Identification of two novel HLA class II alleles, DQB1*0311 and DQB1*0620

Two novel HLA class II alleles have been identified in routine typing of a kidney transplant patient and a cord blood unit from the Australian Cord Blood Bank in Sydney. Sequence analysis of exon 2 of the DQB1 genes revealed the novel polymorphism. A substitution of A to C at nucleotide position 136 has been identified for the DQB1*0311 allele when compared to the closest-matched allele, DQB1*030201. An identical substitution has also been identified for the DQB1*0620 allele when compared to the closest-matched allele, DQB1*0602. The substitution results in an amino acid change from methionine to leucine at position 46 implicating different specificity and affinity of antigen binding.

Identification of two novel HLA class II alleles, DQB1*030503 and DRB1*0447

Two novel human leukocyte antigen (HLA) class II alleles have been identified in routine typing of bone marrow donors for the Australian Bone Marrow Donor Registry in Sydney, Australia. Sequence analysis of exon 2 of both the DQB1 and DRB1 genes revealed the novel polymorphism. A silent substitution of G to A at nucleotide position 210 has been identified for the DQB1*030503 allele when compared to the closest matched allele, DQB1*030501. There is no associated amino acid difference between the translated products of the two alleles. The second new allele is a variant of the DRB1 gene. The DRB1*0447 allele was identified with three nucleotide substitutions compared to the closest matched allele DRB1*0436. There is a silent mutation at nucleotide position 303, G to C and two substitutions at adjacent nucleotide positions 344 and 345, T to G and G to T, respectively. The latter two substitutions result in an amino acid change from valine to glycine at position 86, implicating a different specificity and affinity of antigen binding.

Identification of three novel HLA class I alleles: HLA-B*3928, HLA-B*400104 and HLA-B*4437

Three new human leukocyte antigen (HLA) class I alleles have been identified in the Tissue Typing Laboratory in Sydney, Australia. Sequence analysis of exon 2 and exon 3 of the HLA-B gene revealed the novel polymorphism. A silent substitution of C to T at nucleotide position 369 has been identified for the HLA-B*400104 allele when compared to the closest matched allele, HLA-B*400101. The HLA-B*3928 allele was identified with a nucleotide substitution of G to C at position 362 when compared to the closest matched allele, HLA-B*390101, resulting in an amino acid substitution of Arginine to Threonine. A nucleotide substitution of C to G at position 572 resulting in the amino acid change Serine to Tryptophan was identified in the new allele HLA-B*4437, when compared to the closest matched allele HLA-B*440301. Both amino acid substitutions implicate a different specificity and affinity of antigen binding for the alleles HLA-B*3928 and HLA-B*4437.

A new HLA-B allele, B*1565, identified in three unrelated samples

Anew human leukocyte antigen-B allele, B*1565, has been identified during routine typing of cord blood samples. Subsequently, two individuals from the same family as the first cord blood sample plus two unrelated Australian Bone Marrow Donor Registry samples have been found to carry this novel allele.

HLA-DRB1 and HLA-DQB1 polymorphisms in Pacific Islands populations

Allele frequency distributions of the HLA-DRB1 and HLA-DQB1 genes were investigated in four Pacific Islands populations from the Cook Islands, Samoa, Tokelau and Tonga. Limited diversity was observed for both the HLA-DRB1 and HLA-DQB1 loci. Five HLA-DRB1 alleles were observed to be the most frequent amongst all the studied Pacific Islands populations. They were: HLA-DRB1*0403, HLA-DRB1*08032, HLA-DRB1*09012, HLA-DRB1*11011 and HLA-DRB1*1201. Cook Islanders had the largest number of low frequency DRB1 alleles followed by Samoans, Tokelauans and Tongans, most of which may be attributed to reported non-Polynesian admixture. The most frequently observed DQB1 alleles in the four studied Pacific Islands populations were those of the DQ3 subgroup of alleles HLA-DQB1*03011, HLA-DQB1*0302 and HLA-DQB1*03032 as well as HLA-DQB1*05031 and HLA-DQB1*06011. Cook Islanders had the highest number of rare HLA-DQB1 alleles, the distibution being similar to that of the HLA-DRB1 allele. While, in general, the values of homozygosity for DRB1 and DQB1 were observed to be lower then expected under neutrality, a statistical significance was observed in Tongans, Samoans and Tokelauans for the DQB1 locus and in Tongans for the DRB1 locus. Differences were observed between allele frequency distributions for Tokelauans compared to the other three populations. This was also demonstrated by principal component analysis of DRB1 and DQB1 allele frequencies, which separated the Tokelauan population from Cook Islanders, Tongans and Samoans. Tongans and Samoans were separate from the other Polynesian populations in the phylogenetic trees. Observed allele and haplotype frequencies were found to be in agreement with previously published HLA-DRB and HLA-DQB Polynesian data.

Distribution of HCV genotypes among risk groups in Serbia

Blood samples from 190 patients that were anti-hepatitis C virus (HCV) positive were genotyped and 165 were found to contain HCV-RNA. Genotyping was performed by PCR based on type-specific primers (117 isolates) and LiPA test (48 isolates) and verifying by sequencing. In Serbia, the most frequent genotype was 1b (49.1%), followed by genotype 3 (21.2%) and genotype 1a (8.5%). The frequency of genotypes 2 and 4 was below 5% and mixed infections were encountered in 9.1% of cases. Distribution of genotypes was monitored in different risk groups: intravenous drug abusers, patients under blood transfusion, patients with previous history of surgery, patients undergoing hemodialysis and those with unknown risk factors. Genotype distribution is essentially the same in all the groups, except for the patients undergoing hemodialysis and those with previous history of surgery where significant difference exists compared with the group with unknown route of transmission (p < 0.001 and p < 0.05, respectively). There exists significant age-dependent genotype 3 distribution in Serbian population (p < 0.01).

Nucleotide sequence of exons 2 and 3 of the novel HLA-Cw*12032 allele

A novel HLA-C nucleotide sequence was discovered in an individual of Pacific Island, Tongan ethnicity using sequencing based typing. The sequence was given an official allele designation HLA-Cw*12032 by the WHO Nomenclature Committee for Factors of the HLA System. The novel sequence has 2 bp substitutions compared to the HLA-Cw*1203 at codon 134 "T" to "C" and codon 135 "C" to "G". However, when converted to amino acid sequences HLA-Cw*1203 and HLA-Cw*12032 are identical and would not have direct clinical implications.

HLA-DPA1 and DPB1 polymorphism in four Pacific Islands populations determined by sequencing based typing

Class II HLA-DP antigens are heterodimers comprised of alpha and beta chains coded by HLA-DPA1 and HLA-DPB1 genes. Both genes are polymorphic with substantial variation between different populations world wide. This work describes DPA1 and DPB1 polymorphism in four Pacific Island populations of Cook Islands, Samoa, Tokelau and Tonga, living in New Zealand. Using sequencing based typing four DPA1 alleles and twelve DPB1 alleles were observed in total among the four populations. There are two predominant DPA1 alleles DPA1*01031 and DPA1*02022 and three predominant DPB1 alleles DPB1*02012, DPB1*0401 and DPB1*0501. Fourteen DPA1-DPB1 haplotypes in total are present in these four populations with three predominant haplotypes: DPA1*02022-DPB1*0501, DPA1*01031-DPB1*02012, and DPA1*01031-DPB1*0401. Strong positive and negative disequilibrium was observed for individual DPA1-DPB1 haplotypes. Significant differences in DPA1 and DPB1 allele and haplotype frequencies were observed between Tokelauan and other three populations. Phylogenetic analysis of genetic distances between the four Pacific Island populations and other Asian Oceanian populations have shown that Cook Islanders, Samoans and Tongans are more closely related to Asian populations whereas Tokelauans cluster towards non-Austronesian populations of Papua New Guinea Highlanders and Australian Aborigines.

Feasibility of finding an unrelated bone marrow donor on international registries for New Zealand patients

Allogeneic bone marrow transplantation is the treatment of choice for several hematological conditions. Unfortunately, for the majority (70%) of patients an HLA-matched sibling donor is not available and a matched unrelated donor must be found if they are to proceed to allogeneic transplantation. Most of the donors on international registries are of Caucasian ethnic origin. It has been recognized that patients from certain racial groups have a reduced chance of finding an unrelated donor. This study reports the feasibility of finding an unrelated donor for our local New Zealand patients of Caucasian, New Zealand Maori and Pacific Islander ethnic origin presenting with transplantable hematological conditions at a single center. The search was performed on international registries using HLA-A,B and DR typings for our patients. Six of six and five of six matches were evaluated. We have shown that Maori and Pacific Islanders have significantly lower hit rates than Caucasians when searched for 6/6 antigen matches, but there was no significant difference between the three ethnic groups in finding a 5/6 antigen matched donor. This study supports the policy of the New Zealand Bone Marrow Donor Registry in recruiting New Zealand Maori and Pacific Islanders.