Group-Specific Amplification of cDNA From DRB1 Genes. Complete Coding Sequences of Partially Defined Alleles and Identification of the New Alleles DRB1*040602, DRB1*111102, DRB1*080103, and DRB1*0113

Balas, A.; Vilches, Carlos; Rodrı́guez, Miguel A.; Fernández, B.; Martínez, María Paz; Pablo, Rosario de; García‐Sánchez, Félix; Vicário, José L.

doi:10.1016/j.humimm.2006.09.002

Cited by 10 publications

(3 citation statements)

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“…Santamaria et al (1992) developed an SBT approach focussed on the identification of exon 2 polymorphism by sequencing mRNA templates . Full‐length HLA‐DRB1 RNA sequencing was accomplished since 2005, combining a locus‐specific primer in the 5′ untranslated region (UTR) with a group‐specific primer in the 3′UTR, although the approaches were limited to certain allele groups and required cloning procedures for the separation of some alleles .…”

Section: Introductionmentioning

confidence: 99%

Full‐length HLA‐DRB1 coding sequences generated by a hemizygous RNA‐SBT approach

et al. 2015

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Currently 1582 HLA-DRB1 alleles have been identified in the IMGT/HLA database (v3.18). Among those alleles, more than 90% have incomplete allele sequences, which complicates the analysis of the functional relevance of polymorphism beyond exon 2. The polymorphic index of each individual exon of the currently known allele sequences, shows that polymorphism is present in all exons, albeit not equally abundant. Full-length HLA-DRB1 RNA sequencing identifies polymorphism of the complete coding region. Here we describe a hemizygous full-length RNA sequence-based typing (SBT) approach based on group-specific HLA-DRB1 amplification and subsequent sequencing. RNA full-length sequences can easily be accessed because of the short amplicon length (801 bp). The RNA-SBT approach was successfully validated on a panel of DRB1 alleles having fully known coding sequences according to the IMGT/HLA database, and cover all serological equivalents. Subsequently, the approach was applied on a panel of 54 alleles with incomplete allele sequences, resulting in full-length coding sequences and the identification of one new and one corrected allele. This study shows the universal applicability of the RNA-based sequencing approach to identify full-length coding sequences and to define the polymorphic content of HLA-DRB1 alleles.

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Section: Introductionmentioning

confidence: 99%

Full‐length HLA‐DRB1 coding sequences generated by a hemizygous RNA‐SBT approach

et al. 2015

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“…Thus, a subsequent cloning step is required to achieve allele separation before the products can be sequenced, and this adds on substantial complexity to the assay. We have reported previously PCR amplification of cDNA from specific allele groups using oligonucleotides located at the 5′‐ and 3′‐UT regions of HLA class I and class II genes (8, 9). However, these techniques provide no intronic sequences and require RNA purification, reverse transcription and, often, plasmid cloning.…”

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Allele‐specific amplification of the complete HLA‐C gene from genomic DNA – a novel Cw4 allele (C04:71*) with a Cw1 motif in the peptide‐binding site

et al. 2012

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To determine the complete sequence of a newly identified human leukocyte antigen (HLA)-C allele, we designed a method where the full genomic sequence of HLA-C*04 was amplified in isolation from the patient second HLA-C allele in a single polymerase chain reaction (PCR), using primers spanning its 5'- and 3'-untranslated regions. The new allele, officially designated HLA-C*04:71, differs from HLA-C*04:01:01:01 by two single-nucleotide polymorphisms: one determines substitution of phenylalanine for serine 9 at the B pocket of the peptide-binding site; the second substitution is a new polymorphism in intron 5. Phe-9 is characteristic of Cw1 alleles and its presence in C*04:71 most likely affects its peptide-binding repertoire. The principle we have used for C*04:71 isolation could be adapted for unambiguous sequence-based HLA-C typing of selected samples in a clinical setting.

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“…The IMGT/HLA Database may be accessed via the World Wide Web at: www.ebi.ac.uk/imgt/hla. (Balas et al, 2006) DRB1*1356 (Balas et al, 2006) DRB1*1411 (Balas et al, 2006) DRB1*1446 (Balas et al, 2006) DRB1*1503 (Balas et al, 2006) DRB1*1504 (Balas et al, 2006) DQB1*060302 (Witter et al, 2007) DQB1*0628 (Witter et al, 2007)…”

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Nomenclature for factors of the HLA system, update January 2007*

Marsh

2007

Int J Immunogenetics

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Group-Specific Amplification of cDNA From DRB1 Genes. Complete Coding Sequences of Partially Defined Alleles and Identification of the New Alleles DRB1040602, DRB1111102, DRB1080103, and DRB10113

Cited by 10 publications

References 34 publications

Full‐length HLA‐DRB1 coding sequences generated by a hemizygous RNA‐SBT approach

Full‐length HLA‐DRB1 coding sequences generated by a hemizygous RNA‐SBT approach

Allele‐specific amplification of the complete HLA‐C gene from genomic DNA – a novel Cw4 allele (C04:71*) with a Cw1 motif in the peptide‐binding site

Nomenclature for factors of the HLA system, update January 2007*

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Group-Specific Amplification of cDNA From DRB1 Genes. Complete Coding Sequences of Partially Defined Alleles and Identification of the New Alleles DRB1*040602, DRB1*111102, DRB1*080103, and DRB1*0113

Cited by 10 publications

References 34 publications

Full‐length HLA‐DRB1 coding sequences generated by a hemizygous RNA‐SBT approach

Full‐length HLA‐DRB1 coding sequences generated by a hemizygous RNA‐SBT approach

Allele‐specific amplification of the complete HLA‐C gene from genomic DNA – a novel Cw4 allele (C*04:71) with a Cw1 motif in the peptide‐binding site

Nomenclature for factors of the HLA system, update January 2007*

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Group-Specific Amplification of cDNA From DRB1 Genes. Complete Coding Sequences of Partially Defined Alleles and Identification of the New Alleles DRB1040602, DRB1111102, DRB1080103, and DRB10113

Allele‐specific amplification of the complete HLA‐C gene from genomic DNA – a novel Cw4 allele (C04:71*) with a Cw1 motif in the peptide‐binding site