Sequence-specific Oligonucleotide Probe Method Research Articles

New cost-effective human leukocyte antigen testing algorithm for screening of human leukocyte antigen-matched related donor in thalassemia major patient pretransplant workup

Introduction: India has a huge disease burden of thalassemia major with an estimated 40 million carriers and over a million thalassemia major patients. Very few patients are optimally treated, and the standard of care “hematopoietic stem cell transplant” (HSCT) is out of reach for most patients and their families. The cost of HSCT is significant, and a substantial proportion of it goes to human leukocyte antigen (HLA) testing of family members (HLA screening) in hope of getting a matched related donor (MRD) for HSCT. The aim of this study was to establish that a new proposed testing algorithm of HLA typing would be more cost-effective as compared to the conventional HLA screening within MRD families for possible HSCT. Material and Methods: Buccal swab samples of 177 thalassemia patients and their prospective family donors (232) were collected. Using a new HLA testing algorithm, samples were tested for HLA typing in a sequential manner (first HLA-B, then HLA-A, and finally HLA-DR) using the sequence-specific oligonucleotide probe method on the Luminex platform. Results: The new sequential HLA-A, HLA-B, and HLA-DRB1 testing algorithm showed a 49.1% reduction in cost compared to the conventional HLA testing algorithm. Furthermore, 40 patients (22.59%) were found to have HLA-MRD within the family among other samples that were tested. Conclusion: The new HLA testing algorithm proposed in the present study for identifying MRD for HSCT resulted in a substantial reduction in the cost of HSCT workup.

Human Leukocyte Antigen Examination Using Luminex®-Based Assays for Donor-Recipient Compatibility Assessment in Kidney Transplantation: Our Preliminary Experience

Background: Detection of anti-HLA antibodies (HLAabs) in organ transplantation recipients is vital to determine whether the recipient has specific HLAabs against the donor’s HLA molecules (donor-specific anti-HLA antibodies [DSA]). Methods: This preliminary study involved seven subjects: five without prior HLA sensitization and two with a history of possible HLA sensitization (kidney transplantation and pregnancy). Two of the subjects were siblings, two of the subjects were mother and son, and two of them were first cousins once removed. All the subjects underwent HLA typing, and four of the subjects underwent HLAabs assays using the sequence-specific oligonucleotide probes (SSOP) method. Results: There were 10/16 HLA matches between subjects who were siblings and between subjects who were mother and son, and 6/16 HLA matches were found between subjects who were first cousins once removed. Subjects with previous kidney transplantation developed 59 HLA-Abs toward class I and class II HLA (the mean fluorescence intensity (MFI) value range: 1,003.36 to 12,404.77). HLAabs were also found among subjects without prior HLA sensitization, albeit with relatively lower MFI values. Conclusions: HLA typing and HLAabs detection for donor-recipient compatibility assessment using the SSOP method offers more detailed, semi-quantitative results. Further research involving larger subjects in cohort settings will be useful for profiling MFI cut-off values for HLAabs.

Analysis and verification of a HLA-DQB1*03:90N allele with a single base deletion

To verify a HLA-DQB1*03:90N allele and method to improve the accuracy of HLA typing. 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). 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. 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.

A Comparative Study: Flow Cytometry, Complement-dependent Cytotoxicity, and Luminex Methods

AimThe cell-based flow cytometric and bead-based Luminex crossmatch methods have been used alongside the standard complement-dependent cytotoxic crossmatch (CDCXM) test to detect donor specific anti-HLA antibodies. In this study, it was aimed to compare flow cytometric crossmatch (FCXM), CDCXM, and Luminex donor-specific crossmatch (LM-XM) tests for pre-transplant assessment of patients who applied to Tepecik Education and Research Hospital for kidney transplantation from related or deceased donors. MethodHLA tissue typing of 1120 patients were tested using the sequence specific oligonucleotide probe method with low resolution. FCXM and LM-XM were performed according to the manufacturer's instructions. The CDCXM test was performed according to the standard procedure. The results were analyzed using SPSS version 21.0 software (IBM, Armonk, NY, United States). P < .05 was accepted as statistically significant. ResultsFCXM, CDCXM, and LM-XM tests were performed on 58.2% (n = 652), 91% (n = 1019), and 55.4% (n = 620) of 1120 patients. There were statistically significant differences between FCXM/CDCXM, LM-XM/CDCXM, and FCXM/LM-XM (P < .0001), although there was also a moderate correlation between them (for class I, r = .599, r = .693, and r = .507; for class II, r = .546, r = .471, and r = .495, respectively). The results obtained according to donor type were compatible with the total study group. ConclusionThe utilization of FCXM and/or LM-XM tests together with the CDCXM method before kidney transplantations from related and/or deceased donor may facilitate the determination of target cells of donor-specific antibodies or their antibody class, which may increase the success of transplantation.

A novel analysis strategy for HLA typing using a sequence-specific oligonucleotide probe method.

The technique of reverse sequence-specific oligonucleotide probes (SSOPs) is commonly used in human leukocyte antigen (HLA) typing. In the conventional method for data analysis (exact pattern matching, EPM), the larger is the number of mismatched probes, the longer the time for final typing assignment. A novel strategy, filtering and scoring (FnS), has been developed to easily assign the best-fit allele pair. In the FnS method, candidate alleles and allele pairs were filtered based on (1) subject's ethnicity, and (2) the measured partial reaction pattern with only definitely negative or positive probes. Then, the complete reaction pattern for all probes (CRPoAPs) were compared between the raw sample and expected residual allele pairs to obtain mismatch scores. To compare the FnS and EPM methods, each analysis time (minutes:seconds) for reverse SSOP HLA typing with intermediate resolution (n = 507) was measured. The analysis time with FnS method was shorter than that of the EPM method [00:21 (00:08-01:47) and 01:04 (00:15-23:45), respectively, P < .05]. In addition, the analysis time of the FnS method was relatively constant, regardless of the number of mismatched probes. The alternative approach of filtering based only on definite probes (neglecting ethnicity) took a long time for analysis. However, this approach did not compromise the accuracy. The FnS method showed improved accuracy and efficiency of HLA typing in a comprehensive and quantitative comparison between measured and expected CRPoAPs of candidate allele pairs. Therefore, this analysis strategy might be useful in a clinical setting.

HLA-A, -B, -DRB1 allele and haplotype frequencies of 920 cord blood units from Central Chile

We present human leukocyte antigen (HLA) haplotype and allele/antigenic group frequencies derived from a data set of 920 umbilical cord blood units collected in Central Chile. HLA-A and -B genotypes were typed using sequence specific oligonucleotide probe methods while HLA-DRB1 genotypes were obtained from sequencing-based typing. The most frequent haplotype is A*29~B*44~DRB1*07:01 with an estimated frequency of 2.1%.

Candidate HLA genes for prediction of co-trimoxazole-induced severe cutaneous reactions.

Co-trimoxazole is a sulfonamide-containing antibiotic that is effective in the treatment of several infections and for prophylaxis of Pneumocystis jiroveci pneumonia. This drug has been reported as a common culprit drug for the Stevens-Johnson syndrome (SJS) and for toxic epidermal necrolysis (TEN). Human leukocyte antigens (HLAs) play a key role in the immunopathogenesis of severe cutaneous reactions induced by several drugs. This study investigated the association between the HLA class I and HLA-DRB1 polymorphisms and co-trimoxazole-induced SJS/TEN in a Thai population. Forty-three patients with co-trimoxazole-induced SJS/TEN and 91 co-trimoxazole-tolerant patients were enrolled in the study. HLA class I and HLA-DRB1 were genotyped using the reverse sequence-specific oligonucleotide probe method. The frequencies of three alleles of HLA, namely HLA-B*15:02, HLA-C*06:02, and HLA-C*08:01, were significantly higher in the co-trimoxazole-induced SJS/TEN group compared with controls. The risks for co-trimoxazole-induced SJS/TEN in patients with the HLA-B*15:02, HLA-C*06:02, or HLA-C*08:01 allele were about 3-11-fold higher when compared with those who did not carry one of these alleles. Individuals who carried the HLA-B*15:02-C*08:01 haplotype had a 14-fold higher risk for co-trimoxazole-induced SJS/TEN. Evidence of associations between co-trimoxazole-induced SJS/TEN and HLA alleles including HLA-B*15:02, HLA-C*06:02, and HLA-C*08:01 were found in the study population. These findings may suggest that apart from the HLA molecules, other molecules involved in the molecular pathogenesis of these severe cutaneous adverse drug reactions may play an important role in the susceptibility of individuals to SJS/TEN caused by co-trimoxazole.

HLA-A, -B, -C, and -DRB1 genotyping of 1000 Northern Irish individuals from Belfast, Northern Ireland in the United Kingdom

One thousand individuals from Belfast, Northern Ireland were genotyped at the HLA-A, -B, -C and -DRB1 loci using sequence-specific oligonucleotide probe methods. HLA-A locus genotypes display a minor Hardy–Weinberg (HW) deviation (p=0.0375); HLA-B, -C and -DRB1 genotypes are consistent with expected HW proportions. These genotype data are available in the Allele Frequencies Net Database under identifier AFND 1243.

Lack of association between KIR and HLA-C type and susceptibility to idiopathic bronchiectasis

Idiopathic bronchiectasis is a poorly defined disease characterised by persistent inflammation, infection and progressive lung damage. Natural killer (NK) cells provide a major defense against infection, through the interaction of their surface receptors, including the activating and inhibitory killer immunoglobulin-like receptors (KIR), and human leukocyte antigens (HLA) class I molecules. Homozygosity for HLA-C has been shown in a single study to confer increased genetic susceptibility to idiopathic bronchiectasis. We aimed to assess whether the KIR and HLA repertoire, alone or in combination, may influence the risk of developing idiopathic bronchiectasis, in an independent replication study. In this prospective, observational, case-control association study, 79 idiopathic bronchiectasis patients diagnosed following extensive aetiological investigation were compared with 98 anonymous, healthy, age, sex and ethnically-matched controls attending blood donor sessions in the same geographical location. DNA extraction was performed according to standardised techniques. Determination of presence or absence of KIR genes was performed by a sequence specific oligonucleotide probe method. Allele frequencies for the proposed KIR, HLA-B and HLA-C risk alleles both individually and in combinations were compared. We found no significant differences in allele frequency between the idiopathic bronchiectasis and control samples, whether considering HLA-C group homozygosity alone or in combination with the KIR type. Our results do not show an association between HLA-C and KIR and therefore do not confirm previous positive findings. This may be explained by the lower frequency of HLA-C1 group homozygosity in the control population of the previous study (27.2%), compared to 42.3% in our study, which is consistent with the genetic profiling of control groups across the UK. The previous positive association study may therefore have been driven by an anomalous control group. Further larger prospective multicentre replication studies are needed to determine if an association exists.

40-OR

Genetic control of cytokine production is a feature of variation in cytokine gene regulatory regions that produce low, moderate, or high cytokine production profiles. We have earlier shown that renal allograft recipients carrying low Interleukin-10 (IL-10) producing genotypes have high incidence of chronic allograft failure and graft inflammation. In the present study of a 15-year post transplant follow up, we report the impact of IL-10 gene variants on renal allograft survival. A total of 218 renal transplant recipients with a maximum of 15-year follow-up were recruited. Three variants of IL-10 promoter region (-1082G/A, -819C/T, -592C/A) were analyzed by Luminex based sequence-specific oligonucleotide probe method. Kaplan-Meir (with Log-rank test) and Cox-regression survival analyses using confounding factors like HLA matching, acute rejection as independent variables were performed to assess the impact of IL-10 gene variants on graft survival. Renal transplant recipients carrying low IL-10 producing genotypes had significantly lower graft survival than recipients carrying high IL-10 producing genotypes (65% v/s 92%; p = 0.001; Hazard ratio = 4.35) [Fig. 1]. Renal transplant recipients carrying high IL-10 genotypes have significant better allograft survival. The likely explanation is high IL-10 production contributing to an efficient regulatory immune environment leading to controlled allo-immune responses and better allograft survival.

Short Communication: Association of HLA-A*1101 with Resistance and B*4006 with Susceptibility to HIV and HIV-TB: Anin SilicoAnalysis of Promiscuous T Cell Epitopes

We have shown the association of HLA-A*11 with resistance and HLA-B*40 and -DR2 with susceptibility to HIV and HIV-TB. In the present study, we performed high-resolution subtyping of HLA-A*11 and -B*40 to identify the subtype level association, using the polymerase chain reaction-based sequence-specific oligonucleotide probe method. Underrepresentation of HLA-A*1101 was observed in overall HIV [p(c) = 0.012, OR 0.42 (95% confidence interval (CI) 0.24-0.72)] and HIV(+)TB(+) [p(c) = 0.001, OR 0.18 (95% CI 0.06-0.46)] compared to healthy controls. Significantly higher frequencies of HLA-B*4006 were observed in overall HIV [p = 0.0001, p(c) = 0.004, OR 2.71 (95% CI 1.58-4.75)], HIV(+)TB(-) [p = 0.0003, p(c) = 0.008, OR 2.82 (95% CI 1.56-5.17)], and HIV(+)TB(+) [p = 0.003, p(c) = 0.086, OR 2.56 (95% CI 1.33-4.95)] compared to healthy controls. An in silico analysis of potential T cell epitopes of consensus Gag and Pol sequences of HIV-1 subtype C Indian strains revealed relatively higher number of promiscuous HLA-B40, HLA-DRB1*1501, and -DRB1*1502 (HLA-DR2)-restricted epitopes in contrast to limited numbers of promiscuous binders restricted by HLA-A*1101. The results suggest that HLA-A*1101 may be associated with protection against HIV and the development of TB in HIV patients while HLA-B*4006 may be associated with susceptibility to HIV and TB development in HIV patients. The present study also suggests that the extent of promiscuity of T cell epitopes of HIV-1 subtype C restricted by HLA alleles exerting opposing effects might differ.

Haplotype analysis of HLA‐A, ‐B antigens and ‐DRB1 alleles in south Indian HIV‐1‐infected patients with and without pulmonary tuberculosis

We have shown earlier the association of human leucocyte antigen (HLA)-A11 with resistance and HLA-B40 and -DR2 with susceptibility to HIV and HIV-TB. In the present study, we have attempted to find out the HLA-DR2 subtypes and the possible HLA-A/-B/-DRB1 haplotype combinations that are associated with susceptibility or resistance to HIV and HIV with pulmonary tuberculosis (HIV+PTB+). HLA-DR2 subtyping was carried out by polymerase chain reaction-based sequence-specific oligonucleotide probe method. Overrepresentation of HLA-DRB1*1501 in HIV-positive PTB-negative (HIV+PTB-) patients (P = 0.004, P(c) = 0.06) and -DRB1*1502 in HIV-positive PTB-positive (HIV+PTB+) patients (P = 0.019) was observed as compared to healthy controls. Haplotype analysis revealed an increased frequency of HLA-A2-DRB1*1501 haplotype in HIV+PTB- patients (P = 0.008) and HLA-A2-DRB1*1502 among HIV+PTB+ patients (P = 0.01) compared to healthy controls. The haplotypes B40-DRB1*1501 and B40-DRB1*04 were found to be moderately increased in HIV+PTB(-) and HIV+PTB+ patients (P < 0.05). The study suggests that HLA-A2-DRB1*1501 haplotype may be associated with HIV infection while HLA-A2-DRB1*1502 haplotype might be associated with susceptibility to PTB in HIV patients. Moreover, HLA-B40-DRB1*1501 and HLA-B40-DRB1*04 haplotypes may be associated with susceptibility to HIV infection and to PTB in HIV patients.

HLA-DQB1 and -DPB1 allele profile in HIV infected patients with and without pulmonary tuberculosis of south India

We made an attempt to find out whether Human Leucocyte Antigen (HLA)-DQB1 and -DPB1 alleles are associated with susceptibility or resistance to Human Immunodeficiency Virus (HIV) infection and development of pulmonary tuberculosis (PTB) in HIV infected patients. The allelic profile of HLA-DQB1 and -DPB1 was studied among HIV patients without pulmonary tuberculosis (HIV+PTB−) ( n = 115), HIV patients with pulmonary TB (HIV+PTB+) ( n = 59), HIV negative PTB patients (HIV−PTB+) ( n = 110) and healthy controls ( n = 112) by polymerase chain reaction and sequence specific oligonucleotide probe method. Increased frequency of HLA-DQB1*050301 was observed in HIV+PTB− [ p = 0.024, Odds Ratio (OR) 2.30, 95% Confidence Interval (CI) 1.11–4.90] and HIV+PTB+ patients ( p = 0.044, OR 2.41, 95% CI 1.01–5.73) compared to healthy controls, suggesting that DQB1*050301 may be associated with susceptibility to HIV infection as well as development of PTB in HIV patients. Underrepresentation of HLA-DPB1*1501 was observed in HIV−PTB+ ( p = 0.002, P c = 0.034) and HIV+PTB+ ( p = 0.036) patients compared to healthy controls, suggesting that DPB1*1501 may be associated with protection against PTB development both in HIV positive and negative subjects. Analysis on the amino acid variation in the peptide binding pocket at β69 position of HLA-DPB1 molecules revealed that the β69 arginine containing HLA-DPB1 alleles and the genotype lysine/arginine were underrepresented in HIV−PTB+ (allele: p = 0.003, P c = 0.009; genotype: p = 0.0002, P c = 0.001) and HIV+PTB+ (allele: p = 0.016, P c = 0.048; genotype: p = 0.026). This suggests that HLA-DPB1 alleles with arginine may be associated with protection against development of PTB in both HIV infected as well as uninfected individuals. Further, the haplotypes HLA-DRB1*1502-DPB1*0201 and HLA-DQB1*0601-DPB1*0201 ( P c < 0.001) and HLA-DRB1*1502-DQB1*0601-DPB1*0201 ( p = 0.006, OR 5.09, 95% CI 1.42–22.66) were significantly overrepresented in HIV+PTB+ patients compared to healthy controls suggesting that genetic susceptibility to PTB development in HIV patients may be modulated by interplay between HLA class II alleles, besides HLA class I alleles.

Clinical and genetic risk factors of herpes zoster in patients with systemic lupus erythematosus.

The aim of this study was to determine the clinical and genetic risk factors that influence herpes zoster occurrence in patients with systemic lupus erythematosus (SLE). Three hundred three SLE patients meeting the American College of Rheumatology criteria were enrolled in this study. Herpes zoster was diagnosed when classic grouped vesicles were noted. Medical records were reviewed retrospectively to collect clinical information. For Fc gamma receptor IIa (Fc gamma RIIa) and Fc gamma RIIIa genotyping, polymerase chain reaction (PCR) using allele-specific primers was performed. The PCR sequence-specific oligonucleotide probe method was utilized in human HLA-DRB1 genotyping. Forty-two cases (13.9%) of zoster occurred among 303 SLE patients. The incidence of zoster in patients with SLE was 32.5/1,000 patients per year. Patients who developed zoster had higher rates of lupus nephritis (P = 0.018) and positive anti-Sm antibody (P = 0.019). However, Fc gamma RIIa and Fc gamma RIIIa polymorphism and the HLA-DRB1 genotype did not influence herpes zoster occurrence. Systemic lupus erythematosus patients with lupus nephritis or anti-Sm antibody are at higher risk of herpes zoster. Fc gamma RIIa (H/R131), Fc gamma RIIIa (F/V176), and HLA-DRB1 genetic polymorphisms did not influence the occurrence of herpes zoster in these patients.

Association of HLA class II alleles with preference and intake of dairy milk

The study investigated the possible association between HLA allele frequency and the preference and intake of dairy milk. Ninety-nine Japanese subjects (72 male, 27 female), aged 18–29 years (mean 20.4 years), provided their preference and intake of cow’s milk, by answering ‘like’ or ‘dislike’, and ‘often or daily’ or ‘seldom or never’. Their HLA class II genes (DRB1, DQA1 and DQB1) were analyzed by the polymerase chain reaction sequence specific oligonucleotide probes method. Among the 99 subjects, 37 answered ‘like’ and 62 answered ‘dislike’. For milk intake frequency, 56 of subjects answered ‘often or daily’ and 43 answered ‘seldom or never’. The frequency of HLA-DQA1∗0102 was significantly increased in the ‘dislike’ group for milk preference. The results of the present study suggest that the preference for cow’s milk is negatively associated with the frequency of HLA-DQA1∗0102.

Different distribution of HLA class II alleles according to response to corticosteroid therapy in sudden sensorineural hearing loss.

To investigate the association of HLA class II alleles with the susceptibility to sudden sensorineural hearing loss and with the results of corticosteroid treatment in the Korean population. HLA-DRB1, -DQA1, -DQB1, and -DPB1 genotyping by the sequence-specific oligonucleotide probes method in 41 patients with sudden sensorineural hearing loss and in 206 healthy control subjects. Initial hearing levels at the onset of hearing loss and final hearing levels after treatment were evaluated for the association with HLA class II alleles. Tertiary care referral center, ambulatory and hospitalized care. Forty-one patients (24 men and 17 women; mean age, 49.2 years) were compared with 206 controls. Patients were divided into 2 groups according to their response to corticosteroid therapy (good response vs nonresponse). The frequencies of HLA-DRB1, -DQA1, -DQB1, and -DPB1 alleles were not significantly different between patients and controls (P>.05). When an association between the results of corticosteroid treatment and the frequency of HLA alleles was evaluated, the frequencies of HLA-DRB1*14 (relative risk [RR] = 3.5, P<.02), -DQA1*03 (RR = 4.2, P<.02), and -DQA1*05 (RR = 3.1, P<.03) were significantly increased, but HLA-DQA1*01 (RR = 0.2, P<.004) and -DQB1*06 (RR = 0.2, P<.009) were decreased in the group nonresponsive to corticosteroid therapy, compared with the controls. The distribution of HLA-DQA1*01 (P<.04), -DQB1*06 (P<.02), and -DQA1*03 (P<.003) was significantly different between the responsive and the nonresponsive groups. HLA-DQA1 allelic combination analysis showed that the frequencies of DQA1*03 and *05 had a high RR value in patients with sudden sensorineural hearing loss (RR = 4.1, P<.003) and in patients in the nonresponsive group (RR = 8.9, P<.001), compared with the controls. The presence of HLA class II alleles may be a useful genetic marker in forecasting a prognosis in Korean patients with sudden sensorineural hearing loss.

High frequency of HLA-A∗0103 allele in a Somali population

We report the existence of class I HLA allele A∗0103 in an ethnic group (Somali) where this allele has not been reported. This allele was discovered in a study to examine the relationship between HLA alleles and humoral antibody response to measles vaccine among recent immigrants from Somalia to Olmsted County, Minnesota. We initially used polymerase chain reaction–sequence-specific primers (PCR-SSP) to carry out HLA class I typing. Based on PCR-SSP, 55 subjects were assigned the allele HLA-A∗0101. Following direct DNA sequencing of the PCR products, 37 of the 55 subjects (67.3%) that were initially assigned the A∗0101 allele were found to actually be A∗0103. Our data are significant because it demonstrates that many of the previously typed A∗0101 individuals are actually A∗0103 as the SSP or sequence-specific oligonucleotide probes method cannot distinguish between the two alleles. Lastly, this is the first identification of this allele in the homozygous state.

A polymorphism of the 5' flanking region of tumour necrosis factor α gene is associated with thyroid-associated ophthalmopathy in Japanese.

We have studied the polymorphism of the 5' flanking region of the tumour necrosis factor (TNF)-α gene in order to better understand the genetic background of autoimmune thyroid disorders and thyroid-associated ophthalmopathy. We studied the polymorphism of the 5' flanking region of the TNF-α gene at positions - 1031 (T to C change, termed as - 1031C), - 863 (C to A, - 863 A), - 857 (C to T, - 857T), - 308 (G to A, - 308 A) and - 238 (G to A, - 238 A) in Japanese patients with Graves' disease [n = 173, 62 of whom had associated ophthalmopathy (American Thyroid Association (ATA) class III or greater)] and healthy control subjects (n = 575), using a polymerase chain reaction sequence-specific oligonucleotide probe method. The allele frequency of - 857T in the Graves' disease patients (22.5% vs. 17.7%, OR = 1.35, P = 0.045, corrected P = 0.23) was slightly greater than in the Japanese healthy subjects, respectively. However, the difference was not statistically significant. In Graves' disease patients with evident ophthalmopathy (ATA class III or greater), the allele frequencies of - 1031C and - 863 A were significantly greater than those with no or mild ophthalmopathy (ATA class 0-II) (31.5% vs. 13.5%, OR =2.94, P < 0.0001, corrected P < 0.0005; 23.4% vs. 11.7%, OR =2.30, P = 0.0044, corrected P = 0.022, respectively) and in control subjects. The strength of the association of the polymorphism - 1031C increased with the severity of ophthalmopathy, with odds ratios of 2.36 for ATA class III, and 5.43 for ATA class IV-VI, respectively, compared with Graves' disease with no or mild ophthalmopathy (ATA class 0-II). Although the phenotype frequency of DRB1*0901 was not different among Graves' disease patients with or without ophthalmopathy and control subjects, the phenotype frequency of DRB1*0901(-)/-1031C(+) was significantly increased in Graves' disease patients with ophthalmopathy compared to those with no or mild ophthalmopathy (OR = 4.91, P = 0.0005) or control subjects (OR = 4.59, P < 0.0001). These results suggest that the - 1031C or - 863 A alleles, or a gene in linkage disequilibrium with the TNF-α gene, predispose to the development of ophthalmopathy in Japanese patients with Graves' disease.

Human leukocyte antigen DRB1 1302 protects against bile duct damage and portal lymphocyte infiltration in patients with chronic hepatitis C

Background/Aims: To confirm the immune reaction of hosts in chronic hepatitis C, we examined the association of human leukocyte antigen (HLA) DR with the histopathological outcome including bile duct damage and steatosis, which are characteristic of hepatitis C virus (HCV) infection. Methods: One hundred and fifty-five patients with chronic HCV infection were examined. The pathological appearance of liver biopsy specimens was evaluated by both Knodell's histological activity index and examination of bile duct damage and steatosis. HLA DRB1 was determined by the polymerase chain reaction sequence-specific oligonucleotide probe method. Results: HLA DRB1 1302 was found with significantly higher frequency in patients without than with bile duct damage (34.8% vs. 4.7%, p=0.0001, p corrected by Bonferroni's inequality method=0.002). It was also found more frequently in patients without marked portal lymphocyte infiltration (28.6% vs. 7.7%, p=0.0015, p corrected by Bonferroni's method=0.03). HLA DRB1 1101 was found more frequently in patients without than with piecemeal necrosis ( p=0.004). In contrast, the frequency of HLA DRB1 1502 tended to be higher in patients with than without piecemeal necrosis and marked portal lymphocyte infiltration ( p=0.015 and p=0.03, respectively). HLA DRB1 1201 and 0802 were seen more frequently in bile duct damage-negative ( p=0.02) and piecemeal necrosis-negative patients ( p=0.03), respectively. Interestingly, serum HCV levels of HLA DRB1 1302-positive patients were significantly higher than those of 1302-negative patients (mean: 7.7Meq/ml vs. 3.1Meq/ml, p=0.0007). Conclusion: These findings suggest that some histopathological changes in chronically HCV-infected livers could be caused by the host's immune reaction regulated by HLA DR.

HLA class II haplotype associations with inflammatory bowel disease in Jewish (Ashkenazi) and non-Jewish Caucasian populations

Ulcerative colitis (UC) and Crohn’s disease (CD) are the clinical entities comprising idiopathic inflammatory bowel disease (IBD). Previous studies on the association of IBD and human leukocyte antigen (HLA) class II genes suggested a role for HLA in this disease. Here we present HLA class II (DRB1, DQB1, DQA1, DPB1) allele and haplotype distributions determined using the polymerase chain reaction and sequence-specific oligonucleotide probe methods. A total of 578 UC and CD Caucasian patients and controls from Jewish (Ashkenazi) and non-Jewish populations was examined. Our previously reported association of DR1–DQ5 with CD was attributable to DRB1∗0103. A dramatic association with IBD and the highly unusual DRB1∗0103-DQA1∗0501-DQB1∗0301 haplotype (OR = 6.6, p = 0.036) was found. The more common DR1 haplotype, DRB1∗0103-DQA1∗0101-DQB1∗0501, was also associated with IBD (OR = 3.1, p = 0.014), a result suggesting that interaction between DR and DQ may determine the extent of disease risk. Our previously reported association of DR2 with UC was attributable to DRB1∗1502 (OR = 2.6, p = 0.006). At the DPB1 locus, a significant association of DPB1∗0401 with CD was observed for the combined populations (OR = 1.85, p = 0.007). These observations indicate that some class II alleles and haplotypes confer susceptibility to both UC and CD, implying common immunogenetic mechanisms of pathogenesis, while others confer risk to only one of these diseases, and illustrate the value of DNA HLA typing in disease susceptibility analyses.