Distribution of KIR/HLA alleles among ethnic Han Chinese patients with hepatocellular carcinoma from southern China / 中华医学遗传学杂志

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; P3.84; 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.

Polymorphisms of MICA gene and their linkage disequilibrium with HLA-B among ethnic Han Chinese from Shenzhen / 中华医学遗传学杂志

<p><b>OBJECTIVE</b>To study the distribution of MICA alleles among ethnic Han Chinese blood donors from Shenzhen and their linkage disequilibrium with HLA-B gene.</p><p><b>METHODS</b>For 143 randomly selected blood donors, the MICA and HLA-B alleles were determined with a PCR-sequence based typing (SBT) method. Allelic frequency, haplotypic diversity and linkage disequilibrium were analyzed with a Pypop software.</p><p><b>RESULTS</b>Thirteen MICA and 35 HLA-B alleles were identified among the 143 blood donors, among which MICA*008:01 had the highest frequency (76/286), whilst MICA*008:01-HLA-B*40:01 and MICA*010-HLA-B*46:01 were the most common haplotypes. No novel allele was identified.</p><p><b>CONCLUSION</b>The allele frequencies, haplotype diversities and linkage disequilibrium parameters under a high resolution can facilitate further studies and applications of the MICA and HLA-B genes.</p>

Establishment of a quality control system for HLA allele typing and its key points / 中华医学遗传学杂志

<p><b>OBJECTIVE</b>To list the key points for quality control during HLA-A, B, C, DRB1 and DQB1 allele typing by taking consideration of hardware, software and experimental procedures.</p><p><b>METHODS</b>A total of 10 167 samples from randomly selected healthy blood donors and donor-recipient pairs from Shenzhen were typed for exons 2-4 of HLA-A, B, C, exon 2 of HLA-DRB1, and exons 2 and 3 of HLA-DQB1 by PCR- sequence-based typing. For 56 cases whose forward and reverse sequences were inconsistent, the samples were re-checked by a PCR-sequence specific oligonucleotide probe method. Novel alleles not included in the IMGT/HLA database were cloned and sequenced using in-house primers.</p><p><b>RESULTS</b>Eight novel HLA alleles were identified. A table for key positions of single nucleotide polymorphisms (SNPs) were generated, which summarized the key points for quality control during HLA-A, B, C, DRB1 and DQB1 allele typing. Among the listed SNPs, 3 were located at the HLA-A locus, 8 were at the HLA-B locus, 6 were at the C locus, 6 were at the DQB1 locus, and 4 were at the DRB1 locus. To ensure the quality control, an unique sample number for DNA transferring tubes in the process of experiment should be considered.</p><p><b>CONCLUSION</b>A protocol for quality control should be enforced by checking all of the key points. The SNPs and critical control points of the alleles should be examined to ensure the accuracy of HLA typing results.</p>

Sequencing analysis of a rare human leukocyte antigen, C*08:99, from a volunteer donor of hematopoietic stem cell transplantation / 中国组织工程研究

BACKGROUND:As the sequencing technology has been widely used and high-resolution confirmation of organ transplant matching has been gradualy developed, new human leukocyte antigen (HLA) aleles are emerging. However, the gene frequency of some genes cannot be calculated accurately, and there are rare reports. These genes are often ignored, and it is easy to misjudge their genotypes only according to gene frequency. OBJECTIVE:To test and analyze a rare alele, HLA-C*08:99, from a volunteer donor of hematopoietic stem cel transplantation. METHODS: Genomic DNA was extracted automaticaly from the blood sample by using quick DNA purified kit and amplified by HLA-C locus commercial sequence-based typing kit. The purified PCR product was utilized as the DNA template in the sequencing reaction, and six direct sequencing reactions of PCR product covering exons 2, 3 and 4 in both directions were performed using commercial kit. Four direct sequencing reactions of PCR product covering exon 5 in both directions, exon 6 in forward direction and exon 7 in reverse direction were performed using in-house BigDye terminator cycle sequencing reaction kit. Sequencing reaction products purified by ethanol/sodium acetate/ ethylenediaminetetraacetic acid method were sequenced by ABI PrismTM3730 DNA Sequencer. RESULTS AND CONCLUSION:The alele assignment was analyzed with Assign-SBT 3.6+ software, and the sample HLA-C typing result was C*07:04, 08:99. Increasing the sequencing analysis at exons 5, 6 and 7 of HLA-C locus wil help to make clear the ambiguous SBT result and improve the accuracy of HLA-C typing when it is necessary, which shows important significance in clinical tissue matching. Cite this article:Wang DM, Zou HY, Nie DM, Gao SQ, Wang F.Sequencing analysis of a rare human leukocyte antigen, C*08:99, from a volunteer donor of hematopoietic stem cel transplantation. Zhongguo Zuzhi Gongcheng Yanjiu. 2016;20(1):102-106.

Analysis of ambiguities in HLA sequencing-based typing and its solutions / 中华医学遗传学杂志

<p><b>OBJECTIVE</b>To investigate the number and ratio of ambiguous allele combinations from human leukocyte antigen (HLA) confirmatory test by sequencing based typing for unrelated donor marrow transplantation, and to establish an efficient strategy for identifying such ambiguities.</p><p><b>METHODS</b>A total of 650 donor-receipt samples were genotyped for 5 loci of the HLA gene using an Atria SBT commercial kit. Exons 2, 3 and 4 of HLA-A, -B and -C, exon 2 of HLA-DRB1 and exons 2 and 3 of HLA-DQB1 were tested by routine HLA genotyping. The ratio of usual ambiguous allele combination was calculated. The ambiguities were subjected to further confirmatory test by PCR-SSP or PCR-SBT retest at outside of the routine sequencing region.</p><p><b>RESULTS</b>Among the 650 tested samples, the ratio of ambiguity at HLA-A, B, C, DRB1 and DQB1 were 76.31% (496/650), 91.08% (592/650), 97.69% (635/650), 88.62% (576/650) and 43.38% (141/650), respectively. A total of 36 ambiguous allele combinations inside the routine sequencing region and 22 ambiguous allele combinations outside of the routine sequencing region were discovered. After removing rare alleles based on the Chinese common and well documented (CWD) Allele Table (Version 1.01), 9 ambiguous CWD allele combinations inside the routine sequencing region, including 3 located in HLA-B, HLA-C and 1 located in other three HLA loci were found. Ten ambiguous CWD allele combinations outside of the routine sequencing region, including 4 located in HLA-C, -DRB1 and 1 in HLA-A, -B respectively were determined. All samples with ambiguous CWD allele combinations could be distinguished by high-resolution PCR-SSP commercial kits or PCR SBT retest at outside of the routine sequencing region.</p><p><b>CONCLUSION</b>The common and well documented allele combinations in sequencing-based typing at five HLA loci have been analyzed. Our strategy may provide valuable information for more efficient, low cost and accurate method for high resolution genotyping of HLA genes.</p>

Analysis for 2 samples with HLA-DQB1 allele dropout at exon 2 in sequence-based typing / 中华医学遗传学杂志

<p><b>OBJECTIVE</b>To explore the reason for HLA-DQB1 allele dropout during routine sequence-based typing(SBT) in order to improve the accuracy of typing.</p><p><b>METHODS</b>Two thousand samples derived from HLA high-resolution typing laboratory were typed for HLA-DQB1 locus using an AlleleSEQR HLA-DQB1 SBT kit. Non-conclusive results and "abnormal" sequencing samples were retyped using a LABType rSSO HD HLA-DQB1 kit and further analyzed with both sequence-specific primers and group-specific primers and sequenced for haplotype analysis.</p><p><b>RESULTS</b>Among the 2000 samples, 2 samples with no conclusive result were identified. The heterozygosity was confirmed with both the LAB Type SSO HD HLA-DQB1 kit and PCR-SBT in house method. Subsequent HLA-DQB1 cloning and haplotype sequencing have elucidated that HLA-DQB1*02:02 dropped out at exon 2 for the first sample and HLA-DQB1*02:01:01 dropped out at exon 2 for the second sample during PCR amplification. No novel nucleotide mutation was found.</p><p><b>CONCLUSION</b>Our results indicated that preferential amplification at exon 2 of DQB1 may result in allele dropout in exon 2 sequences during HLA-DQB1 SBT test. This may provide useful information for HLA genotyping.</p>

Sequence analysis of a novel allele HLA-C*01:78 / 中华医学遗传学杂志

<p><b>OBJECTIVE</b>To investigate the genetic basis for a novel allele HLA-C*01:78.</p><p><b>METHODS</b>Genomic DNA was extracted from peripheral blood using a QIAGEN quick DNA extraction kit. The regions encompassing HLA-C from exon 1 to intron 3 and intron 3 to 3'UTR were amplified and cloned using a cloning sequencing kit in order to split the two alleles apart. Selected clones were sequenced to include exons 2 to 4.</p><p><b>RESULTS</b>Sequencing results have indicated the HLA-C alleles of the proband to be a novel C*03:04 allele. The sequence has been submitted to GenBank (KF049216). BLAST analysis has confirmed the novel allele to have one nucleotide difference as C*01:03 at genomic nt316C>A (codon 82CGC>AGC) in exon 2, which has resulted in replacement of one amino acid (82R>S).</p><p><b>CONCLUSION</b>The novel allele has been officially named as C*01:78 by the WHO Nomenclature Committee. The HLA allele type of the proband was therefore A*02:07, 24:02; B*40:01, 46:01; C*01:78, 03:04; DQB1*05:02, 05:02; DRB1*16:02, 16:02.</p>

Result analysis of four human leukocyte antigen rare alleles / 中国组织工程研究

BACKGROUND:Many articles concerned novel al eles reported in China and outside China, but some al eles were detected lately. After that, these al eles were tested again. Because frequencies of these al eles are very low, few relevant articles are reported, so these al eles are ignored easily. OBJECTIVE:To test and identify four human leukocyte antigen rare al eles that patients and donors carries. METHODS:Genomic DNA was extracted automatical y from blood samples using quick DNA purified kit, typed by human leukocyte antigen locus commercial sequence-based typing kits and confirmed by sequence-specific primers high-resolution kits. RESULTS AND CONCLUSION:Four detected rare al eles are B*27:15, B*51:39, C*07:66 and C*08:22. The four above-mentioned human leukocyte antigen rare al eles defined by National Marrow Donor Program are not rare in China. The facts prove that C*08:22 which was defined a rare al ele by National Marrow Donor Program before is a common al ele in Chinese Han nationality.

Analysis of hlgh-resolution human leukocyte antigen matching status for the unrelated donor-receipt pairs matched at low-resolution for HLA-A, HLA-B and HLA-DRB1 / 中华检验医学杂志

le full matching for unrelated donor-receipt pairs. However, HLA-Cw mismatching at antigen level could no longer be ignored. The results indieated that HLA-Cw genotyping should be incorporated into future CMDP unrelated marrow donor routine HLA test.

Identification of human leukocyte antigen-DRB11454 allele and human leukocyte antigen-DRB1 exon 3 sequence information in the Chinese population / 中国组织工程研究

AIM: To identify human leukocyte antigen (HLA)-DRB11454 allele and HLA-DRB1 exon 3 sequence information in the Chinese population, which is significant for organ transplantation, cell transplantation, and human genetics.METHODS: Polymerase chain reaction sequence-based typing (PCR-SBT) was used to identify HLA-DRB1 alleles from 58 donor-recipient individuals who would undergo haemopoietic stem cell transplantation. Medium to high resolution polymerase chain reaction-reverse sequence specific oligonucleotide probe (PCR-RSSOP) was used to identify HLA-DRB1 alleles from 1 268 healthy donors from Guangdong province. The some ambiguous results of HLA-DRB114-associated alleles were confirmed by high resolution polymerase chain reaction-sequence-specific primer typing (PCR-SSP).RESULTS: HLA-DRB11403, 1406, 1410, 1412, 1418, 1425 and 1454 alleles were detected in 1 268 healthy donors.HLA-DRB11454 was confirmed in 8 ambiguous results of HLA-DRB11401/1434/1454 alleles, and HLA-DRB11454 was one of common alleles of HLA-DRB114 allele group in Guangdong population. HLA-DRB114 exon 3 sequence information was confirmed to be polymorphic in Chinese population.CONCLUSION: HLA-DRB11454 and exon 3 of DRB1 are confirmed to be polymorphic in Chinese population, further elucidating that HLA-DRB1 axon 3 sequence information is important for Han population and some minority groups.

Study on HLA alleles and haplotypes of 572 patients with acute lymphoblastic leukemia in southern Chinese Han / 白血病·淋巴瘤

Objective To study the distributive characteristics of HLA-A,B,DRBI alleles and haplotypes patients with ALL in southern Chinese Han.Methods The frequencies of HLA-A,B,DRB1alleles and haplotypes were estimated by Expectation-Maximization method based on the genotypes of 572patients with ALL and 5645 unrelated health donors,and then compared by chi-square test.Results The frequencies of HLA-A33(7.15%vs 9.3%,OR=0.73,P＜0.05),B58(5.93%vs 8.75%,OR=0.64,P＜0.05),DRB1*17(5.15%vs 6.30%,OR=0.82,P＜0.05)alleles and HLA-A33-B58-DRB1*17(2.46%vs 4.14%,OB=0.35,P＜0.05)haplotype were significantly lower in ALL patient groups than that in controls.The frequencies of HLA-A3(2.1%vs 1.26%,OR=1.7,P＜0.05),B51(7.25%vs 5.78%,OR=1.3,P＜0.05)and DRB*12 (16.13%vs 12.99%,OR=1.35,P＜0.05)alleles and A2-B51-DRB1*12(1.24%vs.0.89%,OR=1.66,P＜0.05)haplotype were significantly higher in ALL patient groups than that in controls.Conclusion These results indieated that HLA-A33-B58-DRB1*17 haplotype was a associated with a diminished incidence of ALL.and HLA-A3 auele or A2-B51-DRB1*12 haplotype was weakly associated with ALL.

Molecular polymorphism and the distribution of HLA B-27 subtypes in southern Chinese Han patients with Ankylosing Spondylitis and healthy controls / 中国输血杂志

Objective To study the molecular polymorphism and the distribution of HLA-B27 subtypes in southern Chinese Han patients with Ankylosing Spondylitis and healthy controls.Methods A total of 46 samples form southern Chinese Han patients with AS and 80 non-related blood samples from healthy peripheral blood stem cell donors with B27-positive identified by rSSO Lumminex flow array assay were subjected to sequencing analysis of exon 2 ,3 and 4 of HLA-B gene by the sequence-based typing,the purified products of sequencing reaction were electrophoresed on ABI 3730 DNA sequencer and the designation of HLA-B27 allele was accomplished using the Assign3.5 software. The ambiguities and the detected "rare" alleles were confirmed using the PCR-SSP commercial kit. Results In the 46 B27-positive patients with the diagnosis of AS,four alleles,namely B2704,B2705,B2707 and B2724 were determined. The frequencies for these four alleles were 82.98%(39/47),12.77%(6/47),2.13%(1/47) and 2.13%(1/47),respectively. In the 80 B27-positive control individuals,seven B27 related alleles were identified. The frequency for the two dominant subtype B2704 and B2705 were 57.32%(47/82) and 26.83%(22/82),respectively. Both the B2706 and B2707 were observed 5 times with a frequency of 6.10%(5/82),three alleles B2703,B2715 and B2724 were detected only once with a frequency of 1.22%(1/82).Conclusion Our study shows that HLA-B2704 and B2705 were the predominant subtypes in normal healthy controls,however,B2704 was the predominant subtype for the AS group in southern Chinese Han patients.

Polymorphism of HLA-A,B and DRB1 alleles and their haplotypes in Chinese Man bone marrow donors / 中国输血杂志

ObjectiveTo analyze the polymorphism of HLA-A,B,and DRB1 alleles and their haplotypes in Chinese Man population.Methods Frequencies of HLA-A,B and DRB1 alleles and haplotypes were estimated by maximum-likelihood estimation method based on the genotypes of 2183 Chinese Man bone marrow donors.ResultsA total of 18 HLA-A alleles,44 HLA-B alleles and 15 HLA-DRB1 alleles were detected in Man population,and the most frequent alleles were A*02,A*11,A*24,A*30,A*33,B*13,B*35,B*46,B*51,B*40(B60),B*40(B61),B*15(B62),DRB1*04,DRB1*07,DRB1*08,DRB1*09,DRB1*11,DRB1*12,DRB1*13,DRB1*14 and DRB1*15.A*30-B*13,A*02-DRB1*15,B*13-DRB1*07 and A*30-B*13-DRB1*07 were the most frequent haplotypes in Man population for A-B,A-DRB1,B-DRB1 and A-B-DRB1 haplotype,respectively.The number of haplotypes with frequency ≥ 0.01 for A-B,A-DRB1 and B-DRB1 haplotype was 31,24 and 27,respectively,and ≥ 0.005 for A-B-DRB1 haplotype was 32.There were 14 in A-B,3 in A-DRB1,14 in B-DRB1 and 38 in A-B-DRB1 haploypes that showed strong linkage disequilibrium with ALD≥0.40.ConclusionsThe distribution of HLA-A,B and DRB1 alleles and haplotypes in Man population was similar to that in Northern Chinese Han population.