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【Objective】 To study the concordance of identifying the presence or absence of KIR genes using flow reverse sequence-specific oligonucleotide probe (Flow-rSSO) hybridization and sequencing based typing-PCR (PCR-SBT) methods. 【Methods】 A total number of 131 cases of DNA samples from Han population were subjected to identify the presence or absence of all 16 KIR genes by Flow-rSSO method, and then sequenced at coding sequence for all 14 functional KIR genes using our in-house KIR PCR-SBT assay. The concordance of identifying the presence or absence of all functional KIR genes by Flow-rSSO and PCR-SBT was analyzed. Samples with inconsistent initial results were re-tested using the Flow-rSSO commercial kits with different Lot number, and further tested using the PCR-SSP commercial kit. 【Results】 The presence or absence of 14 functional KIR genes for 129 of 131 samples were completely in accordance via the PCR-SBT and Flow-rSSO methods. Two samples, one with 3DL1 negative, the other with both 2DS3 and 2DS5 negative initially-identified by Flow-rSSO, were actually all positive tested by PCR-SBT. Further retest by Flow-rSSO commercial kits with different Lot number and PCR-SSP commercial kit indicated that the two samples were all positive, which agreed well with PCR-SBT results. 【Conclusion】 In this paper, the initial test results of the presence or absence of KIR genes identified by Flow-rSSO for 2 samples were wrong, which indicated the importance of carrying out the quality control for reagents in KIR gene testing.
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Psoriasis is an auto-immune skin disease affecting skin, nails and joints. The association of HLA with psoriasis is already established with HLA- C*06 known to be associated strongly with the disease. We wanted to determine the HLA -A & HLA-B pattern and its association with psoriasis in a Tamil speaking ethnic population.METHODSA total of 100 psoriasis patients attending the Dermatology OPD at SRMC were taken up for the study. This was a case control study and hence 100 voluntary blood donors donating at the SRMC Hospital blood bank were taken up for study as controls. Voluntary blood donors are considered as healthy normal individuals and hence chosen as controls. All the 100 patients and 100 controls were typed for HLA (Human Leucocyte Antigen) - A & B by PCR-SSP (Polymerase Chain Reaction-Sequence Specific Primers) and the results were analysed statistically using OpenEpi software (2 X 2 table). The Odds Ratio (OR), p (probability) value, and 95% confidence interval were the statistical tests which were studied.RESULTSHLA-A*02, 24 and HLA-B*35 were found to be strongly associated with psoriasis among Tamil speaking ethnic population.CONCLUSIONSThere are different HLA – A & B alleles associated with psoriasis in Tamil ethnic population in comparison with other ethnic studies
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Prevalence of psoriasis is 1-3% in India. HLA-C*06 has been shown to be strongly associated with psoriasis in different ethnic populations. This study was carried out to determine the association of HLA-C in psoriasis patients in a south Indian ethnic population.METHODSA total of 200 samples were included in the study. In all, 100 psoriasis patients and 100 healthy controls were studied. HLA-C typing was done by PCR-SSP method. Results were analysed statistically using open epi software (2 X 2 table). The Odds ratio (OR), p (probability) value, and 95% confidence interval were the statistical tests applied and analysed.RESULTSA total of 14 different HLA-C alleles were identified in both 100 cases and 100 controls. Among the 14 different HLA-C alleles, the alleles which were found to be strongly associated with psoriasis which were statistically significant were both HLA-C*06 and HLA-C*07. HLA-C*06 was found to be present in 52% of the patients and HLA-C*07 was found to be present in 33% of the patients. HLA-C*06 was found to be strongly associated with the disease in 52% of the patients.CONCLUSIONSThis study confirms HLA-C*06 association with psoriasis which is in concordance with other previous studies.
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Objective To investigate the ambiguity results distribution of HLA-A,B and DRB1 gene sequence-base typing in Guangxi population and to propose the way to resolve.Methods HLA-A,B and DRB1 genes of 1 000 donors in the Guangxi branch bank of China'bone marrow bank were genotyped by PCR-SBT,and then the ambiguity results distribution of the three loci was analyzed.The typing ambiguities resultswere resolved by high-resolution polymerase chain reaction-sequence-specific primers(PCR-SSP) and group specific sequencing primer(GSSP) methods,respectively.Results Among 1 000 samples,at least 1 locus in HLA-A,B and DRB1 genes in 96.7％ samples appeared the ambiguity results,in which the proportions of HLA-A,B and DRB1 loci appearing ambiguity results were 65.7 ％,58.8 ％ and 77.2 ％ respectively.For the samples of detected ambiguity results,single using the GSSP method could resolve the ambiguity typing results of 87.37％ HLA-A,93.54％ HLA-B and 60.49％ HLA-DRB1,using high-resolution PCR-SSP could resolve the ambiguity typing results of 12.63 ％ HLA-A,4.76 ％ HLA-B and 15.29 ％ HLA-DRB1,and the rest 1.70 ％ HLA-B and 24.22 ％ HLA-DRB1 ambiguity results were resolved by both GSSP and high-resolution PCR-SSPs method.Conclusion GSSP and high-resolution PCR-SSPs methods have high abilities to solve HLA ambiguity results both locate inside and outside the sequencing region,respectively.GSSP and high-resolution PCR-SSPs methods are supplement for each other,which can effectively resolve the problem of ambiguity results in high resolution HLA typing.
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BACKGROUND: Recombination (crossing over) may generate novel haplotypes that can be beneficial to a population against recently introduced pathogens. It may lead to the generation of new alleles. SETTINGS AND DESIGN: A prospective study at a tertiary care centre. AIM: To report two rare cases of crossing over in HLA region. MATERIALS AND METHODS: Tissue-typing was done by sequence specific primers (SSP) for DR locus and by both SSP and serology for Class I which was reconfirmed on fresh samples. RESULTS: In one patient crossing over had taken place in the region of A locus resulting in inheritance of A*01 instead of expected A*11. In second family crossing over had taken place in region of DRB1 locus and the sibling inherited DRB1*08 instead of DRB1*10. CONCLUSIONS: Possibility of recombination must be considered when interpreting implausible tissue-typing results of families worked up for BMT.
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Asian People/genetics , Family , Histocompatibility Antigens , HLA Antigens/genetics , Family , HLA Antigens/genetics , Histocompatibility Antigens , Humans , India , Major Histocompatibility Complex , Recombination, GeneticABSTRACT
Objective To understand the association of human leukocyte antigen (HLA)-DRB polymorphism and patients diagnosed as hemorrhagic fever with renal syndrome (HFRS). Methods HLA-DR allele polymorphism was detected by PCR-sequence specific primers (PCR-SSP). Hantavirus (HV) typed as Hantaan virus (HTNV) and Seoul virus (SEOV) in patients were detected by RT-heminested PCR. Results The gene frequency of DRB1*0401-0411, *1001 and *1101-1105 in HFRS case group were 3.1%, 2.2% and 15.7% respectively. Compared with control group, it was significant higher in HFRS case group (RR=13.87, 9.72 and 2.00 respectively with Chi-square value as 10.006,6.324 and 6.472 respectively, P<0.05). When compared with HFRS case group, the gene frequency of DRB1*1501-1502, DRB4 and DRB5 in control group were 11.0%, 19.0% and 16.9% respectively, markedly lower than in patients (RR=0.45, 0.58 and 0.23 respectively. Chi-square values were 6.138, 4.583 and 21.076 respectively, P<0.05). There was no significant difference in other HLA-DR gene frequencies. Mixed infection was found in Hubei, with HTNV slightly more than SEOV. Distinct hantaviruses could coexist in either different or the same geographic or ecological zores in Hubei province. Patients with HLA-DRB1*1101-1105 alleles were 81.8%(27/33) infected by HTNV and only 18.2% infected by SEOV, which had significant difference (P<0.05). Conclusion DRB1*0401-0411,*1001 and *1101-1105 were possibly associated with increased susceptibility to HV infection. On the other hand there was an inverse correlation among HFRS, DRB1*1501-1502, DRB4 and DRB5.
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Objective To investigate the killer cell lg-like receptors (KIR) gene frequency of HIV-1 infected slow progressors(SP) and typical progressors(TP), and to analyze the interaction between KIR alleles and the progression of HIV-1 infection in Chinese population. Methods Eighty-one HIV-1 posi-tive individuals including 43 SPs and 38 TPs were recruited. Carriage of KIR genes was assessed using poly-merase chain reaction sequence-specific primers (PCR-SSP) assays. Results KIR2DS3 gene frequency was significantly lower in SP group (3.6%) than that in TP group (14.2%), P =0. 018 ,OR =0. 210,95% CI =0.053-0.833. The number of activating KIR genes was less in SP group than that in TP group, but was not significant (P = 0. 208). Conclusion Lower KIR2DS3 gene frequency may potentially be associated with slower progression to AIDS in Chinese population.
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Objective To study the polymorphism of human platelet antigens among unrelated Guangzhou blood donors with PCR-SSP,in order to provide basic data for population studies and clinical transfusion practice.Methods Blood samples from 706 unrelated blood donors in Guangzhou were genotyped for each of the HPA1—6,15 systems by PCR-SSP.Gene frequencies and genotype frequencies were analyzed by statistical methods.Results HPA-3 and-15 had the greatest heterozygosity with a gene frequency of 0.2918,0.4830,0.2252 for HPA-3a/a,HPA-3a/b,HPA-3b/b,and 0.2691,0.5170,0.2139 for HPA-15a/a,HPA-15a/b,HPA-15b/b.The a/a homozygosity was predominant in HPA-1,-2,-4,-5,with a frequency ranged from 0.9583 to 0.9993,while HPA b/b was not found among them.The frequency of HPA-lb and HPA-4b was very low,which was 0.0028 and 0.0007,respectively.In our study,HPA-1 frequency was significantly different from that of the north Chinese,English,and American Indian(P
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BACKGROUND: Rapid platelet engraftment has several economic benefits by reducing the cost of supportive therapy as well as reducing the risk of fatal bleeding due to severe thrombocytopenia. Based on these considerations, we genotyped human platelet alloantigens (HPA) to evaluate the effect of minor transplantation antigen mismatches on the rate and speed of platelet recovery and clinical outcome of transplantation. METHODS: Thirty-five patients with various hematologic diseases transplanted between January 2001 and August 2004 were included. Genomic DNA was isolated from peripheral blood of donor-recipient pairs before transplantation. HPA-1, -2, -3, -4, -5, and -6 genotyping was performed by poly-merase chain reaction (PCR)-sequence specific primers (SSP). The effects of HPA compatibility on platelet recovery, incidences of graft-versus-host disease (GVHD) and relapse, and overall survival was investigated. RESULTS: There were no significant differences in platelet recovery according to HPA matching status. We observed no statistically significant differences in the occurrence of relapse and overall survival according to HPA-1, -2, and -3 matched/mismatched groups of patients, whereas HPA-3 mismatching was found to have a significant effect on GVHD development. There was also no difference in GVHD occurrence according to HPA-1 and -2 matched or mismatched transplants. CONCLUSIONS: Since platelet recovery in the HPA-1, -2, -3, and -5 matched/mismatched groups is not significantly different, the seems that platelet glycoprotein (GP) does not seem to act as a factor influencing the homing of hematopoietic stem cells. The finding that HPA-3 incompatibility may be involved in GVHD can be of importance. If a role for HPA-3 as minor histocompatibility antigens is confirmed by additional studies, we can ameliorate the outcome of allogeneic stem cell transplantation by typing of HPA and selecting the most closely related donors.
Subject(s)
Humans , Antigens, Human Platelet , Blood Platelets , DNA , Glycoproteins , Graft vs Host Disease , Hematologic Diseases , Hematopoietic Stem Cell Transplantation , Hematopoietic Stem Cells , Hemorrhage , Incidence , Minor Histocompatibility Antigens , Recurrence , Stem Cell Transplantation , Thrombocytopenia , Tissue DonorsABSTRACT
Objective The purpose of this study was to determine the value of K-ras mutation in DNA extracted from the plasma as clinical indicator of colorectal cancer. Methods Point mutation at codon 12 of K-ras gene was assayed by polymerase chain reaction of sequence-specific primers in DNA extracted from the plasma and tumors from 32 patients with colorectal cancer. The mutation was further confirmed by dideoxy-mediated chain-termination method of DNA sequencing. Results Fourteen patients (44%) had a codon 12 K-ras mutation within their primary tumors and identical mutations were found in the plasma DNA of 13 patients (93%). Mutant DNA was not detected in the plasma specimens of 18 patients whose tumors tested negative for K-ras alterations or in 5 healthy control subjects. Conclusion Preliminary results suggest the detection of K-ras mutations in circulating DNA extracted from the plasma specimens may have some clinical uti- lity in the detection of colorectal cancer.