Genetic Variability and Linkage Disequilibrium Within the DP Region in the CEPH Families

ABSTRACT: A PCR-based SSO-assay has been developed to characterize the allelic polymorphism at the HLA-DPA1 locus. To validate the performance of this assay, 77 samples were typed side by side in a blinded fashion by the SSO assay and sequencing-based typing (SBT); 100% concordance was seen between the two methods. To address questions of genetic variability and linkage disequilibrium within the class II region, 478 members of the 37 original Caucasian Centre d’Etude du Polymorphisme Humain (CEPH) families were typed for DPA1 using the SSO assay providing information on 247 independent chromosomes. Six of the eight known DPA1 alleles were detected in this population; DPA1*0103 was the most frequent allele. Analysis of the distribution of allele and haplotype frequencies using the homozygosity statistic suggests that balancing selection does not appear to be acting on the DPA1 locus nor on the functional DP heterodimer in this population. Family data permits the unambiguous assignment of haplotypes. Of the 247 independent chromosomes analyzed, 24 distinct DPA1-DPB1 haplotypes were identified with DPA1*0103-DPB1*0401 being the most common. Twelve of the 18 DPB1 alleles identified in this population have an exclusive association with one DPA1 allele. Of the remaining six DPB1 alleles, four are present at a frequency of >3% and show preferential association with just one DPA1 allele. Calculation of the normalized disequilibrium parameter (D′) shows 13 DP haplotypes to be in significant positive disequilibrium. These data suggest there is strong linkage disequilibrium between the DPA1 and DPB1 loci in this Caucasoid population and provide a basis with which to study linkage disequilibrium in other ethnic groups as well as analyze the evolutionary forces which govern allelic and haplotypic variation.     

Genetic analysis of the hypervariable region of the human astrovirus nsP1a coding region: design of a new RFLP typing method

Human astroviruses (HAstV) are causative agents of viral gastroenteritis worldwide. A hypervariable region (HVR) is located close to the C-terminus of the nsP1a, and recent data support the involvement of the HVR-containing nonstructural protein in viral RNA replication processes, suggesting a correlation between variability in this region and pathogenic properties. The HVR of the C-terminal nsP1a coding region of 104 wild-type and reference isolates of HAstV was sequenced. A phylogenetic analysis was performed to identify different genotypes, and a restriction fragment length polymorphism (RFLP) method was designed. An extensive nucleotide and deduced amino acid sequence variability was observed, as well as many insertions and deletions that retained the reading frame. The resultant phylogenetic tree supported the subdivision of HAstV into the two previously described major genetic groups, genogroup A and B, and the identification of 12 genotypes (9 within genogroup A, and 3 within genogroup B), which could be identified by RFLP. A correlation analysis was performed between genotype information and viral load using information from 35 clinical samples. Significant differences were observed between the viral load in clinical samples and certain HAstV genotypes that belonged to the same serotype, confirming the influence of C-terminal nsP1a variability on the viral replication phenotype. The use of the new RFLP typing method based on the HVR of the C-terminal nsP1a coding region by diagnosticians would help to understand the relationship between different genotypes and the severity of the gastroenteritis.     

HLA中部区域多态性反映单体型遗传保守性

对２８个代表１２种不同的ＨＬＡ单体型的细胞株同时进行Ｃ４、ＣＹＰ２１、ＢＡＴ３的ＲＦＬＰ检测，观察到了７种不同的Ｃ４－ＣＹＰ２１－ＢＡＴ３的ＲＦＬＰ结构形式。结果显示：Ｃ４－ＣＹＰ２１－ＢＡＴ３基因结构具有高度的多态性，且具有祖传单体型性质和祖传单体型特异性性质。本项研究表明，ＨＬＡ祖传单体型在遗传与进化过程中是高度保守的。本文还对祖传单体型研究的意义及随机个体单体型分型的可能性进行了探讨。     

Comparison of HLA-DRB1 typing by DNA-RFLP, PCR-SSO and PCR-SSP methods and their application in providing matched unrelated donors for bone marrow transplantation

Abstract: The aim of the study was to devise a strategy for large batch analysis to determine HLA Class II alleles exhibited by candidate bone marrow transplant donors and prospective recipients using previously published DNA-based typing techniques. Special attention was directed towards the technical aspects of procedures, the level of typing resolution and the speed of data analysis. 200 blood samples from volunteer bone marrow transplant donors typed serologically for HLA-DR and DQ were further investigated using three DNA-based typing methods: (i) restriction fragment length polymorphism (RFLP) analysis, (ii) polymerase chain reaction (PCR) amplification and subsequent hybridisation with sequence specific oligonucleotide probes (PCR-SSO), and (iii) PCR amplification with sequence specific primers (PCR-SSP) to resolve the DRB1* specificity of each individual. In general, the HLA-DR results obtained using PCR-SSO and PCR-SSP correlated well with each other. However, discordant results were obtained between PCR and RFLP based typing in 21 cases, especially in relation to DRB3* alleles associated with the DRB1 gene. These differences were due to three problems pertaining to RFLP analysis: i) alleles with identical DRB, DQA and DQB fragment sizes, ii) reliance on DQA and DQB results to assign the DRB genotype, and iii) a "new polymorphism" of DR7, in a DR7 homozygous, exhibiting a fragment similar in size to DR8. Our findings suggested a strategy requiring PCR-SSO analysis for initial low resolution class II typing involving large numbers of samples, while the use of PCR-SSP is reserved for small numbers of samples, for urgent samples or for situations where higher resolution is required. As the PCR-based methods are relatively quick, precise, simple and inexpensive, they have replaced RFLP analysis and become the routine approach for DR' typing in our laboratory.     

Unclassified serovars of Chlamydia trachomatis isolated from Japanese infants

Objective: To analyze antigenic and genetic variations of Chlamydia trachomatis among the serovars obtained from Japanese infants.
Methods: The polymerase chain reaction (PCR) was used to amplify a large part of the major outer-membrane protein gene, and restriction fragment length polymorphism (RFLP) was used to identify the serovars of C. trachomatis from nasopharyngeal and conjunctival swabs from Japanese infants and neonates.
Results: The typing of 10 nasopharyngeal isolates gave the following results: seven E, one H, and two unclassified serovars. The typing of seven conjunctival isolates gave the following results: five D, one F, and one unclassified serovar. Reactive patterns of these unclassified strains, determined by PCR-RFLP, to monoclonal antibodies were different from those of 15 reference serovars.
Conclusions: Characterization of unclassified variants will allow more detailed epidemiologic studies of perinatal C. trachomatis infections in Japan.     

Oligoclonal interspecific origin of ‘North Indian’ and ‘Chinese’ sugarcanes

Sugarcanes consist of several groups of complex polyploid forms. The origin of North Indian and Chinese sugarcanes (referred to as S. barberi and S. sinense) was investigated using genomic in-situ hybridization (GISH), detection of species-specific repeated sequences and RFLP. GISH proved their interspecific hybrid origin. Together with the distribution of species-specific repeated sequences and earlier RFLP data, the results show that both taxa are derived from interspecific hybridization between S. officinarum and S. spontaneum and that no other genus has been directly involved. RFLP indicates that the clones are clustered into a few groups, each derived from a single interspecific hybrid that has subsequently undergone a few somatic mutations. These groups correspond quite well with those already defined based on morphological characters and chromosome numbers. However, the calculated genetic similarities do not support the existence of two distinct taxa. The North Indian and Chinese sugarcanes represent a set of horticultural groups rather than established species.     

Analysis of HLA-DRB and -DQB gene RFLPs in DR7 homozygous cell lines: associations with Dw11, Dw17 and DB1

The DR7-associated Dw specificities, Dw11, Dw17 and DB1 were investigated with regard to DRB- and DQB-gene polymorphism, as revealed by RFLP analysis using the restriction enzyme TaqI. In the 22 DR7 homozygous cell lines investigated, each of these Dw specificities was found to correlate to one specific RFLP defined DR-DQ haplotype. In addition, a clear linkage disequilibrium to a specific HLA-B locus allele for each Dw specificity was noted, indicating that the Dw subtypes of DR7 often are associated with a conserved HLA-B-DR-DQ haplotype. Only one genetically homozygous cell line, PLH, deviated from these correlations. This cell line, notably derived from an individual with a deletion of the 21-hydroxylase B-gene (21-OHB), caries the HLA haplotype Bw47, DR7, DQw2, DB1, but displayed a DRB RFLP otherwise found in association with Dw17.     

Molecular epidemiology characterization of the urinary excretion of polyomavirus in healthy individuals from Portugal--a Southern European population

The human polyomaviruses--BKV and JCV--are members of Polyomaviridae family and after primary infections they persist as latent infection especially in the kidneys. BKV reactivation is mainly related to urinary tract diseases and JCV reactivation can induce the disease progressive multifocal leukoencephalopathy. The aim of our study was to characterize the excretion of polyomaviruses in urine samples of healthy individuals from a Portuguese population. We analyzed 498 DNA samples using PCR-RFLP, the sequence amplified consisted in 176 or 173 bp within the antigen T region. Our results indicate that 23.9% of the samples were positive for JCV, 1.8% positive for BKV and 74.3% of the individuals were negative for both viruses. We observed an increased prevalence of JCV shedding in male individuals in comparison to female (P = 0.026). Furthermore, the shedding of both polyomaviruses was influenced by the age of individuals with a significant increase in individuals with more than 56 years old (P = 0.005). Our results show that the shedding of polyomavirus in urine of healthy individuals is highly variable between genders, is influenced by age and differs from region to region. Further studies are needed to evaluate the prevalence of polyomaviruses in healthy individuals, in order to understand the biological behaviour of these viruses.     

The 1858T PTPN22 gene variant contributes to a genetic risk of type 1 diabetes in a Ukrainian population

The 1858T variant of the protein tyrosine phosphatase gene, PTPN22, is associated with an increased risk of several autoimmune diseases. The aim of this study has been to investigate the possible association of 1858C-->T PTPN22 polymorphism and type 1 diabetes (T1D) in Caucasians from Ukraine. Overall, the distribution of 1858 PTPN22 genotypes differed significantly between the T1D patient group (n = 296) and the control group (n = 242) (P = 0.0036). When both groups were classified according to sex, the TT genotype and T allele showed a statistically significant higher frequency in T1D female patients (5.9 and 22.8%, respectively) in comparison with the female controls (0 and 11.9%) (P = 0.008 for both analyses). The patients with the TT genotype were significantly younger at the onset of T1D compared with those with genotypes TC and CC (P = 0.035 and 0.019, respectively). In our Ukrainian Caucasian cohort, we confirmed the association between T1D and the PTPN22,1858T allele.     

Polymorphisms in the tumor necrosis factor (TNF) genes are associated with susceptibility to effects of ultraviolet-B radiation on induction of contact hypersensitivity

We investigated the allelic distributions of single nucleotide polymorphisms (SNPs) of the TNFA, TNFB and IKBL genes, 3 microsatellites within the tumor necrosis factor (TNF) region of HLA locus, and the HLA phenotypes as well as the TLR4 gene in Chromosome 9 in 26 healthy Caucasian volunteers. These individuals were also assessed as ultraviolet B (UVB)-susceptible (S) or UVB-resistant (R). Our results identified 12 UVB-S and 14 UVB-R individuals. Attempts to correlate particular HLA-A, -B, -C, and -DR antigens with the UVB phenotypes failed. Similarly, attempts to correlate SNP at the NcoI-RFLP within intron 1 of the TNFB, IKBL and TLR4 gene with UVB phenotypes also failed. However, microsatellite analyses of TNFa, TNFc, and TNFd markers revealed a significant increase in the frequencies of TNFa2 in UVB-S individuals (P=0.00032) and of TNFd3 in UVB-R individuals (P=0.012). Moreover, DNA sequencing analyses of 5 SNPs of the TNFA promoter region revealed a significant increase in the frequency of the allele B of the TNFA gene (TNFApB) representing the nucleotide A at position -863 and C at position -1031 (P=0.015). Since it is known that TNFa2 and TNFApB is a high TNF-alpha responder, whereas TNFd3 is a TNF-alpha low responder, we propose that the TNF region of HLA contains polymorphic genes that confer susceptibility and resistance to the deleterious effects of UVB radiation on the induction of contact hypersensitivity. This proposal is consistent with previous reports that a unique microsatellite region of the Tnfa gene in mice contains alleles that dictate the UVB-dependent phenotypes in mice, and implicate TNF-alpha as the primary mediator of the immune-damaging effects of UVB radiation.