HLA‐DQB1 sequencing‐based typing updated

Dijk, Anouk van; Melchers, Rowena C A; Tilanus, M.G.J.; Rozemuller, Erik H.

doi:10.1111/j.1399-0039.2006.760_5.x

Cited by 13 publications

(10 citation statements)

References 5 publications

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“…Discordant calls were attributable to a combination of sensitivity errors occurring 0.7% (5 out of 766), in which CAPSeq analysis of next-generation sequences identified heterozygous genotypes as homozygous, and specificity errors occurring 0.3% (2 out of 766) in which an alternate genotype was called (Table 2). Sensitivity errors also referred to as “allele dropout” result from unbalanced amplification of HLA alleles, exhibit low Call Rates, and most likely result from nucleotide polymorphisms that influence amplification efficiency [26], [27]. This can lead to reporting of an individual as homozygous due to the resulting unbalanced representation of the two alleles.…”

Section: Resultsmentioning

confidence: 99%

Clustering and Alignment of Polymorphic Sequences for HLA-DRB1 Genotyping

Ringquist

Bellone

et al. 2013

PLoS ONE

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Located on Chromosome 6p21, classical human leukocyte antigen genes are highly polymorphic. HLA alleles associate with a variety of phenotypes, such as narcolepsy, autoimmunity, as well as immunologic response to infectious disease. Moreover, high resolution genotyping of these loci is critical to achieving long-term survival of allogeneic transplants. Development of methods to obtain high resolution analysis of HLA genotypes will lead to improved understanding of how select alleles contribute to human health and disease risk. Genomic DNAs were obtained from a cohort of n = 383 subjects recruited as part of an Ulcerative Colitis study and analyzed for HLA-DRB1. HLA genotypes were determined using sequence specific oligonucleotide probes and by next-generation sequencing using the Roche/454 GSFLX instrument. The Clustering and Alignment of Polymorphic Sequences (CAPSeq) software application was developed to analyze next-generation sequencing data. The application generates HLA sequence specific 6-digit genotype information from next-generation sequencing data using MUMmer to align sequences and the R package diffusionMap to classify sequences into their respective allelic groups. The incorporation of Bootstrap Aggregating, Bagging to aid in sorting of sequences into allele classes resulted in improved genotyping accuracy. Using Bagging iterations equal to 60, the genotyping results obtained using CAPSeq when compared with sequence specific oligonucleotide probe characterized 4-digit genotypes exhibited high rates of concordance, matching at 759 out of 766 (99.1%) alleles.

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Section: Resultsmentioning

confidence: 99%

Clustering and Alignment of Polymorphic Sequences for HLA-DRB1 Genotyping

Ringquist

Bellone

et al. 2013

PLoS ONE

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“…To verify the assay, 36 control DNAs were allelotyped using a DQB1 exon 2 sequencing-based typing technique adapted from van Dijk et al 12 and sequences were compared to MLPA results. Agreement was 100% between both techniques.…”

Section: Methodsmentioning

confidence: 99%

“…The following allele combinations were indistinguishable by our MLPA method: (*0601/*0601) vs. (*0601/*0602); (*0603/*0603) vs. (*0602/*0603); (*0604/*0604) vs. (*0604/*0609); and (*0602/*0604) vs. (*0603/*0604) vs. (*0603/*0609). Sequencing-based typing 12 was used to distinguish these cases.…”

Section: Methodsmentioning

confidence: 99%

Association ofHLA-DQB1alleles with risk of follicular lymphoma

Akers

Curry

Conde

et al. 2010

Leukemia & Lymphoma

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In a recent genome-wide association study of follicular lymphoma (FL), we identified novel risk alleles on chromosome 6p21.33 that appeared to be part of an extended haplotype including HLA-DRB1*0101, DQA1*0101, and DQB1*0501. To follow up on these findings, we obtained 2–4 digit HLA-DQB1 allelotypes on a subset of 265 FL cases and 757 controls using a novel assay that applies multiplexed ligation-dependent probe amplification (MLPA). We confirmed a positive association between FL and the HLA-DQB1*05 allele group (OR=1.70, 95% CI 1.28–2.27; adjusted p-value=0.013) and also identified an allele group inversely associated with FL risk, HLA-DQB1*06 (OR=0.51, 95% CI 0.38–0.69; adjusted p-value=4.46×10−5). Although these findings require verification, the role of HLA class II proteins in B-cell survival and proliferation make this a biologically plausible association.

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“…High‐resolution sequence‐based typing was used for the determination of the second and the third exons of DQA1 and DQB1 loci: these exons respectively encode for the α1 and β1 regions of the HLA‐DQ antigen cleft. The primers for amplifications and sequencing are listed in Table 1: they were used according to references (29, 30). Conditions for the polymerase chain reaction (PCR) assay by custom‐designed primers were as follow: 10 min at 95°C, 35 cycles of 30 s at 95°C, 1 min at 53.5°C, 30 s at 72°C and a final extension of 7 min at 72°C.…”

Section: Hla Typingmentioning

confidence: 99%

Genetic response to an environmental pathogenic agent: HLA‐DQ and onchocerciasis in northwestern Ecuador

et al. 2011

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The aim of this study is to explore human leukocyte antigen (HLA)-DQ variability in two populations (Cayapas Amerindians and Afro-Ecuadorians) who live near one another along the Cayapa River and who are exposed to the same environmental stresses, such as infection by Onchocerca volvulus. HLA-DQA1 and HLA-DQB1 of 149 unrelated individuals (74 Cayapas and 75 Afro-Ecuadorians) have been analyzed. HLA high-resolution molecular typing was performed by sequence-based typing, sequence-specific oligonucleotides hybridization and sequence-specific primer (SSP) amplification. The comparison between affected (cases) and unaffected people (controls) in both populations shows the key role of several HLA-DQA1 alleles in susceptibility and protection against onchocerciasis. In both populations, there is strong evidence related to the protective role of DQA1*0401 against onchocerciasis. Alleles HLA-DQA1*0102 and *0103 seem to represent risk factors in Afro-Ecuadorians, while HLA-DQA1*0301 is only a suggestive susceptibility allele in Cayapas. These findings represent new positive/negative associations with onchocerciasis in South America, whereas previous findings pertained only to African populations.

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HLA‐DQB1 sequencing‐based typing updated

Cited by 13 publications

References 5 publications

Clustering and Alignment of Polymorphic Sequences for HLA-DRB1 Genotyping

Clustering and Alignment of Polymorphic Sequences for HLA-DRB1 Genotyping

Association ofHLA-DQB1alleles with risk of follicular lymphoma

Genetic response to an environmental pathogenic agent: HLA‐DQ and onchocerciasis in northwestern Ecuador

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