Elucidation of Exon 1, 4, and 5 Sequences of 39 Infrequent HLA-B Alleles

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

doi:10.1016/j.humimm.2005.01.006

Cited by 3 publications

(3 citation statements)

References 42 publications

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“…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

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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.

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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

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“…Although polymorphism outside exons 2 and 3 might not have a direct function in the binding of peptides, they still show a certain degree of polymorphism, as was shown in previous studies for HLA‐B and ‐C . It is hypothesized that exon 4 polymorphism might play a role in indirectly affecting peptide binding by influencing the β2‐microglobulin binding to the α3 domain .…”

Section: Introductionmentioning

confidence: 99%

An improved and validated RNA HLA class I SBT approach for obtaining full length coding sequences

et al. 2014

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The functional relevance of human leukocyte antigen (HLA) class I allele polymorphism beyond exons 2 and 3 is difficult to address because more than 70% of the HLA class I alleles are defined by exons 2 and 3 sequences only. For routine application on clinical samples we improved and validated the HLA sequence-based typing (SBT) approach based on RNA templates, using either a single locus-specific or two overlapping group-specific polymerase chain reaction (PCR) amplifications, with three forward and three reverse sequencing reactions for full length sequencing. Locus-specific HLA typing with RNA SBT of a reference panel, representing the major antigen groups, showed identical results compared to DNA SBT typing. Alleles encountered with unknown exons in the IMGT/HLA database and three samples, two with Null and one with a Low expressed allele, have been addressed by the group-specific RNA SBT approach to obtain full length coding sequences. This RNA SBT approach has proven its value in our routine full length definition of alleles.

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“…Previously published partial exon 1, exon 4, intron 4, exon 5 sequences of B*40:01:01 (B60), B*40:02 (B61), B*40:03 (B61), B*40:05 (B61), B*40:08 (B61), B*40:10 (B60) and B*40:35 (B61) confirm and point to the correlation of the gene polymorphism with the antigen groups as indicated between brackets. Based upon the sequence polymorphism, B*40:12 (intron 4 and exon 5) and B*40:16 (exon 4, intron 4 and exon 5), for which the serological equivalent is unknown, belong to the B60 antigen lineage . However, whereas neural network analysis could not assign the antigen groups , the expert assignment of B*40:12 is indeed B60/B48, but for B*40:16 experts assigned B61 in contrast to the gene polymorphism.…”

mentioning

confidence: 99%

Identification of a new allele polymorphism (HLA‐B40:79*) and correlation with the HLA‐B40 (B60 and B61) antigens

2013

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Elucidation of Exon 1, 4, and 5 Sequences of 39 Infrequent HLA-B Alleles

Cited by 3 publications

References 42 publications

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

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

An improved and validated RNA HLA class I SBT approach for obtaining full length coding sequences

Identification of a new allele polymorphism (HLA‐B40:79*) and correlation with the HLA‐B40 (B60 and B61) antigens

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Elucidation of Exon 1, 4, and 5 Sequences of 39 Infrequent HLA-B Alleles

Cited by 3 publications

References 42 publications

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

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

An improved and validated RNA HLA class I SBT approach for obtaining full length coding sequences

Identification of a new allele polymorphism (HLA‐B*40:79) and correlation with the HLA‐B40 (B60 and B61) antigens

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Product

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Identification of a new allele polymorphism (HLA‐B40:79*) and correlation with the HLA‐B40 (B60 and B61) antigens