ABSTRACT
The non-classical HLA-G*01:55 allele differs from G*01:01:12 at one position in exon 4.
Subject(s)
Alleles , Asian People , Exons , HLA-G Antigens , Histocompatibility Testing , Humans , HLA-G Antigens/genetics , Base Sequence , Sequence Analysis, DNA , China , Codon , East Asian PeopleABSTRACT
MICB*002:06 differs from MICB*002:01:01 by one nucleotide change at nucleotide 33 in exon 1 from C to T.
Subject(s)
Exons , Histocompatibility Antigens Class I , Humans , Histocompatibility Antigens Class I/genetics , Histocompatibility Antigens Class I/immunology , Alleles , Base Sequence , Sequence Analysis, DNA/methods , Histocompatibility Testing , Sequence Alignment , CodonABSTRACT
One nucleotide substitution in codon 30 of HLA-DRB4*01:03:01:01 results in a novel allele, HLA-DRB4*01:179.
Subject(s)
Alleles , Exons , HLA-DRB4 Chains , Histocompatibility Testing , Humans , Base Sequence , Codon , HLA-DRB4 Chains/genetics , Sequence Alignment , Sequence Analysis, DNAABSTRACT
We report a novel HLA-DRB3*03 allele, now named DRB3*03:65, identified by next-generation sequencing.
Subject(s)
Exons , HLA-DRB3 Chains , Histocompatibility Testing , Humans , Alleles , Base Sequence , Codon , East Asian People , High-Throughput Nucleotide Sequencing , HLA-DRB3 Chains/genetics , Sequence Analysis, DNA/methodsABSTRACT
HLA-A*31:01:53 differs from HLA-A*31:01:02:01 by one nucleotide change at nucleotide 900 in exon 5 from G to A.
Subject(s)
Alleles , Asian People , Exons , HLA-A Antigens , High-Throughput Nucleotide Sequencing , Humans , Asian People/genetics , Base Sequence , Codon , East Asian People , Histocompatibility Testing/methods , HLA-A Antigens/genetics , Polymorphism, Single Nucleotide , Sequence Analysis, DNA/methodsABSTRACT
OBJECTIVE: To investigate the accuracy of next-generation sequencing technology (NGS) in detecting the polymorphisms of HLA-DRB1, DQB1, DQA1, DRB3, DRB4, DRB5, DPA1 and DPB1 alleles in randomly-selected unrelated healthy individuals from Shenzhen Han population, investigate the potential reason for HLA-DRB1 allele dropout in routine NGS, and establish an internal quality control system. METHODS: NGS-based HLA class II genotyping was performed on 1 012 samples using the MiSeqDxTM platform. The suspected missed alleles indicated by the quality control software and HLA-DRB1 homozygotes were confirmed by PCR-SSOP or PCR-SBT methods. RESULTS: A total of 139 alleles were detected, including HLA-DRB1(45), DRB3(7), DRB4(5), DRB5(7), DQA1(17), DQB1(21), DPA1(10) and DPB1(27). HLA-DRB1*09:01(17.09%),15:01(10.72%); DRB3*02:02(25.99%),03:01(10.18%); DRB4*01:03(36.46%); DRB5*01:01(15.42%); DQA1*01:02(20.01%),03:02(17.19%); DQB1*03:01(19.47%),03:03(17.98%), 05:02(11.66%), 06:01(10.67%); DPA1*02:02(54.45%), 01:03(31.18%) and DPB1*05:01(39.13%), 02:01(16.90%) alleles were the most common alleles in Shenzhen Han population (frequencies >10%). There was no statistical difference between the gene frequencies of HLA-DRB1 and DQB1 loci in our study. The HLA Common and Well-Documented Alleles in China (CWD2.4) (χ2=12.68, P >0.05). 94 cases of HLA-DRB1 homozygous samples detected by NGS were retested by PCR-SSOP or SBT method, and one case of allele dropout at HLA-DRB1 locus was found. SBT method confirmed that the allele of DRB1*04:03 was missed. The laboratory internal quality control system was established. Two cases of new alleles were detected and named by WHO Nomenclature Committee for Factors of the HLA System. CONCLUSION: The HLA genotyping results based on NGS showed a significantly lower ambiguity rate. The HLA class II alleles exhibit genetic polymorphism in the Han population of unrelated healthy individuals in Shenzhen. The independent method based on NGS in clinical histocompatibility testing has limitations and requires internal quality control strategies to avoid allele-dropout events.
Subject(s)
East Asian People , Genotype , High-Throughput Nucleotide Sequencing , Histocompatibility Antigens Class II , Humans , Alleles , Gene Frequency , Polymorphism, Genetic , East Asian People/genetics , Histocompatibility Antigens Class II/geneticsABSTRACT
Compared with HLA-DRB1*09:01:02:05, the alleles HLA-DRB1*09:57 and HLA-DRB1*09:58 each show one nucleotide change, respectively.
Subject(s)
Alleles , Asian People , Base Sequence , Exons , HLA-DRB1 Chains , Humans , HLA-DRB1 Chains/genetics , Asian People/genetics , Histocompatibility Testing , China , Sequence Analysis, DNA/methods , Sequence Alignment , Codon , East Asian PeopleABSTRACT
The novel HLA-A*33:244 allele contains a c.553G>A substitution in exon 3 compared with A*33:03:01:01.
Subject(s)
HLA-A Antigens , High-Throughput Nucleotide Sequencing , Humans , Alleles , Exons/genetics , HLA-A Antigens/geneticsABSTRACT
HLA-A*30:211 differs from HLA-A*30:01:01:01 by one nucleotide change at nucleotide 344 in exon 3 from G to C.
Subject(s)
High-Throughput Nucleotide Sequencing , Nucleotides , Humans , Alleles , China , HLA-A Antigens/geneticsABSTRACT
HLA-B*13:179 differs from HLA-B*13:99 by one nucleotide substitution at position 829(A>G) in exon 4.
Subject(s)
East Asian People , High-Throughput Nucleotide Sequencing , Humans , Alleles , Asian People/genetics , HLA-B Antigens/geneticsABSTRACT
One nucleotide substitution in codon 116 of HLA-B*40:06:01:12 results in a novel allele, HLA-B*40:537.
Subject(s)
East Asian People , HLA-B Antigens , Humans , Alleles , High-Throughput Nucleotide Sequencing , Histocompatibility Testing , HLA-B Antigens/genetics , Sequence Analysis, DNAABSTRACT
B*15:664 differs from B*15:02:01:01 by one nucleotide change at nucleotide 755 in exon 4 from C to G.
Subject(s)
HLA-B Antigens , Humans , Alleles , East Asian People/genetics , High-Throughput Nucleotide Sequencing , HLA-B Antigens/genetics , NucleotidesABSTRACT
HLA-B*40:01:83, carrying a single nucleotide substitution in exon 5 is described.
Subject(s)
Genes, MHC Class I , HLA-B Antigens , Humans , Alleles , Exons/genetics , HLA-B Antigens/genetics , Nucleotides , High-Throughput Nucleotide SequencingABSTRACT
OBJECTIVE: To confirm the HLA genotypes of the samples including 4 cases of magnetic bead probe HLA genotyping result pattern abnormality and 3 cases of ambiguous result detected by PCR sequence-specific oligonudeotide probe (SSOP) method. METHODS: All samples derived from HLA high-resolution typing laboratory were detected by PCR-SSOP. A total of 4 samples of magnetic bead probe HLA genotyping result pattern abnormality and 3 samples of ambiguous result were further confirmed by PCR sequence-based typing (SBT) technology and next-generation sequencing (NGS) technology. RESULTS: A total of 4 samples of magnetic bead probe HLA genotyping result pattern abnormality were detected by PCR-SSOP method. The results of SBT and NGS showed that the HLA-A genotype of sample 1 did not match any known genotypes. NGS analysis revealed that the novel allele was different from the closest matching allele A*31:01:02:01at position 154 with G>A in exon 2, which resulting in one amino acid substitution at codon 28 from Valine to Methionine (p.Val28Met). The HLA-C genotype of sample 2 was C*03:119, 06:02, sample 3 was C*03:03, 07:137, and sample 4 was B*55:02, 55:12. A total of 3 samples with ambiguous result were initially detected by PCR-SSOP method. The re-examination results of SBT and NGS showed that the HLA-B genotype of sample 5 was B*15:58, 38:02, sample 6 was DRB1*04:05, 14:101, and sample 7 was DQB1*03:34, 05:02. Among them, alleles C*03:119, C*07:137 and DRB1*14:101 were not included in the Common and Well-documented Alleles (CWD) v2.4 of the Chinese Hematopoietic Stem Cell Donor Database. CONCLUSION: The abnormal pattern of HLA genotyping results of magnetic probe by PCR-SSOP method suggests that it may be a rare allele or a novel allele, which needs to be verified by sequencing.
Subject(s)
High-Throughput Nucleotide Sequencing , Technology , Humans , Alleles , Polymerase Chain Reaction , Genotype , Histocompatibility Testing/methodsABSTRACT
HLA-C*03:566 differs from HLA-C*03:04:01:02 by one nucleotide substitution at nucleotide 92 in exon 2 from A to G.
Subject(s)
East Asian People , HLA-C Antigens , Humans , HLA-C Antigens/genetics , Alleles , NucleotidesABSTRACT
Identification of the novel HLA-DQB1*04:90 allele that differs from DQB1*04:01:01:01 at nucleotide 183 in exon 2 from A to T.
Subject(s)
East Asian People , Humans , AllelesABSTRACT
HLA-DRB1*14:239 differs from HLA-DRB1*14:03:01 by one nucleotide substitution in codon 82 in exon 2.
Subject(s)
HLA-DRB1 Chains , Humans , HLA-DRB1 Chains/genetics , Alleles , Base Sequence , Exons/genetics , MutationABSTRACT
The HLA-DRB3*02:02:19 allele differs from DRB3*02:02:01:02 by a single nucleotide change in exon 2.
Subject(s)
Nucleotides , Alleles , Exons/genetics , HLA-DRB1 Chains/genetics , HLA-DRB3 Chains/genetics , Histocompatibility Testing , HumansABSTRACT
Identification of the novel HLA-C*15:192 allele that differs from HLA-C*15:02:01:01 at one position in exon 2.
Subject(s)
HLA-C Antigens , High-Throughput Nucleotide Sequencing , Alleles , China , Genes, MHC Class I , HLA-C Antigens/genetics , HumansABSTRACT
One nucleotide substitution in codon 90 of HLA-A*11:01:01:01 results in a novel allele, HLA-A*11:399.