Complete coding sequences and haplotypic associations of HLA‐B*0707, ‐B*1524, ‐B*4405, ‐B*4802, ‐DRB1*0409, ‐DRB1*0411, ‐DRB1*1115, ‐DRB1*1305, and the novel allele ‐DRB1*0709. Group‐specific amplification of cDNA from DRB1 alleles associated to DRB3 and DRB4

Vilches, Carlos; Sepúlveda, S; Balas, A.; Solís, R; Mj, Avilés Inglés; Estefanía, E; Gómez‐Lozano, Natalia; Jl, Vicario; dePablo, R

doi:10.1111/j.1399-0039.2005.00407.x

Cited by 10 publications

(4 citation statements)

References 52 publications

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“…Family segregation allowed to define the haplotype including this new allele as A*0101, B*0777, Cw*070201, DRB1*150101, DQB1*060201. Its closest allele B*0707 was first defined in a Caucasian individual (3) and more recently completely characterized in a sample with a mixed Venezuelan and Spanish ancestry (4). Both B*0707 bearing samples showed haplotypic association with A*01 and Cw*07 as here described for B*0777.…”

supporting

confidence: 51%

HLA‐B0777 allele differs from B0707 by a single residue in the antigen binding groove

et al. 2009

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supporting

confidence: 51%

HLA‐B0777 allele differs from B0707 by a single residue in the antigen binding groove

et al. 2009

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“…It is difficult to obtain the full‐coding sequences from genomic DNA because the full‐length genomic sequences of HLA‐DRB1 alleles are spanned from 10 to 15 kb. Some investigation had used the protocol from cDNA to obtain HLA‐DRB1 alleles complete coding region (8–16). Santamaria et al (10) described a cDNA approach for HLA‐DRB1 alleles sequencing and Vilches et al (11) had established a group‐specific amplification method for HLA‐DRB1 alleles from cDNA.…”

Section: The Primers Information For Hla‐drb1 Cdna Amplification and mentioning

confidence: 99%

Analysis of the complete cDNA sequences of HLA‐DRB1 alleles with group‐specific amplification primers in the Chinese Han population

Zhu

Tao

et al. 2011

Tissue Antigens

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Currently for the majority of HLA-DRB1 alleles the focus has been mainly on exon 2 and complete cDNA sequences of HLA-DRB1 alleles are rare. In this study, we analyzed the complete coding sequences of partial alleles of HLA-DRB1 locus. The cDNA was amplified by polymerase chain reaction using the group-specific primers located in the 5'- and 3'-untranslated regions to obtain the complete coding sequences. The amplification products were sequenced using an ABI BigDye® Terminator Cycle Sequencing kit. The HLA-DRB1 allele phylogenetic tree was analyzed by dnaman software. Full-length cDNA sequences of 22 HLA-DRB1 alleles were obtained in this study. HLA-DRB1*08:09, DRB1 *12:02:01, and DRB1*13:12 alleles were first reported for complete coding sequences. The sequences of exon 1 of HLA-DRB1*04:06:01, DRB1*08:03:02, and DRB1 *14:07:01 were newly presented. The complete coding sequences of HLA-DRB1 *01:01:01, DRB1*03:01:01:01, DRB1*04:01:01, DRB1*04:05:01, DRB1*07:01:01: 01, DRB1*09:01:02, DRB1*10:01:01, DRB1*11:01:01, DRB1*12:01:01, DRB1*13: 01:01, DRB1*13:02:01, DRB1*14:04, DRB1*14:54, DRB1*15:01:01:01, DRB1*15: 02:01, and DRB1*16:02:01 were identical to those previously reported. Forty polymorphic positions in complete coding sequences outside exon 2 of these HLA-DRB1 alleles were confirmed. According to the phylogenetic tree of full-length coding sequence, the HLA-DRB1 allele was classified into seven major allelic lineages. In conclusion, a protocol for HLA-DRB1 cDNA amplification and sequencing was improved and the data may help to determine the polymorphism of coding sequences outside exon 2.

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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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Complete coding sequences and haplotypic associations of HLA‐B0707, ‐B1524, ‐B4405, ‐B4802, ‐DRB10409, ‐DRB10411, ‐DRB11115, ‐DRB11305, and the novel allele ‐DRB1*0709. Group‐specific amplification of cDNA from DRB1 alleles associated to DRB3 and DRB4

Cited by 10 publications

References 52 publications

HLA‐B0777 allele differs from B0707 by a single residue in the antigen binding groove

HLA‐B0777 allele differs from B0707 by a single residue in the antigen binding groove

Analysis of the complete cDNA sequences of HLA‐DRB1 alleles with group‐specific amplification primers in the Chinese Han population

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

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Complete coding sequences and haplotypic associations of HLA‐B*0707, ‐B*1524, ‐B*4405, ‐B*4802, ‐DRB1*0409, ‐DRB1*0411, ‐DRB1*1115, ‐DRB1*1305, and the novel allele ‐DRB1*0709. Group‐specific amplification of cDNA from DRB1 alleles associated to DRB3 and DRB4

Cited by 10 publications

References 52 publications

HLA‐B*0777 allele differs from B*0707 by a single residue in the antigen binding groove

HLA‐B*0777 allele differs from B*0707 by a single residue in the antigen binding groove

Analysis of the complete cDNA sequences of HLA‐DRB1 alleles with group‐specific amplification primers in the Chinese Han population

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

Contact Info

Product

Resources

About

Complete coding sequences and haplotypic associations of HLA‐B0707, ‐B1524, ‐B4405, ‐B4802, ‐DRB10409, ‐DRB10411, ‐DRB11115, ‐DRB11305, and the novel allele ‐DRB1*0709. Group‐specific amplification of cDNA from DRB1 alleles associated to DRB3 and DRB4

HLA‐B0777 allele differs from B0707 by a single residue in the antigen binding groove

HLA‐B0777 allele differs from B0707 by a single residue in the antigen binding groove