HLA A*, B*-BF* AND C4 A*, ALLELE ASSOCIATIONS,WITH SPECIAL REFERENCE TO BF*S07, IN THE TUNISIAN POPULATION

The HLA A*2, Bw*50-BF*S07-C4 A*2, B*l linkage group was transmitted unambiguously in four unrelated Tunisian families. In one of these, another allele association, also carrying BF*S07, HLA A*9, Bw*50-BF* S07-C4 A*1, B*1, was encountered. The previously reported linkage disequilibrium between BF*S07 and HLA Bw*50, a subtypic speficity of HLA Bw*21, is confirmed in our study. The C4 A*2, B*1, haplotype, rare in the other populations until now studied, seems more frequent in Tunisia since it has been also found linked to HLA A* 11, B*27 and BF*S in one of these familie. Other allele associations were unambiguously demonstrated with predominantly the C4 A*3, B*1 haplotype, particularly a rare HLA A*3, B*18-BF* F1-C4 A*3, B*1 linkage group. A silent gene at the C4 A locus was found linked to HLA B*.     

Association of C4B deficiency (C4B*Q0) with erythema nodosum in leprosy

A considerable number of studies have postulated significant associations between susceptibility to the different clinical manifestations of leprosy and the MHC, In this investigation, the association between the MHC class III complement proieins C2, BF, C4A and C4B and leprosy in a patient population of Southern Brazil was studied. A total of 109 non-related leprosy patients was investigated; 73 presented wilh lepromatous leprosy (LL), 46 of Ihem had the immunopathological reaction of erythema nodosum (ENL), the remaining 36 were tuberculoid, borderline and indeterminate leprosy (TIBL) patients. The control group included 172 healthy individuals matched with the patients according lo their ethnic and geographical origin, C2, BF, C4A and C4B allotypes were determined by slandard technologies including Western blots for C2 and C4 variant alleles wilh monoclonal and polyclonal antibodies. Non-expressed (‘silent’) C4 alleles in hemizygously deficient individuals were estimated semiquantitatively on the basis of the C4A and C4B isolype ratio and by the M ASC (‘minimal chi-square’) method. The results showed a significantly elevated presence of the non-expressed C4B allele (C4B*Q0) in the LL and ENL patient groups in comparison with the controls. The most signifieant difference was observed in the ENL group when compared with the controls. In addition, all patients who were homozygously C4B-deficient had ENL, and most of them had the BF*F1 allele. The comparison between LL patients with and without ENL also showed a statistically significant difference in the presence of C4B*Q0, indieating thai C4B deficiency itself is associated with EN L. The relative risk of LL patients with the C4B*Q0 allele suffering from ENL was 53 compared with LL palients without C4B*Q0, Since immune complexes (IC) are considered to be the palhogenic cause of ENL, our findings indicate thai C4B deficieney may play an important role in the abnormal immune response against Myeobaeterium leprae and in the lack of IC clearance, leading to ENL reactions. Individuals wilh this allele seem to be at a higher risk of developing pathologieal immune reactivity in lepromatous leprosy.     

Effect of different genetics variants: CYP2C9*2, CYP2C9*3 of cytochrome P-450 CYP2C9 and 1639G>A of the VKORC1 gene; On acenocoumarol requirement in Moroccan patients

Coumarin derivatives such as acenocoumarol represent the therapy of choice for the long-term treatment and prevention of thromboembolic diseases. Many genetics determinants involved in the metabolism of acenocoumarol have been shown to influence the anticoagulant dosage. The aim of this work was to evaluate, for the first time in Maghreb, the allelic frequencies of CYP2C9*2, CYP2C9*3 and VKORC1 -1639G>A mutations, and to establish the role of this polymorphisms in modulating the acenocoumarol requirement in Moroccan patients receiving anticoagulation treatment. Three groups of patients, with low, medium, or high acenocoumarol dose requirements were studied. Genetic analyses of VKORC1 -1639G>A, CYP2C9*2, and CYP2C9*3, were performed in 114 Moroccan patients with stable acenocoumarol dose. The results showed that the allelic frequencies of the three mutations studied was varies, most of patients having CYP2C9*2 and CYP2C9*3 mutations belong to a group with low dose of acenocoumarol, with P-value of 0.0082 and the single patient with CYP2C9*3 on homozygous form belongs to the same group and carried the A allele for VKORC1 gene. In conclusion, the present study confirmed the large interindividual variability in acenocoumarol maintenance dose due to CYP2C9*2, CYP2C9*3 and VKORC1 -1639G>A polymorphisms, and demonstrated that these alleles modulates sensitivity to acenocoumarol, a finding indicating that a reduced initial loading dose of acenocoumarol should be used in carriers of this allele, also, she indicates the usefulness of predictive testing concerning these mutations when an hypocoagulability is installed and not explained by the dose of VKA.     

THE HLA-DRB1*0405 HAPLOTYPE IS MOST STRONGLY ASSOCIATED WITH IDDM IN ALGERIANS

Insulin-dependent diabetes mellitus (IDDM) in Caucasians is strongly associated with HLA-DR3-DQ2 and DR4-DQ8. In order to investigate the HLA class II associations with IDDM in Algerians, we have used polymerase chain reaction (PCR) and sequence specific oligonucleotide analysis (SSO) to identify DQA1, DQB1, and DRB1 alleles, haplotypes and genotypes in 50 unrelated IDDM patients and 46 controls from a homogeneous population in Western Algeria. Both DRB1*0301-DQA1*0501-DQB1*0201 (DR3-DQ2) and DRB1*04-DQA1*0301-DQB1*0302 (DR4-DQ8) haplotypes were found at increased frequencies among the patients compared to controls (45% vs. 13%, RR = 5.5, P_c < 10^-5 and 37% vs. 4%, RR = 12.9, P_c < 10^-4, respectively). Among the latter, in contrast to other Caucasian populations, only DRB1*0405-DQA1*0301-DQB1*0302 was significantly increased in the Algerian patients (25% vs. 1% in controls, RR = 30.3, P_c < 10^-3). Accordingly, the highest risk of disease was observed in DRB1*0301-DQA1*0501-DQB1*0201/DRB¹*0405-DQA1*0301-DQB1*0302 heterozygotes (34% in patients vs. 0% in controls; RR = 49; P_c < 10^-3). This observation and its comparison with DR-DQ haplotypes in other ethnic groups suggest that the DRB1*0405 allele which encodes an Asp57-negative β chain may contribute to IDDM susceptibility in a similar way as Asp57-negative DQβ chains.     

CYP2C19 genetic polymorphism in the Vietnamese population

Abstract

Background: Genetic polymorphism of CYP2C19 has been shown to affect enzyme activity and thereby contribute to inter-individual variability in drug metabolism and response. The complete genetic variation of CYP2C19 in Vietnam still remains obscure even though data of common alleles in Vietnamese Kinh have been reported.

Aim: To establish the extent of CYP2C19 polymorphism in Vietnamese.

Subjects and methods: The promoter and all nine exons of CYP2C19 in 100 healthy unrelated Vietnamese Kinh subjects were sequenced. Additionally, the CYP2C19 variants, *2, *3 and *17 were analysed by RFLP-PCR in 275 subjects of four minor ethnic groups in Vietnam (Tay, Muong, H’Mong and Nung).

Results: In 100 Kinh subjects, the percentages of CYP2C19*1, CYP2C19*2, CYP2C19*3 and CYP2C19*17 alleles were 76%, 20.5%, 2.5% and 1%, respectively. Three novel variants in introns 2, 5 and 8 had no impact on mRNA splicing according to the Human Splicing Finder. The prevalence of CYP2C19*17 in Vietnamese Kinh was significantly lower compared with figures found in Western Asia and Europe, while CYP2C19*2 frequency was statistically higher than that in Western Asia and several countries in Europe. The frequency of CYP2C19*2 in Kinh was significantly lower than in the other four ethnic minorities.

Conclusion: These results provide information on CYP2C19 polymorphism in the Vietnamese population, which could be useful for optimising drug therapies and precision medicine studies.     

Characterization of two hybrid C4 allotypes (C4A*12 and C4B*3) by electrophoretic, serological and restriction fragment length polymorphism analyses

Informative pedigree analysis of two rare C4 allotypes is reported. One proband was C4A deficient as a consequence of having one haplotype with a deleted C4A gene, and the second haplotype with two C4B genes--one encoding the common C4B*1 and one encoding a unique hybrid gene product C4B*3. C4B*3 had approximately normal C4B hemolytic activity, a single alpha-chain of MR 94,000 by SDS-PAGE but was positive for Rg:1,2 by hemagglutination inhibition (HAI) and for Rg:1 by Western blotting. The hybrid nature was confirmed by RFLP analysis with a Rg:1-associated fragment by Eco0109 digestion but no C4A-associated fragments by N1aIV digestion were identified. A gene conversion at Locus I which included just the C4 isotype region could explain the structure of C4B*3. The second pedigree had a Rodgers negative C4A*12 allotype. This C4A gene, which segregated with a single 7.0 kb TaqI fragment, encoded a C4A alpha-chain, which was negative for Rg:1 epitope. The affected haplotype lacked the Rg:1-associated fragment by Eco0109 digestion yet had the C4A specific N1aIV digestion fragment. These studies successfully employed RFLP analyses to confirm serologic and electrophoretic observations.     

Familial C4B deficiency and immune complex glomerulonephritis

Homozygous complement C4B deficiency is described in a Southern European young female patient with Membranoproliferative Glomerulonephritis (MPGN) type III characterized by renal biopsies with strong complement C4 and IgG deposits. Low C4 levels were independent of clinical evolution or type of immunosuppression and were found in three other family members without renal disease or infections. HLA typing revealed that the patient has homozygous A*02, Cw*06, B*50 at the class I region, and DRB1*08 and DQB1*03 at the class II region. Genotypic and phenotypic studies demonstrated that the patient has homozygous monomodular RCCX in the HLA class III region, with single long C4A genes coding for C4A3 and complete C4B deficiency. Her father, mother, son and niece have heterozygous C4B deficiency. The patient's deceased brother had a history of Henoch–Schönlein Purpura (HSP), an immune complex-mediated proliferative glomerulonephritis. These findings challenge the putative pathophysiological roles of C4A and C4B and underscore the need to perform functional assays, C4 allotyping and genotyping on patients with persistently low serum levels of a classical pathway complement component and glomerulopathy associated with immune deposits.     

HLA‐A*11:53 is shown to be identical to the corrected A*11:02:01 allele sequence

According to the IMGT/HLA Database, the DNA sequence of A*11:53 is identical to A*11:02:01 in exons 2, 3, 4 and 5 except at codon 276. A*11:53 was reported as a rare variant of A*11, while A*11:02:01 was understood to be the second most frequently observed variant of A*11 after A*11:01:01 in Taiwanese. We sequenced HLA‐A locus exons 2, 3, 4 and 5 of Taiwanese blood donors (n = 50) previously typed to carry A*11:02:01. We found out all of their sequences are identical to A*11:53 in exons 2, 3, 4 and 5′ part of exon 5 including codon 276.     

Protective Effect of HLA-DRB1*11 and Predisposition of HLA-C*04 in the Development of Severe Liver Damage in Brazilian Patients with Chronic Hepatitis C Virus Infection

The objective of this study was to investigate human leucocyte antigen (HLA) genes in patients chronically infected with hepatitis C virus (HCV) and to analyse the possible role of these genes in the progression of chronic hepatitis C. One hundred and forty‐five (145) Brazilian patients infected only with HCV genotype 1 were evaluated. HLA class I (A*, B*, C*) and class II (DRB1*, DQA1*, DQB1*) typing were carried out by PCR‐SSO, through Luminex technology. Associations were found with protection against development of liver damage by both DRB1*11 (5.0% versus 18.2%, P = 0.0016, OR = 0.23, CI 95% = 0.09–0.58; Pc=0.0208) and DRB1*11‐DQA1*05‐DQB1*03 haplotype (4.2% versus 15.3%, P = 0.0032; OR = 0.24, CI 95% = 0.08‐0.64). Liver damage was associated with HLA‐C*04 in patients with <20 years of infection (38.4% versus 9.1%, P = 0.002, OR = 6.25, CI 95% = 1.97–19.7; Pc=0.0238). It is concluded that HLA alleles can influence the development of liver damage in HCV type‐1 chronically infected Brazilian patients.     

Distribution of polymorphisms in the CYP2C9 gene and CYP2C19/CYP2C9 haplotypes among Venezuelan populations

Background: Polymorphisms with decreased enzyme activity of their gene products have been reported in region CYP2C with population variations in haplotype structure.

Aim: To estimate the allelic and genotypic frequencies of variants CYP2C9*2 and CYP2C9*3 and of CYP2C9/CYP2C19 haplotypes in Venezuelan populations.

Subjects and methods: Six hundred and thirty-four individuals from nine admixed populations (AP) and the Warao indigenous group were studied. Allelic frequencies, linkage disequilibrium and genetic distances for haplotypes were calculated and compared within Venezuela and with data available in the literature.

Results: Heterogeneity in the distribution of CYP2C9 alleles and CYP2C9/CYP2C19 haplotypes among the AP and the Warao was observed. The joint frequency of haplotypes, with at least one non-functional variant, shows values in AP between 21–41%, while in Warao it reaches 5%. The haplotype that includes the Asian and rare Latin America CYP2C19*3 allele was detected in most AP and in Warao. Pairwise Fst values showed that the Warao was an outlier compared with the AP, while these are closer to European-derived populations. No significant correlation was found between haplotype frequencies and admixture.

Conclusions: These results support the need to understand the distribution of genomic biomarkers related to the metabolism of drugs, for planning national public health strategies.     

Combined Heterozygous Deficiency of the Classical Complement Pathway Proteins C2 and C4

Genetic deficiencies of components of the classical pathway of complement activation are associated with an increased risk for the development of autoimmune and immune complex-mediated diseases. In the present study we report on the molecular and clinical features associated with combined heterozygous C4 and C2 deficiency in 15 individuals investigated within six families. Approximately 30% of the individuals manifested SLE or another autoimmune condition. Heterozygous C2 deficiency was related to a 28-bp deletion in the C2 gene (C2 deficiency type I), in most cases within the HLA-A25 B18 C2Q0 BfS C4A4B2 DR2 haplotype. Among 13 partial C4-deficient haplotypes transmitted, 8 carried C4A*Q0 alleles and 5 C4B*Q0 alleles. In seven cases the C4A*Q0 alleles were associated with a deletion of the C4A/CYP21P genes within the HLA-B8 C2C BfS C4AQ0B1 DR3 haplotype. In three cases, the C4B*Q0 allele was associated with a deletion of the C4B/CYP21P genes within the HLA-B18 C2C BfF1 C4A3BQ0 DR3 haplotype. In the other cases, C4A*Q0 or C4B*Q0 was dependent on as yet uncharacterized defects in the C4 gene or in C4 gene expression. In view of the relatively high frequency of heterozygous C4 deficiency in the normal Caucasian population, the expected frequency of the combined deficiency should approximate 0.001.     

A case report of a patient carrying CYP2C9*3/4 genotype with extremely low warfarin dose requirement

We report a case of intolerance to warfarin dosing due to impaired drug metabolism in a patient with CYP2C9*3/*4. A 73-yr-old woman with atrial fibrilation was taking warfarin. She attained a high prothrombin time international normalized ratio (INR) at the standard doses during the induction of anticoagulation and extremely low dose of warfarin (6.5 mg/week) was finally chosen to reach the target INR. Genotyping for CYP2C9 revealed that this patient had a genotype CYP2C9*3/*4. This is the first Korean compound heterozygote for CYP2C9*3 and *4. This case suggests the clinical usefulness of pharmacogenetic testing for individualized dosage adjustments of warfarin.     

Investigation of Killer Cell Immunoglobulin‐Like Receptors KIR2DL2 and KIR2DL3 Diversity and Identification of Ten Novel KIR2DL3 Alleles in the Chinese Han Population

KIR2DL2 and KIR2DL3 are important inhibitory receptors that recognize a subset of HLA‐C allelic products carrying Ser77 and Asn80. In this study, we have determined KIR2DL2 and KIR2DL3 diversity in the Chinese Han population by a PCR sequence‐based typing. Based on sequencing, the coding regions of 166 Chinese Han individuals, seven new polymorphic sites (238G>A, 405G>A, 476A>G, 550G>A, 608G>A, 789T>C, 947T>C) were found. KIR2DL2*00301, *00101, KIR2DL3*00101,*00201,*013, *015 and ten new KIR2DL3 variants (KIR2DL3*00105, 00106, 00107, 00108, 019, 020, 021, 022, 023 and 024) were identified, of which KIR2DL3*00101 was the most frequent allele. Compared with the sequences of KIR2DL3*00101, all sequences of 2DL3*00105, 2DL3*00106, 2DL3*00107 and 2DL3*00108 had one nucleotide substitution(789T>C, 261C>T, 489G>A and 405G>A),but none resulted in amino acid change. An A>G substitution was observed in nucleotide position 476 in 2DL3*019, 608 G>A in 2DL3*020, 824T>C in 2DL3*021 and 238 G>A in 2DL3*023. In addition, 2DL3*022 probably arose from 2DL3*00201 with a nucleotide substitution G>A at 550. There were more HLA‐C1 positive individuals than HLA‐C2. In conclusion, the data of allelic polymorphism for KIR2DL2 and KIR2DL3 were obtained in the Chinese Han population and ten novel KIR2DL3 alleles were identified.     

Association of alcohol dehydrogenase 2*1 allele with liver damage and insulin concentration in the Japanese

The Japanese have a polymorphism in the alcohol dehydrogenase 2 gene (ADH2). The alleles of ADH2 (ADH2*1 and ADH2*2) encode more active and less active forms for ethanol metabolism, respectively. We examined whether liver damage and the insulin–glucose axis vary according to ADH2 genotype in the Japanese. The 2,232 subjects (1,126 men and 1,106 women) were recruited from a population-based prospective cohort study. Clinical evaluations including alcohol consumption, percentage of alcohol drinkers, plasma glucose, HbA1c, insulin, AST, ALT, -GTP, and prevalence of diabetes were compared among the ADH2 genotypes. The percentage of drinkers, alcohol consumption, AST, ALT, and -GTP were higher in group ADH2*1/1 than in group ADH2*1/2 or ADH2*2/2 (all P<0.05). Hence, ADH2*1/1 is associated with excess alcohol intake and liver disorders. However, the prevalence of diabetes did not differ among the three groups. For the glucose–insulin axis, we examined subjects who did not receive insulin therapy or oral anti-diabetes medication. While amounts of alcohol consumed and glucose levels were nearly the same between ADH*1/2 and ADH2*2/2, insulin concentrations were lower in ADH2*2/1 than in ADH2*2/2 (P<0.05 in men). This finding suggests that the ADH2*1 allele is associated with a lower insulin concentration when alcohol intake is light or moderate. It also suggests that the genetic effect of ADH2*1 plays an important role in alcohol drinking behavior and in the occurrence of liver injury, but the effect is so mild that it does not influence the glucose–insulin axis or prevalence of diabetes.     

C2_4_4 microheterogeneity and HLA Class I

The microheterogeneity of the tetranucleotide repeat locus C2_4_4 situated in the HLA class I region (6p21.3) was investigated by sequencing 50 alleles in an Austrian population sample of 240 unrelated Caucasoid individuals. Several different sequences were found in alleles of the same length. Analysis of the associations between the sequenced C2_4_4 alleles and HLA class I showed a strong linkage disequilibrium between the C2_4_4*9 sequence variants and two different HLA class I haplotypes, as well as between the most common *17 sequence and one HLA-ABC haplotype. No clear cut association could be observed in C2_4_4*16 and *18. The results of this study demonstrate that the exclusive use of microsatellite polymorphisms for the definition of HLA haplotypes is generally not possible.     

PHENOTYPES OF THE FOURTH COMPLEMENT COMPONENT (C4) IN BLACK AMERICANS FROM THE SOUTHEASTERN UNITED STATES

C4 is composed of two tightly linked genes (C4A and C4B) lying within the major histocompatibility complex of chromosome 6 that can be demonstrated by agarose gel electrophoresis. Seven alleles and five alleles at the C4A and C4B loci, respectively, were detected in 169 black individuals from the southeastern United States. Furthermore, the phenotypic frequencies of C4A6, C4A5, C4A4, C4B4, C4B3, and C4BQO were significantly different between black and white Americans.     

THE EFFECT OF TNF*B GENE POLYMORPHISM ON TNF-α AND -β SECRETION LEVELS IN PATIENTS WITH INSULIN-DEPENDENT DIABETES MELLITUS AND HEALTHY CONTROLS

TNF-α and -β have been implicated in the development of HLA-associated autoimmune diseases. It has been suggested that inter-individual differences in the secretion levels of these cytokines may contribute to the predisposition of certain individuals to the development of diseases such as insulin-dependent diabetes mellitus (IDDM). We have investigated whether a diallelic TNF*B polymorphism detected using the enzyme Ncol influences the TNF-α and/or -β secretory capacity of peripheral blood mononuclear cells (PBMC) from PHA stimulated healthy individuals and IDDM patients. We have shown that the level of TNF-β secreted correlates with the TNF*B genotype in healthy individuals: those with the TNF B*2 allele secreted significantly higher levels of TNF-β (P= 0.025) than those with the TNF*B1 allele. In IDDM patients, the reverse situation was observed, with those patients with the TNF*B1 allele secreting higher levels of TNF-β than those with the TNF*B2 allele. No correlation was found between TNF-α levels and TNF*B genotype. Furthermore, when IDDM patients and controls were matched for TNF*B genotype, the IDDM patients with the TNF*B2 allele secreted significantly lower levels of TNF-β than controls with this allele. On analysis of IDDM-susceptible extended HLA haplotypes in the homozygous groups, 4/7 IDDM patients with the TNF*B2 allele were Bw62-DR4 compared with 0/16 matched controls. Thus, the extended haplotype Bw62-DR4-TNF*B2/2 rather than IDDM per se is almost certainly responsible for the depressed TNF-β secretion found in the IDDM-TNF*B2 homozygous cohort.     

HLA-DR4 SUBTYPE AND -B ALLELES IN DQB1*0302-POSITIVE HAPLOTYPES ASSOCIATED WITH IDDM

We determined the distribution of DR4 subtypes in 309 DQB1*0302-positive haplotypes found in insulin-dependent diabetes mellitus (IDDM) patients and 70 control haplotypes present only in healthy family members. An increased frequency of DRB1*0401 allele (74.4% vs. 55.7%, P = 0.003) and a decrease of DRB1*0404 allele (23.6% vs. 40.0%, P = 0.0064) was revealed. A further analysis of extended haplotypes demonstrated strong linkages between various B alleles and DRB1*04 subtypes. HLA-B39 was more frequent in DRB1*0404–DQB1*0302-positive IDDM haplotypes compared with control ones (37.0% vs. 14.3%, P = 0.049), suggesting an involvement of the region telomeric to HLA-DRB1 in the susceptibility to IDDM.     

Detection and identification of cytochrome P-450 2C9 alleles *1, *2, and *3 by high-resolution melting curve analysis of PCR amplicons

High-resolution melting curve analysis using a fluorescent DNA binding dye can detect sequence variations in a closed-tube system without labeled primers or probes. We developed and verified a melting analysis assay for common single nucleotide polymorphisms of cytochrome P-450 (CYP) 2C9 that affect warfarin metabolism. We used this method to genotype 84 patients receiving warfarin. For wild-type, *1/*1, 50% fluorescence corresponded to a mean+/-SD of 87.17+/-0.05 degrees C, whereas *2/*2 was 0.4 degrees C lower. The *1/*2 melting curve was easily distinguished from *1/*1 and *2/*2 based on transition temperature and shape. Exon 7 showed a more complex melting curve; however, genotypes *1/*1, *1/*3, and *3/*3 were easily distinguishable. Melting curves were highly reproducible (SD of temperature for multiple fluorescence values 0.04 degrees C-0.11 degrees C; mean, 0.06 degrees C). Heterozygotes (*1/*2 or *1/*3) required significantly lower mean maintenance warfarin doses compared with wild-type (30.67 and 29.56 vs 42.81 mg/wk; P<.05). High-resolution melting analysis provides a simple and accurate method for genotyping of CYP2C9.