OBJECTIVE: To delineate a deletional mutation of the HLA-B gene in a Chinese pedigree. METHODS: A female patient with acute myeloid leukemia who had visited Liuzhou People's Hospital in April 2022 was selected as the study subject. Routine human leukocyte antigen (HLA) was determined by using PCR-sequence specific oligonucleotide polymorphism (PCR-SSOP) and PCR-sequence-based typing (PCR-SBT) methods. Next generation sequencing (NGS) was used to validate the candidate variant in the HLA-B gene. RESULTS: The PCR-SBT and SSOP results for the HLA-B locus were inconsistent for the patient and her daughter. The SSOP results of the two individuals were HLA-B*35:01, 40:02 and HLA-B*35:01, 40:01, respectively. However, the PCR-SBT results has indicated a mismatch with the nearest HLA-B*35:01 at exon 4. NGS results showed that the HLA-B*35:01 had a 9 bp deletion in the intron 5. The patient's husband was HLA-B*40:01, 58:01, which was normal. CONCLUSION The variant in intron 5 of the HLA-B gene in this pedigree has mapped to a primer-binding region for the SBT reagent, which has affected the accuracy of PCR-SBT results.
Humans ; Female ; Alleles ; Pedigree ; HLA Antigens/genetics* ; HLA-B Antigens/genetics* ; China ; Histocompatibility Testing/methods* ; Sequence Analysis, DNA/methods*

OBJECTIVE: To delineate the characteristics of a novel HLA-DQB1 allele identified during routine HLA matching in a leukemia family. METHODS: The mother and brother of the patient were subjected to PCR sequence-specific oligonucleotide probe (SSOP), PCR sequence-based typ1ing (SBT), as well as next-generation sequencing (NGS). RESULTS: PCR-SBT revealed that the patient's mother and brother's HLA-DQB1 sequences did not fully match with any known allele combination. NGS revealed that the novel allele has differed from the closest matched DQB1*03:02 with a T>G substitution at position 233 in exon 2, which resulted in substitution of Valine at codon 46 by Glycine. Pedigree analysis confirmed that the novel HLA-DQB1 allele was inherited from his mother. CONCLUSION A novel HLA-DQB1 allele has been identified through next generation sequencing and was officially named as HLA-DQB1*03:362 by the World Health Organization HLA Factor Nomenclature Committee.
Alleles ; Base Sequence ; HLA-DQ beta-Chains/genetics* ; Humans ; Male ; Nucleotides ; Polymorphism, Single Nucleotide ; Sequence Analysis, DNA

OBJECTIVE: To verify a HLA-DQB1*03:90N allele and method to improve the accuracy of HLA typing. METHODS: A total of 2265 hematopoietic stem cell donors from Shenzhen Branch of China Marrow Donor Program in 2018 were initially detected by a PCR sequence-specific oligonucleotide probe (SSOP) method. Among these, a rare HLA-DQB1 allele was identified by sequence-based tying (SBT) and Ion Torrent S5 next generation sequencing (NGS). RESULTS: The SSOP typing result suggested the HLA-DQB1 to be a rare allele, while an insertion and a deletion was suspected in its exon 2 by SBT, which were confirmed by NGS as DQB1*03:90N and DQB1*06:01, respectively. CONCLUSION Rare alleles suspected by the SSOP method should be verified by other methods to ensure the accuracy of HLA genotyping. Rare alleles formed by deletions can be detected by NGS with accuracy.

OBJECTIVE: To assess the association of KIR/HLA alleles with hepatocellular carcinoma (HCC) and hepatitis B virus (HBV) infection among ethnic Han Chinese patients from southern China. METHODS: For 95 patients with HCC and 171 healthy controls, the genotype of HLA-C alleles was determined with a PCR sequence-specific oligonucleotides typing method on an Illumina GenDx NGSgo platform. Genotypes comprised of HLA-C and KIR gene alleles were also subjected to statistical analysis. RESULTS: In total 16 KIR genes (2DL2, 2DS2, 2DS3, 2DS5, 3DS1, 2DS1, 2DL5, 2DS4, 3DL1, 3DP1, 2DL3, 2DP1, 3DL3, 2DL1, 3DL2 and 2DL4) were discovered in the two groups. The frequencies of KIR2DL3 alleles and combinational genotypes of KIR2DL3/HLA-C1C2 were significantly lower in the patient group compared with the controls (0.9368 vs. 0.9883, χ²>3.84; P<0.05, OR = 0.1; 0.0112 vs. 0.2663, χ²>3.84; P<0.05, RR = 0.03). The frequency of HLA-C2C2 genotype of the patient group was significantly lower than that of the controls (0.0316 vs. 0.2690, P<0.05, RR = 0.09), while the frequency of HLA-C1C2 genotype was significantly higher than that of the controls (0.2316 vs. 0.0058, P<0.05, RR = 51.23). CONCLUSION Above results suggested that the KIR2DL3 allele is associated with lower risk for HCC. There may be individual difference in patients with HCC and HBV infection but various combinations of KIR/HLA alleles.
Alleles ; Carcinoma, Hepatocellular ; genetics ; China ; Gene Frequency ; Genotype ; Humans ; Liver Neoplasms ; genetics ; Polymorphism, Genetic ; Receptors, KIR

ObjectiveTo investigate the genetic polymorphism of 42 short tandem repeats （STRs）， including 41 non-CODIS loci from the Shenzhen Han population and evaluate their potential values in forensic application. MethodsIn our research， the AGCU 21+1 STR kit and Microreader™ 23sp Direct ID System were applied to analyze the polymorphism of STR loci from 435 unrelated individuals of Shenzhen Han population. Modified-Powerstates and Arlequin v3.5 software were used to analyze the allele frequencies and forensic parameters， and perform the Hardy-Weinberg equilibrium test. ResultsA total of 418 alleles were detected from 435 unrelated individuals in Shenzhen， all consistent with Hardy-Weinberg equilibrium （P>0.05/42）， with the allele frequency ranging from 0.001 1 to 0.552 9. Besides， the discrimination power （DP） ranged from 0.798 8 （D1S1627） to 0.968 6 （D7S3048）， the polymorphic information content （PIC） ranged from 0.568 0 （D1S1627） to 0.859 8 （D7S3048）， and the heterozygosity （H） ranged from 0.627 6 （D1S1627） to 0.878 2 （D20S470）. Among all the STRs tested in the study， both D1S1656 and D21S1270 have 16 alleles and show the highest polymorphism. In comparison， only five alleles were observed in the D4S2408 locus， which displays the least polymorphism. ConclusionsThe 42 autosomal STR loci with high genetic polymorphism in Shenzhen Han population showed potential as an effective means for individual identification and paternity testing， especially in the cases with single parent or mutation detected. The obtained information can provide basic data for STR population genetics.