant (B*560502) in the Korean population.

We report here a new HLA-B*56 allele, B*560502, identified by sequencing-based typing in the Korean population. HLA-B*560502 differs from B*560501 by a single nucleotide at position 141 in exon 2 (T(r)C). This single nucleotide substitution may not result in an amino acid difference in the alpha1 domain at residue 23. The putative haplotype involving B*560502 may be A*24-DRB1*1201-DQA1*0503-DQB1*0304-DPB1*0202.

Identification of a new HLA-B allele, B*3705 containing a Bw6 sequence motif.

HLA-B37, which is Bw4 type antigen frequently found in linkage disequilibrium with A1, Cw6 and DR10 in all ethnic groups, generally has a very low frequency all over the world. We report a new HLA-B*37 allele, B*3705, identified in two potential bone marrow donors in the Korean population. B*3705, which has the Bw6 nucleotide segment, differs from B*3701 in three nucleotide positions: 311, 317 and 319 in exon2. The serological profile of B*3705 did not exhibit the B37 specificity. The putative haplotype associated with B*3705 in the Korean population could be A*02-Cw*0602-DRB1*1001-DQA1*0101-DQB1*0501-DPB1*02011.

Identification of HLA-A*11 variant (A*1107) in the Korean population.

We report here a new HLA-A*11 allele, A*1107, identified by sequencing based typing in the Korean population. The full-length sequencing of A*1107 was conducted on cDNA. HLA-A*1107 differs from HLA-A*1101 by a single nucleotide at position 399 of codon 109 in exon3 (TTC-->TTA), leading to an amino acid change from phenylalanine to leucine. But the serological profile of HLA-A*1107 did not exhibit the altered HLA-A11.

Distribution of seven polymorphic markers and haplotypes within the human TNF gene cluster in Koreans.

We examined the distribution of polymorphic elements within the tumor necrosis factor (TNF) gene cluster in 133 normals and in 20 Korean families and compared our data with the results of Caucasians. The genotypes that are shown frequently are TNF a6 (33.8%), TNF b5 (46.6%), TNF c1 (79.3%), TNF d3 (34.6%), TNF e3 (86.5%), TNFB*2 (51.5%), and TNF(-308) A (91.4%). In comparison, TNFa 6 (33.8%), TNFa 13 (4.1%), TNFb 5 (46.6%), TNFd 1 (7.5%), TNFd 3 (34.6%), TNFe 3 (86.5%), TNFe 4 (6.8%), and TNF(-308) A (91.3%) were found more frequently in Koreans than Caucasians (p < 0.01). TNFa 14, TNFa 15, TNFd 8, and TNFe 4 alleles were found only in Korean controls. However, TNFb 6 and TNFb 7 alleles were not found in this study. From the TNF gene of TNFa, TNFb, TNFc, TNFn, TNF(-308), TNFd, and TNFe, 49 different TNF haplotypes were found in 20 Korean families. These data suggest that the TNF microsatellite haplotypes constitute a highly polymorphic system and that will provide useful information on the association between the TNF marker and the immune disease.