Naming HLA diversity: A review of HLA nomenclature.

The development of a standardized HLA nomenclature has been critical in our understanding of the HLA system and in facilitating the clinical applications of HLA. The Nomenclature Committee for Factors of the HLA System, established in 1968, has overseen the development and usage of nomenclature based on serologic specificities, cellular responses, and DNA sequences. Their decisions have been guided by community consensus reached through 17 international workshops beginning in 1964 and continuing today.

Next generation sequencing characterizes HLA diversity in a registry population from the Netherlands.

Next generation DNA sequencing is used to determine the HLA-A, -B, -C, -DRB1, -DRB3/4/5, and -DQB1 assignments of 1009 unrelated volunteers for the unrelated donor registry in The Netherlands. The analysis characterizes all HLA exons and introns for class I alleles; at least exons 2 to 3 for HLA-DRB1; and exons 2 to 6 for HLA-DQB1. Of the distinct alleles present, there are 229 class I and 71 class II; 36 of these alleles are novel.

Continue to focus clinical decision-making on the antigen recognition domain for the present.

Next generation DNA sequencing has facilitated the routine characterization of complete HLA gene sequences. These data complement structural and functional studies of HLA elements encoded outside of the exons specifying the antigen recognition domain. This commentary is focused on evaluating whether the interpretation of HLA clinical typing results should expand the region of the HLA gene considered in the assignment from the exon(s) encoding the antigen recognition domain to the full gene sequence.

Characterizing alleles with large deletions using region specific extraction.

Two novel HLA class II alleles, DRB4*03:01N and DQB1*03:276N, containing large deletions were identified during routine typing. Extraction of DNA encompassing the deletions was carried out with a panel of capture oligonucleotides followed by whole genome amplification. Next generation DNA sequencing was then used to characterize the sequences.

KIR3DL1/HLA-B Subtypes Govern Acute Myelogenous Leukemia Relapse After Hematopoietic Cell Transplantation.

Purpose Disease relapse remains a major challenge to successful outcomes in patients who undergo allogeneic hematopoietic cell transplantation (HCT). Donor natural killer (NK) cell alloreactivity in HCT can control leukemic relapse, but capturing alloreactivity in HLA-matched HCT has been elusive. HLA expression on leukemia cells-upregulated in the post-HCT environment-signals for NK cell inhibition via inhibitory killer immunoglobulin-like (KIR) receptors and interrupts their antitumor activity.

Combining one-step Sanger sequencing with phasing probe hybridization for HLA class I typing yields rapid, G-group resolution predicting 99% of unique full length protein sequences.

Background: Sanger-based DNA sequencing of exons 2+3 of HLA class I alleles from a heterozygote frequently results in two or more alternative genotypes. This study was undertaken to reduce the time and effort required to produce a single high resolution HLA genotype.

Materials And Methods: Samples were typed in parallel by Sanger sequencing and oligonucleotide probe hybridization.

Allelic variation of killer cell immunoglobulin-like receptor 2DS5 impacts glycosylation altering cell surface expression levels.

Natural killer cell stimulatory receptor gene, KIR2DS5, is polymorphic. While KIR2DS5*002 is most frequently observed, other alleles have also been found. The proteins encoded by these alleles (KIR2DS5*002-*009) are expressed at varying levels on the surface of NKL and Jurkat transfectants.

Human leukocyte antigen (HLA) typing by DNA sequencing.

DNA sequencing is a powerful technique for identifying allelic variation within the human leukocyte antigen (HLA) genes. Sequencing is usually focused on the most polymorphic exons of the class I (HLA-A, -B, -C) and class II (HLA-DR, -DQ, and -DP) genes. These exons encode the antigen recognition site, the region of the HLA molecule that binds peptides and interacts with the T cell receptor for antigen and natural killer cell immunoglobulin-like receptors (KIR).

DAP12 impacts trafficking and surface stability of killer immunoglobulin-like receptors on natural killer cells.

KIR aid in the regulation of NK cell activity. In this study, the effect of the interaction between the KIR2DS and their adapter, DAP12, was investigated beyond the previously defined signaling function. Flow cytometry analysis showed enhanced KIR2DS surface expression on NKL cells when cotransfected with DAP12.

Allelic variation in KIR2DL3 generates a KIR2DL2-like receptor with increased binding to its HLA-C ligand.

Although extensive homology exists between their extracellular domains, NK cell inhibitory receptors killer Ig-like receptor (KIR) 2DL2*001 and KIR2DL3*001 have previously been shown to differ substantially in their HLA-C binding avidity. To explore the largely uncharacterized impact of allelic diversity, the most common KIR2DL2/3 allelic products in European American and African American populations were evaluated for surface expression and binding affinity to their HLA-C group 1 and 2 ligands. Although no significant differences in the degree of cell membrane localization were detected in a transfected human NKL cell line by flow cytometry, surface plasmon resonance and KIR binding to a panel of HLA allotypes demonstrated that KIR2DL3*005 differed significantly from other KIR2DL3 allelic products in its ability to bind HLA-C.

The impact of HLA unidirectional mismatches on the outcome of myeloablative hematopoietic stem cell transplantation with unrelated donors.

The impact of HLA homozygosity at mismatched (MM) loci on the outcome of 2687 myeloablative unrelated donor hematopoietic cell transplantations performed for malignant disease was evaluated among 4 groups: 7/8 bidirectional MM transplants (donor and recipient heterozygous MM, n = 1393), 7/8 host-versus-graft (HVG) vector MM (recipient homozygous, n = 112), 7/8 graft-versus-host (GVH) vector MM (donor homozygous, n = 119), and 8/8 matches (n = 1063). Multivariate analyses found 7/8 GVH (P = .001) and bidirectional MM groups (P < .

Allele-level haplotype frequencies and pairwise linkage disequilibrium for 14 KIR loci in 506 European-American individuals.

The immune responses of natural killer cells are regulated, in part, by killer cell immunoglobulin-like receptors (KIR). The 16 closely-related genes in the KIR gene system have been diversified by gene duplication and unequal crossing over, thereby generating haplotypes with variation in gene copy number. Allelic variation also contributes to diversity within the complex.

Definitions of histocompatibility typing terms.

Histocompatibility testing for stem cell and solid organ transplantation has become increasingly complex as newly discovered HLA alleles are described. HLA typing assignments reported by laboratories are used by physicians and donor registries for matching donors and recipients. To communicate effectively, a common language for histocompatibility terms should be established.

Definitions of histocompatibility typing terms: Harmonization of Histocompatibility Typing Terms Working Group.

Histocompatibility testing for stem cell and solid organ transplantation has become increasingly complex as newly discovered human leukocyte antigen (HLA) alleles are described. HLA typing assignments reported by laboratories are used by physicians and donor registries for matching donors and recipients. To communicate effectively, a common language for histocompatibility terms should be established.

The characteristics of allelic polymorphism in killer-immunoglobulin-like receptor framework genes in African Americans.

The frequencies of alleles of killer cell immunoglobulin-like receptor genes, KIR3DL3 and KIR3DL2, and the carrier frequency of KIR2DL4 alleles have been determined from a population of African Americans (n = 100) by DNA sequencing of the coding regions. Fifty alleles of KIR3DL3 were observed with the most frequent, KIR3DL3*00901 (13%). KIR3DL2 was also diverse; 32 alleles with KIR3DL2*00103 the most frequent (17%).

Human leukocyte antigen-A, -B, -C, -DRB1 allele and haplotype frequencies in Americans originating from southern Europe: contrasting patterns of population differentiation between Italian and Spanish Americans.

High-resolution DNA sequencing was used to identify the human leukocyte antigen (HLA) -A, -B, -C, and -DRB1 alleles found in 552 individuals from the United States indicating Southern European (Italian or Spanish) heritage. A total of 46 HLA-A, 80 HLA-B, 32 HLA-C, and 50 DRB1 alleles were identified. Frequent alleles included A*02:01:01G (allele frequency = 0.

Thirty allele-level haplotypes centered around KIR2DL5 define the diversity in an African American population.

KIR2DL5 alleles were physically linked to alleles at adjacent KIR loci to define this region of KIR haplotypes in 55 gene-positive random African Americans. The majority carried KIR2DL5B. Three KIR2DL5A and six KIR2DL5B alleles that have been previously described and 11 novel KIR2DL5 alleles were identified by DNA sequencing.

HLA-A disparities illustrate challenges for ranking the impact of HLA mismatches on bone marrow transplant outcomes in the United States.

HLA disparity between hematopoietic stem cell donors and recipients is one of the most important factors influencing transplant outcomes, but there are no well-accepted guidelines to aid in selecting the optimal donor among several HLA mismatched donors. In this report, HLA-A is used as a model to illustrate factors that are barriers to delineating the relationship between specific HLA mismatches and transplant outcomes in the United States. Patients in this investigation received transplants for hematologic malignancies that were facilitated by the National Marrow Donor Program (NMDP) between 1990 and 2002 (n = 4226).

In contrast to other stimulatory natural killer cell immunoglobulin-like receptor loci, several KIR2DS5 alleles predominate in African Americans.

The five two-domain stimulatory KIR genes carried by 100 random African Americans were characterized by DNA sequencing of genomic DNA covering the majority of coding exons. The frequency of individual loci was similar to that found in European Americans, with the exception of a reduced frequency for KIR2DS1 in African Americans. New alleles were identified at the KIR2DS1 (*008), KIR2DS2 (*006), KIR2DS3 (*00104, *00105, *00106, *004), KIR2DS4 (*00103, *00104, *009, *011, *012, *013), and KIR2DS5 (*006, *007, *00801, *00802, *009) loci.

Promoter variants of KIR2DL5 add to diversity and may impact gene expression.

Sequencing of polymerase chain reaction (PCR)-amplified genomic DNA encompassing the putative proximal promoter and the coding region was used to identify KIR2DL5 alleles from 77 unrelated Caucasian individuals. PCR and sequencing were used to link each new allele to its neighboring KIR locus to identify 2DL5A or 2DL5B loci. Allele 2DL5A*001 was found in 24 of the 37 2DL5 positive individuals; 2DL5B*0020101 and 2DL5A*0050101 were also observed.

Limited allelic diversity of stimulatory two-domain killer cell immunoglobulin-like receptors.

Genomic sequencing was used to characterize most of the coding regions of the five two-domain stimulatory killer cell immunoglobulin-like receptor (KIR) loci from 80 unrelated, primarily Caucasian, individuals. Specific loci were present in from 26% (KIR2DS3) to 98% (KIR2DS4) of individuals. The number of known alleles present varied from one (KIR2DS1, KIR2DS5) to five (KIR2DS4).

Estimation of HLA-A, -B, -DRB1 haplotype frequencies using mixed resolution data from a National Registry with selective retyping of volunteers.

Large registries of volunteer hematopoietic stem cell donors typed for HLA contain potentially valuable data for studying haplotype frequencies in the general population. However the usual assumptions for use of the expectation-maximization (EM) algorithm are typically violated in these registries. To avoid this problem, previous studies using registry data have reduced the HLA typings to low-resolution and/or excluded subjects who were selected for testing on behalf of a specific patient ("patient-directed" typings).