Sequence-Based Typing of the HLA-A10/A19 Group and Confirmation of a Pseudogene Coamplified With A*3401

Swelsen, Wendy; Voorter, Christina E.M.; Berg‐Loonen, Ella M. van den

doi:10.1016/j.humimm.2005.01.005

Cited by 9 publications

(11 citation statements)

References 30 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Although the precise genomic location of HLA-Y remains unknown, linkage disequilibrium between HLA-Y and a subset of HLA-A demonstrates its presence in the MHC. HLA-Y has been detected on all haplotypes that have HLA-A * 2901 , * 3001 , * 33 , * 3401 , or * 6802 and on most haplotypes that have HLA-A * 0203 , * 0205 , and * 31 (55, 56, 58, 59). The HLA-A alleles associated with HLA-Y are more frequent in non-Caucasian populations and we estimate that ∼20% of the human population carry HLA-Y .…”

Section: Resultsmentioning

confidence: 99%

Although Divergent in Residues of the Peptide Binding Site, Conserved Chimpanzee Patr-AL and Polymorphic Human HLA-A*02 Have Overlapping Peptide-Binding Repertoires

Gleimer

Wahl

Hickman

et al. 2011

The Journal of Immunology

View full text Add to dashboard Cite

Patr-AL is an expressed, non-polymorphic MHC class I gene carried by ∼50% of chimpanzee MHC haplotypes. Comparing Patr-AL+ and Patr-AL- haplotypes showed Patr-AL defines a unique 125kb genomic block flanked by blocks containing classical Patr-A and pseudogene Patr-H. Orthologous to Patr-AL are polymorphic orangutan Popy-A and the 5′ part of human pseudogene HLA-Y, carried by ∼10% of HLA haplotypes. Thus the AL gene alternatively evolved in these closely related species to become classical, non-classical and non-functional. Although differing by 30 amino acid substitutions in the peptide-binding α1 and α2 domains, Patr-AL and HLA-A*0201 bind overlapping repertoires of peptides; the overlap being comparable to that between the A*0201 and A*0207 subtypes differing by one substitution. Patr-AL thus has the A02 supertypic peptide-binding specificity. Patr-AL and HLA-A*0201 have similar three-dimensional structures, binding peptides in similar conformation. Although comparable in size and shape, the B and F specificity pockets of Patr-AL and HLA-A*0201 differ in both their constituent residues and contacts with peptide anchors. Uniquely shared by Patr-AL, HLA-A*0201, and other members of the A02 supertype are the absence of serine at position 9 in the B pocket and the presence of tyrosine at position 116 in the F pocket. Distinguishing Patr-AL from HLA-A*02 is an unusually electropositive upper face on the α2 helix. Stimulating PBMC from Patr-AL- chimpanzees with B cells expressing Patr-AL, produced potent alloreactive CD8 T cells with specificity for Patr-AL and no crossreactivity toward other MHC class I, including HLA-A*02. PBMC from Patr-AL+ chimpanzees are tolerant of Patr-AL.

show abstract

Section: Resultsmentioning

confidence: 99%

Although Divergent in Residues of the Peptide Binding Site, Conserved Chimpanzee Patr-AL and Polymorphic Human HLA-A*02 Have Overlapping Peptide-Binding Repertoires

Gleimer

Wahl

Hickman

et al. 2011

The Journal of Immunology

View full text Add to dashboard Cite

show abstract

“…SBT of HLA‐A, ‐B and ‐Cw was performed as described previously (4–9) by heterozygous amplification and sequencing of the complete exons 2 and 3. If this did not result in an allele typing to the four‐digit level at the time of analysis, additional exons and/or allele‐specific sequencing was performed until an unequivocal four‐digit typing result was obtained.…”

Section: Methodsmentioning

confidence: 99%

“…If this did not result in an allele typing to the four-digit level at the time of analysis, additional exons and/or allele-specific sequencing was performed until an unequivocal four-digit typing result was obtained. Additional exons 1 and 4 for HLA-A and 1, 4 and 5 for HLA-B and -Cw were sequenced using amplification primers located in the adjacent introns as described (4,(9)(10)(11)(12)(13)(14). For allele-specific sequencing, in-house custom group-specific amplification primers were used (4,(15)(16)(17)(18)(19)(20)(21).…”

Section: Sequence-based Typingmentioning

confidence: 99%

Reanalysis of sequence‐based HLA‐A, ‐B and ‐Cw typings: how ambiguous is today’s SBT typing tomorrow

Voorter¹,

Mulkers²,

Liebelt³

et al. 2007

Tissue Antigens

View full text Add to dashboard Cite

The permanently increasing number of human leukocyte antigen (HLA)-alleles and the growing list of ambiguities require continuous updating of high-resolution HLA typing results. Two different kinds of ambiguities exist: the first, when two or more allele combinations have identical heterozygous sequences, and the second, when differences are located outside the analyzed region. The number of HLA-A, B and C alleles recognized in 1999 was almost tripled in 2006. Two hundred individuals, sequence-based typing (SBT) typed in the period from 1999 to 2002, were reanalyzed using the 2006 database. A final allele typing result of at least four digits was obtained for HLA-A, -B and -C by heterozygous sequencing of exons 2 and 3 and, if necessary, additional exons and/or allele-specific sequencing. Storage of the individual sequences in a specially developed database enabled reanalysis with all present and future HLA releases. In the 5-year period HLA-A, -B and -C typing results became ambiguous in 37%, 46% and 41% of the cases. Most were because of differences outside the analyzed region; ambiguities because of different allele combinations with identical heterozygous sequences were present in 7%, 8% and 13% of the HLA-A, -B and -C typings. These results indicate that within 5 years, approximately half of the HLA SBT typings become ambiguous.

show abstract

“…Heterozygous sequencing of the A locus, performed as described previously (3), revealed the presence of two mismatches with the known alleles A*0201, *1106/1112. For A*0201, *1106, the mismatches were located at positions 282 and 341, whereas for A*0201, *1112, they were located at 282 and 292.…”

mentioning

confidence: 94%

“…To characterize the new allele, allele‐specific sequencing of exons 2 and 3 was performed using a group‐specific 5′ primer (5′‐GGAGAAGCAAGGGGCCCT‐3′) located in intron 1 combined with the generic 3′ primers A97104 and A96090 as described previously (3). In addition, the sequences of exons 1 and 4 were determined.…”

mentioning

confidence: 99%

A novel HLA‐A11 allele, A1118, identified by sequence‐based typing†

et al. 2006

View full text Add to dashboard Cite

show abstract

Sequence-Based Typing of the HLA-A10/A19 Group and Confirmation of a Pseudogene Coamplified With A*3401

Cited by 9 publications

References 30 publications

Although Divergent in Residues of the Peptide Binding Site, Conserved Chimpanzee Patr-AL and Polymorphic Human HLA-A*02 Have Overlapping Peptide-Binding Repertoires

Although Divergent in Residues of the Peptide Binding Site, Conserved Chimpanzee Patr-AL and Polymorphic Human HLA-A*02 Have Overlapping Peptide-Binding Repertoires

Reanalysis of sequence‐based HLA‐A, ‐B and ‐Cw typings: how ambiguous is today’s SBT typing tomorrow

A novel HLA‐A11 allele, A1118, identified by sequence‐based typing†

Contact Info

Product

Resources

About

Sequence-Based Typing of the HLA-A10/A19 Group and Confirmation of a Pseudogene Coamplified With A*3401

Cited by 9 publications

References 30 publications

Although Divergent in Residues of the Peptide Binding Site, Conserved Chimpanzee Patr-AL and Polymorphic Human HLA-A*02 Have Overlapping Peptide-Binding Repertoires

Although Divergent in Residues of the Peptide Binding Site, Conserved Chimpanzee Patr-AL and Polymorphic Human HLA-A*02 Have Overlapping Peptide-Binding Repertoires

Reanalysis of sequence‐based HLA‐A, ‐B and ‐Cw typings: how ambiguous is today’s SBT typing tomorrow

A novel HLA‐A*11 allele, A*1118, identified by sequence‐based typing†

Contact Info

Product

Resources

About

A novel HLA‐A11 allele, A1118, identified by sequence‐based typing†