Identification of a new HLA-C allele, Cw*0316, by sequence-based typing

The presence of a new allele, Cw*0316, was detected in a Caucasian individual through an unusual association. Molecular typing of the individual by sequence-specific primers and sequence-specific oligonucleotides showed the presence of B*58, B*41 and Cw*17. Sequence-based typing revealed the additional presence of another human leucocyte antigen-C allele. The new allele showed four nucleotide differences with Cw*030202 at positions 559, 560, 589 and 594 in exon 3, leading to three codon changes, codons 187, 197 and 198. This resulted in two amino acid substitutions at positions 163 (L-T) and 173 (K-E) of the mature protein, which proved sufficient to abrogate serological reactivity with Cw3-specific sera.     

Identification of an HLA-C variant allele, Cw*0805, by sequencing based typing

Abstract: We have identified a. variant HLA-C allele, Cw*0805, in DNA isolated from a blood sample used in the UK National External Quality Assessment Scheme for Histocompatibility and Immunogenetics. The DNA was initially typed by PCR-SSP and PCR-SBT as Cw*0802, 1602 with a single mismatch in exon 2 of one of the alleles. The two HLA-C alleles were separated by locus- and allele-speciflc PCRs and sequencing analysis showed that the Cw*0802 allele was variant in this sample, with a single mismatch in exon 2 at position 289.     

Sequencing based typing for HLA-C. Identification of three new alleles: Cw*0307, Cw*0502 and Cw*0504

HLA-C has been described as a transplantation locus in the unrelated bone marrow transplantation setting, and noticeably the number of mismatches between HLA-A,-B,-DRB1 compatible pairs is considerably high. Sequencing based typing (SBT) is an accurate and efficient methodology utilised in the HLA class I and II allele level of resolution. SBT for HLA-C locus was applied on a sample of 40 HLA-A,B,DRB1,DRB3/4/5,DQB1-compatible bone marrow recipient-donor pairs, and 3 new HLA-C alleles have been found. Cw*0307, well defined by serology as Cw3, showed two amino acid changes at the NK motif 77-80 regarding all described Cw*03 alleles, N77K80 instead of S77N80. Two new Cw*05 alleles were described, Cw*0502 properly typed by serology, and Cw*0504 that behaves as a short antigen. Cw*0502 differed from Cw*0501 by only one nucleotide at exon 3, that generated an amino acid replacement at codon 177, K to E. Cw*0504 differs from Cw*0501 by two clustered amino acid positions (114 and 116) placed at the peptide binding site. The rate of new HLA-C alleles found in this small series evidences a high grade of hidden HLA-C diversity in the Spanish population, particularly in the well-defined serologic specificities.     

HLA-C typing of eleven Papua New Guineans: identification of an HLA-Cw4/Cw2 hybrid allele

HLA-C polymorphism of 11 individuals from Papua New Guinea was studied by serology and DNA typing (SSP ARMS-PCR). To resolve certain discrepancies HLA-C alleles were cloned and sequenced. Five alleles were identified by sequencing, four of which; Cw*0304, Cw*0401, Cw*12022 and Cw*1502 have been identified previously in other populations. The fifth allele, which was found in four individuals is a novel HLA-C allele. The new allele, called HLA-Cw*0403 is most similar to HLA-Cw*0401, differing by 10 nucleotides, 9 of which are located in the region from nucleotide 98 to 218. This region of Cw*0403 is identical to both HLA-Cw*0201 and Cw*02022. The 9 nucleotide differences between Cw*0401 and Cw*0403 result in 6 amino acid differences in the α1 domain. These amino acids in Cw*0403 may contribute to the serological typing of some, but not all Cw*0403 expressing cells. The Final difference between Cw*0401 and Cw*0403 is a coding substitution at nucleotide 979 in exon 5. The guanine found in Cw*0403 is identical to all HLA-C alleles except HLA-Cw*0401, which has an adenine. The Cw*0403 allele was most likely formed by a gene conversion event between Cw*02 and Cw*04, involving a minimum of 121 to a maximum of 215 nucleotides.     

Identification of a novel HLA-C allele, Cw*0406, in a Singapore Malay

A novel allele, C*0406, has been identified and is characterised by a single nucleotide substitution at position 196 of exon 3 when compared with its closest related allele, C*0403. The latter is found in 4/69 Chinese and 7/80 Malays while Cw*0406 was found in only one Malay individual within the study populations. The data suggest that Cw*0406 may have arisen as a relatively recent genetic event either by gene conversion or as a simple point mutation variant of Cw*0403.     

Identification of the novel HLA-C allele Cw*0751

We report the novel HLA-Cw allele HLA-Cw*0751. The allele was identified during routine sequence-based typing in our laboratory. The novel allele is identical to Cw*07020101 except for a single nucleotide change in codon 90.2 in position 268. HLA-Cw*0751 allele possesses an adenine at position 268 in exon 2, while HLA-Cw*07020101 has a cytosine at this position. Although this substitution does not change serologic reactivity of HLA-Cw7 molecule, it changes the amino acid at codon 90 from an aspartic acid to an alanine. Aspartic acid is polar and acidic, while alanine is non-polar and neutral.     

A new pair of HLA-C alleles, Cw* 12042 and Cw*1203, differing at the KIR-related dimorphism of codons 77–80

Abstract: A previously unknown HLA-C variant of the Cw*12 group was identified by PCR-SSP from genomic DNA of cell NDS-JD. Molecular cloning and nucleotide sequence analysis permitted the characterization of the complete coding region of this new allele, Cw*12042. The new variant differs from the recently reported Cw*12041 by two silent changes at exons 2 and 3, and from Cw*1203 by coding changes at codons 77 and 80. Cw*1203 (Ser-Asn) and Cw*12042 (Asn-Lys) constitute the second known example of HLA-C alleles only differing at the KIR-related dimorphism of residues 77–80. The new allele is associated in cell NDS-JD with the haplotype HLA-A*2403, Cw*12042, B*51, DRB1*1502, DRB5*0102, DQB1*0601, possibly related from the evolutionary aspect to the ancestral haplotype A*2402, Cw*1202, B*5201, DRB1*1502, DRB5*0102, DQBl*0601.     

Two new HLA Cw* alleles,Cw*0105 and Cw*1405, detected by sequence based typing

During recent years, the view of the relative importance of the HLA Cw locus has undergone substantial change. From being an HLA locus with both limited polymorphism and biological significance there are now more than a hundred different alleles known and the biological importance of HLA Cw, both as a transplantation antigen and as a receptor for NK cells, is well established. Sequence based typing has been shown to be a powerful tool, especially for HLA Cw typing. Here we describe two new HLA Cw* alleles found during routine typing of potential bone marrow donors and hematological patients. The HLA Cw*0105 differs from Cw*0102 at positions 361 and 368 in exon 3 leading to a Trp to Arg and Cys to Ser substitution, respectively. HLA Cw*1405 differs from Cw*14021 by a single nucleotide substitution at position 368. This mutation results in an amino acid substitution of Phe for Tyr.     

A novel HLA-Cw*03 allele, Cw*033802, identified by sequence-based typing

New allele Cw*033802 showed one nucleotide difference with Cw*0338 at codon 99 (TAC-->TAT).     

Characterization of a new HLA-C allele: Cw*1606

HLA-Cw*16 is a relatively common HLA-C specificity among Caucasoids, with Cw*1601 being the most frequent allele. We report herein the identification by sequence-based typing of a new HLA-Cw*16 allele in a Spanish Caucasoid blood donor. The novel allele, designated Cw*1606, differs from Cw*1601 by two nucleotide changes at positions 361 (T to A) and 368 (A to C) in exon 3, which leads to two amino acid changes from Trp (TGG) to Arg (AGG) and from Tyr (TAT) to Ser (TCT) at codons 97 and 99 in the alpha2 domain, respectively. Sequence comparisons suggest that the new HLA-Cw*1606 variant could have arisen from an intralocus gene conversion event.     

Molecular cloning of two new HLA-C alleles: Cw*1801 and Cw*0706

Nucleotide sequence analysis of the HLA-C alleles of the GB92 cell line, heterozygous for B*8101 and B*4407, revealed the existence of two new allelic variants: Cw*1801 and Cw*0706. The former allele, initially detected as a PCR-SSP variant, displays a hybrid aspect, sharing sequence motifs with Cw*07 at exons 1 and 2, and with'Cw*04 at distal exons. In serological assays, Cw*1801 is only recognized by some cross-reactive sera. Cw*0706 shows a primary structure closely related to previously known Cw7 alleles, but carries new sequence motifs at its 3'-end. Preliminary data indicate that Cw*1801 is associated to B*8101 and that Cw*0706, B*4407 could account for a part of the Cw7, B44 haplotypes observed in African populations.     

Characterization of a new HLA-C allele: Cw*0719

We describe a new human leukocyte antigen (HLA)-Cw*07 allele that differs from Cw*0718 by a single-coding nucleotide. DNA-based genotyping identified a clinical sample from a Black African-American patient that differed from known Cw alleles. The allele was amplified independently with a haplo-specific primer and sequenced in its entirety.     

Identification of a novel HLA-Cw*07 variant (Cw*0714) in a German Caucasian family

We report herein the identification of a new HLA-Cw*07 allele in two members of a German Caucasian family. This novel allele, designated as Cw*0714, differs from Cw*07011 and Cw*0706 by two nucleotide changes: one at codon 66 (AAC-->AAG) in the exon 2, leading to an amino acid change from Asn to Lys; and another silent substitution at codon 99 (TAT-->TAC) in the exon 3. The latest substitution (T-->C at the third position of codon 99) was not seen in any of the HLA-Cw*07 alleles reported so far, thus being characteristic to the new HLA-Cw*0714 allele.     

Characterization of a new HLA-C allele in a Chinese family by sequence-based typing: HLA-Cw*0348

The novel human leukocyte antigen (HLA)-Cw*0348 allele was identified by sequence-based typing in a Chinese family. This allele shows that the sequences of exons 1–3 of HLA-Cw*0348 are identical to those of HLA-Cw*030401 except for a nucleotide substitution that changes CCG to CTG at codon 57, resulting in an amino acid change from Pro to Leu in the protein, and this is a unique nucleotide change among the HLA-C alleles, suggesting a point mutation mechanism. The extended haplotype carrying the new allele was deduced from the family group typing and defined as A*110101, B*1301, Cw*0348, DRB1*0405, and DQB1*0402.     

Identification of the very uncommon allele HLA-Cw*0716 in a Caucasian renal transplant recipient: extension of the exon 4 sequence

This report describes the unknown exon 4 sequence of the rare human leukocyte antigen-Cw*0716 allele, identified in a Caucasian renal transplant recipient from Italy. This sequence is identical to the Cw*070101 allele, and this result allowed us to confirm the hypothesis of the generation of Cw*0716 allele by an interallelic recombination event between Cw*0701/0706/0718 and Cw*020202 allele.     

Elongation of the cytoplasmic domain,due to a point deletion at exon 7, results in an HLA-C null allele,Cw*0409 N

The development of molecular techniques for HLA typing has allowed the identification of genes previously assigned as serologic blank alleles. Lack or poor cell surface expression has been found for molecules coded by HLA-A, -B, -DRB4, -DRB5, and -DPB1 genes. In this report we describe the first HLA-C gene encoding for a null cell surface molecule. HLA-Cw*0409 N shows a point deletion at position 1095 within exon 7. This mutation provokes a codon reading shift, generating a new translation stop codon 97 bp downstream to that described in alleles normally expressed. This new stop codon location implies the presence of 32 extra amino acid residues in the cytoplasmic domain. Transfection experiments suggest that elongation of the cytoplasmic domain in Cw*0409 N would be the cause of cell surface expression failure, although Cw*0409 N heavy chain is able to create stable complexes with beta2-microglobulin. HLA-C fragment length analysis in a small selected group of samples with B44-Cblk haplotypic associations allowed us to identify two additional subjects showing both a serologic silent Cw*04 allele and a point base deletion at the 3' end of the HLA-C gene. This finding indicates that the allele frequency of Cw*0409 N within serologic C blank alleles would be appreciable, although basically restricted to the (A23)-Cw*0409 N-B*4403-DR7-DQ2 haplotype.     

The new HLA-Cw*0442 allele possibly generated by a recombination event involving Cw*04010101 and Cw*1801

A new human leukocyte antigen-C (HLA-C) allele Cw*0442 was identified in a Spanish Caucasian patient by sequencing-based typing (SBT). HLA-Cw*0442 differs from Cw*04010101 by three amino acid replacements at positions 9 (S>D), 11 (S>A), and 14 (W>R).