Refined information on alleles belonging to the C*07:01/07:06/07:18 group in the Korean population

Lee, Kyung Wha; Jung, Y.-A.

doi:10.1016/j.humimm.2011.05.002

Cited by 3 publications

(9 citation statements)

References 32 publications

(31 reference statements)

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“…To discriminate C*07:18 from C*07:06 and C*07:01:01 , exons 5 and 6, respectively, should additionally be sequenced, explaining why all three of these alleles were reported as C*07:01 in previous reports where only exons 2–4 were sequenced. Lee et al showed that 96.6% of C*07:01 alleles previously reported in Koreans were found to be C*07:06 by additional sequencing of exon 5 . However, the results of this study results indicate that the remaining C*07:01 alleles could be identified as C*07:18 if exon 6 is also sequenced.…”

Section: Discussioncontrasting

confidence: 81%

See 1 more Smart Citation

Estimation of the 6‐digit level allele and haplotype frequencies of HLA‐A, ‐B, and ‐C in Koreans using ambiguity‐solving DNA typing

et al. 2014

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Because Korean society is fast becoming multi-ethnic, the determination of ambiguous human leukocyte antigen (HLA) types using HLA allele frequencies is becoming less applicable. In this study, we focused on the development of new technical methods to directly resolve the ambiguities arising from HLA genotyping. One hundred and fifty unrelated healthy Korean adults were included in this study. All alleles from each HLA locus were first divided into 2-4 groups, with each group amplified in a single PCR tube (multi-group-specific amplification, MGSA). To resolve phase ambiguities, some allele groups were also amplified separately in small group-specific amplification (SGSA) tubes. In order to then resolve incomplete sequence ambiguities, primers for MGSA and SGSA were initially designed to cover additional exons. If needed, a heterozygous ambiguity resolving primer (HARP) or sequence specific primer (SSP) was also used. When MGSA and SGSA methods were applied, the rate of phase ambiguity was greatly reduced to an average of 6% (1.3% in HLA-A, 15.7% in -B, and 2.0% in -C). Additional HARP and SSP methods could resolve all the phase ambiguities. Using our proposed method, we also detected three alleles that have not been previously reported in Korea, C*04:82, C*07:18, and C*08:22, and report 6-digit level HLA allele and haplotype frequencies among Koreans. In conclusion, the use of MGSA/SGSA for the initial amplification step is a cost-effective method facilitating timely and accurate reporting, given the continuing increase in the ethnic diversity of the Korean population. The MGSA described here can be applicable to various populations and thus could be shared by the majority of HLA typing laboratories. However, efforts to solve HLA ambiguity should continue, because SGSA, HARPs and SSPs would be specific to a particular population.

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Section: Discussioncontrasting

confidence: 81%

“…In this analyses, all incomplete sequence ambiguities were resolved and the alleles HLA‐C*04:82, C*07:18 , and C*08:22 , which have not been reported in previous studies, were identified . These three alleles were identified through the sequencing of additional exons for HLA class I.…”

Section: Discussionmentioning

confidence: 99%

Estimation of the 6‐digit level allele and haplotype frequencies of HLA‐A, ‐B, and ‐C in Koreans using ambiguity‐solving DNA typing

et al. 2014

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“…The HLA distribution in anti-LGI1 encephalitis was largely homogenous, as characterized by the DRB1*07:01-DQB1*02:02 haplotype in 10 of the 11 patients and the C*07:06-B*44:03-DRB1*07:01-DQB1*02:02 haplotype in 7 patients (Fig 1F). [26][27][28] There is approximately a 0.074% (approximately 38,000 people in South Korea) probability, which is not impossible, for any Korean to have these two haplotypes randomly by simple calculation. 3 and 4) had exactly the same alleles (Supplementary Table 2), which correspond to two conserved haplotypes of A*33:03-C*07:06-B*44:03-DRB1*07:01-DQB1*02:02 (haplotype frequency of 2.99% in Korean general population) and A*11:01-C*04:01-B*15:01-DRB1*04:06-DQB1*03:02 (haplotype frequency of 1.24%).…”

Section: Discussionmentioning

confidence: 99%

“…24 Briefly, the genotypes of the HLA-A, B, C, DRB1, and DQB1 genes of each subject were determined at the four-digit allele level using direct DNA sequence analysis following established protocols (Biowithus, Seoul, Korea). The previously reported HLA frequencies in the Korean population were used for the healthy control group values, [26][27][28] which comprises 485 healthy subjects genotyped by sequence-specific oligonucleotide probes. HLA-A, B, and C belong to HLA class I, whereas HLA-DRB1 and DQB1 belong to HLA class II.…”

Section: Hla Genotypingmentioning

confidence: 99%

Anti‐LGI1 encephalitis is associated with unique HLA subtypes

Kim

Moon

Sunwoo

et al. 2017

Annals of Neurology

150

112

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“…The obtained electropherograms were processed by using Assign SBT (Conexio Genomics, Fremantle Western Australia, Australia). To resolve ambiguity in C*07:01/07:06/07:18 group, exon 5 sequences of HLA-C were further analyzed, as described previously [ 14 ].…”

Section: Methodsmentioning

confidence: 99%

Allele and Haplotype Frequencies of Human Leukocyte Antigen-A, -B, -C, -DRB1, and -DQB1 From Sequence-Based DNA Typing Data in Koreans

Roh

et al. 2015

Ann Lab Med

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BackgroundData on allele frequencies (AFs) and haplotype frequencies (HFs) of HLA-C and -DQB1 are limited in Koreans. We investigated AFs and HFs of HLA-A, -B, -C, -DRB1, and -DQB1 in Koreans by high-resolution sequence-based typing (SBT).MethodsHematopoietic stem cells were obtained from 613 healthy, unrelated donors to analyze HLA-A, -B, -C, -DRB1, and -DQB1 genotypes by using AlleleSEQR HLA-A, -B, -C, -DRB1, and -DQB1 SBT kits (Abbott Molecular, USA), respectively. Alleles belonging to HLA-C*07:01/07:06 group were further discriminated by using PCR-sequence specific primer analysis. AFs and HFs were calculated by direct counting and maximum likelihood method, respectively.ResultsIn all, 24 HLA-A, 46 HLA-B, 24 HLA-C, 29 HLA-DRB1, and 15 HLA-DQB1 alleles were identified. AFs and HFs of HLA-A, -B, and -DRB1 were similar to those reported previously. For the HLA-C locus, C*01:02 was the most common allele, followed by C*03:03, C*03:04, C*14:02, C*03:02, and C*07:02 (AF ≥7%). AFs of C*07:01 and C*07:06 were 0.16% and 3.18%, respectively. For the HLA-DQB1 locus, DQB1*03:01 was the most common allele, followed by DQB1*03:03, *03:02, *06:01, *05:01, *04:01, and *06:02 (AF ≥7%). AFs of DQB1*02:01 and DQB1*02:02 were 2.12% and 6.69%, respectively. HFs of A*33:03-C*07:06 and C*07:06-B*44:03 were 3.09% and 3.10%, respectively, while those of DRB1*07:01-DQB1*02:02 and DRB1*03:01-DQB1*02:01 were 6.61% and 2.04%, respectively.ConclusionsThis study reported AFs and HFs of HLA, including HLA-C and -DQB1, in Koreans by using high-resolution SBT. These data can be used to resolve ambiguous results of HLA typing for organ and hematopoietic stem cell transplantations.

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Refined information on alleles belonging to the C*07:01/07:06/07:18 group in the Korean population

Cited by 3 publications

References 32 publications

Estimation of the 6‐digit level allele and haplotype frequencies of HLA‐A, ‐B, and ‐C in Koreans using ambiguity‐solving DNA typing

Estimation of the 6‐digit level allele and haplotype frequencies of HLA‐A, ‐B, and ‐C in Koreans using ambiguity‐solving DNA typing

Anti‐LGI1 encephalitis is associated with unique HLA subtypes

Allele and Haplotype Frequencies of Human Leukocyte Antigen-A, -B, -C, -DRB1, and -DQB1 From Sequence-Based DNA Typing Data in Koreans

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