Polymorphisms within the HLA-DRw6 haplotype. I. Restriction fragment length variation and its correlation with serology

The Dw6/DRw6 complex, one of the MHC class II specificities that can be defined by cellular techniques and by serology, probably has one or more immunoregulatory functions. To obtain information on the molecular structure of the DRw6 region, we studied several DRw6 homozygous cell lines, of which three were of consanguineous origin. DNA-DNA hybridization comprised the use of seven restriction enzymes in combination with three DR beta cDNA probes. The obtained results were compared with similar analyses of an HLA homozygous cell panel, expressing DR1-w8 specificities. This comparison indicated that in DRw6 homozygous individuals the coding potential for DR beta chains resembles closely that of all other DR specificities, thus identifying DRw6 as a regular DR region. In addition, we found a restriction fragment length pattern unique for DRw6, indicating the possibility to type for DRw6 by DNA-DNA hybridization. Comparisons within the DRw6 cell panel revealed the occurrence of several HLA class II DNA subtypes. These subdivisions partly correlated with serologically obtained reaction patterns. No correlation, however, could be observed between the different DNA subtypes and cellular reaction patterns as obtained by MLC and T cell cytotoxicity.     

A distinct HLA-DRw8 haplotype characterizes patients with juvenile rheumatoid arthritis

We studied the first domain of the HLA-DRB1, HLA-DQA1, and HLA-DQB1 loci of 67 HLA-DRw8-positive Caucasians including 43 with early-onset pauciarticular juvenile rheumatoid arthritis (EOPA-JRA, alternatively known as early-onset pauciarticular juvenile chronic arthritis). Serology, restriction fragment length polymorphism (RFLP), and polymerase chain reaction (PCR) oligotyping revealed that 62, including all the EOPA-JRA patients, carried the HLA-DRB1*0801, DQA1*0401, DQB1*0402 genotype. Approximately onefifth of the controls carried atypical HLA-DRB1, HLA-DQA1, and/or HLA-DQB1 loci on their HLA-DRw8 haplotype confirmed by family studies. DNA sequences of HLA-DRB1, DQA1, and DQB1 alleles in patients and controls were identical to those previously reported. Disease association studies in 113 EOPA-JRA patients and 207 controls unselected for HLA-DRw8 revealed that the HLA-DRB1*0801, DQA1*0401, DQB1*0402 genotype was associated with a higher relative risk (RR) for disease (RR = 12.8, ² = 48.8, P < 10^–4) than was the serologically defined presence of HLA-DRw8 (RR = 8, ² = 39, P < 10^–4). Further analysis suggested that the DQ genes on HLA-DRw8 haplotypes are as likely as the DR genes to contribute to the pathogenesis of EOPA-JRA. This study increases to five the number of HLA-DR/DQ haplotypes identified in HLA-DRw8 Caucasians.The nucleotide sequence data reported in this paper have been submitted to the GenBank nucleotide sequence database and have been assigned the accession number M34308.     

HLA-DRw6 and renal allograft rejection.

HLA-DRw6-positive patients are "high responders" to certain renal allograft antigens. A study was therefore conducted of the outcome of 247 first renal allografts in 74 DRw6-positive and 173 DRw6-negative recipients. The effectiveness of matching for HLA-DR determinants in both groups was also analysed. The one-year graft survival in DRw6-positive patients was 59% as compared with 75% in DRw6-negative recipients (p = 0.012). A striking difference between the two groups was that HLA-DR matching significantly improved renal allograft survival only in the DRw6-positive patients. In those patients the one-year survival of HLA-DR-identical grafts was 95% as compared with only 38% for 2-DR mismatched grafts (p = 0.009). In DRw6-negative patients only a slight beneficial effect of HLA-DR matching was observed (83% versus 72% at one year for the 0-DR and 2-DR mismatched grafts, respectively) (p greater than 0.05). These findings are clear evidence that DRw6-positive patients (about a quarter of the patients on the waiting list of Eurotransplant) should be given HLA-DR-identical kidney transplants only.     

Polymorphisms within the HLA-DR3 haplotypes

HLA-DR molecules were isolated from eight different HLA-DR3 homozygous B-cell lines by immunoprecipitation with monoclonal antibodies, and they were subsequently analyzed by two-dimensional gel electrophoresis. We found that HLA-DR3 homozygous B-cell lines of consanguineous origin express two types of HLA-DR molecules. One type of HLA-DR molecule was present in all the cell lines tested, whereas the second DR molecule appears to be polymorphic. DNA isolated from the different HLA-DR3 homozygous cell lines was studied by Southern blot analysis to determine whether any DR restriction fragment length polymorphism could be observed. Polymorphisms detected at both the product and genomic level have been compared to each other, and their relations to the serological (HLA-DR) and cellular (HLA-D and LB-Q1) typing data will be discussed.No reprints available     

Biochemistry of HLA-DRw6: evidence for seven distinct haplotypes

The DRw6 specificity, which has a frequency of 11% in the Caucasian population, cannot be positively defined, since no monospecific allo-antiserum is available. This particular status among DR specificities led us to study the DRw6 haplotypes at the molecular level. We performed 2D-PAGE analysis of HLA-DR molecules in 44 different DRw6 haplotypes. The data were obtained from six homozygous typing cells, eight families informative for the segregation of the DRw6 haplotype, and 15 unrelated donors. Five unique beta-chain electrophoretic patterns were detected, indicating the existence of five structurally distinct DRw6 beta-chains. Each haplotype expresses one or two beta-chains. The different combinations of the DR beta-chains present in a single haplotype allow to characterize seven unique DRw6 haplotypes. In contrast to what has been previously found for DR2 and DR4, there is no DR beta-chain common to all the DRw6 cells. Correlation of the biochemical data with the recent serologic (DRw13 vs DRw14) and cellular (Dw9, Dw18, Dw19) splits of the DRw6 specificity will be discussed.     

Mitochondrial genome haplotype hypervariation within the isopod parasitic nematode Thaumamermis cosgrovei

Characterization of mitochondrial genomes from individual Thaumamermis cosgrovei nematodes, obligate parasites of the isopod Armadillidium vulgare, revealed that numerous mtDNA haplotypes, ranging in size from 19 to 34 kb, are maintained in several spatially separated isopod populations. The magnitude and frequency of conspecific mtDNA size variation is unprecedented among all studied size-polymorphic metazoan mitochondrial genomes. To understand the molecular basis of this hypervariation, complete nucleotide sequences of two T. cosgrovei mtDNA haplotypes were determined. A hypervariable segment, residing between the atp6 and rrnL genes, contributes exclusively to T. cosgrovei mtDNA size variation. Within this region, mtDNA coding genes and putative nonfunctional sequences have accumulated substitutions and are duplicated and rearranged to varying extents. Hypervariation at this level has enabled a first insight into the life history of T. cosgrovei. In five A. vulgare hosts infected with multiple nematodes, four carried nematodes with identical mtDNA haplotypes, suggesting that hosts may become infected by ingesting a recently hatched egg clutch or become parasitized by individuals from the same brood prior to dispersal of siblings within the soil.     

Transgenic mice with -6A haplotype of the human angiotensinogen gene have increased blood pressure compared with -6G haplotype

Hypertension is a serious risk factor for cardiovascular disease, and the angiotensinogen (AGT) gene locus is associated with human essential hypertension. The human AGT (hAGT) gene has an A/G polymorphism at -6, and the -6A allele is associated with increased blood pressure. However, transgenic mice containing 1.2 kb of the promoter with -6A of the hAGT gene show neither increased plasma AGT level nor increased blood pressure compared with -6G. We have found that the hAGT gene has three additional SNPs (A/G at -1670, C/G at -1562, and T/G at -1561). Variants -1670A, -1562C, and -1561T almost always occur with -6A, and variants -1670G, -1562G, and -1561G almost always occur with -6G. Therefore, the hAGT gene may be subdivided into either -6A or -6G haplotypes. We show that these polymorphisms affect the binding of HNF-1α and glucocorticoid receptor to the promoter, and a reporter construct containing a 1.8-kb hAGT gene promoter with -6A haplotype has 4-fold increased glucocorticoid-induced promoter activity as compared with -6G haplotype. In order to understand the physiological significance of these haplotypes in an in vivo situation, we have generated double transgenic mice containing either the -6A or -6G haplotype of the hAGT gene and the human renin gene. Our ChIP assay shows that HNF-1α and glucocorticoid receptor have stronger affinity for the chromatin obtained from the liver of transgenic mice containing -6A haplotype. Our studies also show that transgenic mice containing -6A haplotype have increased plasma AGT level and increased blood pressure as compared with -6G haplotype. Our studies explain the molecular mechanism involved in association of the -6A allele of the hAGT gene with hypertension.     

Phylogeographic relationships within the Mediterranean turbot inferred by mitochondrial DNA haplotype variation

The Mediterranean turbot Psetta maxima consists of two main genetically distinct lineages (western Mediterranean and 'eastern secluded Mediterranean' basins) as investigated by mitochondrial DNA analysis. Within the latter lineage, most haplotypes from the Sea of Azov were endemic and more than half of them derived from a single ancestral haplotype shared among all the eastern Mediterranean areas. There was no relation between morphotype variation in bony tubercles and mitochondrial genealogy.     

Analysis of the HLA-DRw8 haplotype: Recognition by HTC typing of three distinct antigen complexes in Caucasians,Native Americans,and Orientals

We have used seven HLA-D homozygous typing cells (HTC) in a comparative study of the DRw8 antigen complex in three racial groups. Three distinct HLA-D specificities were recognized, each associated with HLA-DRw8. Four of the HTC defined a DRw8-associated HLA-D specificity designated 8.1, one defined a specificity designated 8.2, and two defined a specificity designated 8.3. Each of the three specificities showed an association with a distinct racial group: Dw"8.1" in Caucasians, Dw"8.2" in Pacific Northwest Indians, and Dw"8.3" in Orientals. An informative primed lymphocyte (PLT) cell generated against a Dw"8.1" haplotype was able to distinguish 8.1 from 8.2 and 8.3. Using selected anti-DRw8 sera, a serologic distinction between 8.1 and 8.3 could also be made. It was thus possible, by using both cellular and serologic techniques in a comparative population study, to recognize at least three HLA-D-defined splits of the DRw8 haplotype.     

Epigenetic patterns within the haplotype phased fig (Ficus carica L.) genome

Due to DNA heterozygosity and repeat content, assembly of non‐model plant genomes is challenging. Herein, we report a high‐quality genome reference of one of the oldest known domesticated species, fig (Ficus carica L.), using Pacific Biosciences single‐molecule, real‐time sequencing. The fig genome is ~333 Mbp in size, of which 80% has been anchored to 13 chromosomes. Genome‐wide analysis of N⁶‐methyladenine and N⁴‐methylcytosine revealed high methylation levels in both genes and transposable elements, and a prevalence of methylated over non‐methylated genes. Furthermore, the characterization of N⁶‐methyladenine sites led to the identification of ANHGA, a species‐specific motif, which is prevalent for both genes and transposable elements. Finally, exploiting the contiguity of the 13 pseudomolecules, we identified 13 putative centromeric regions. The high‐quality reference genome and the characterization of methylation profiles, provides an important resource for both fig breeding and for fundamental research into the relationship between epigenetic changes and phenotype, using fig as a model species.     

A putative disease-associated haplotype within the SCN1A gene in Dravet syndrome

Dravet syndrome (DS), previously known as severe myoclonic epilepsy of infancy, is one of the most severe forms of childhood epilepsy. DS is caused by a mutation in the neuronal voltage-gated sodium-channel alpha-subunit gene (SCN1A). However, 25–30% of patients with DS are negative for the SCN1A mutation screening, suggesting that other molecular mechanisms may account for these disorders. Recently, the first case of DS caused by a mutation in the neuronal voltage-gated sodium-channel beta-subunit gene (SCN1B) was also reported. In this report we aim to make the molecular analysis of the SCN1A and SCN1B genes in two Tunisian patients affected with DS. The SCN1A and SCN1B genes were tested for mutations by direct sequencing. No mutation was revealed in the SCN1A and SCN1B genes by sequencing analyses. On the other hand, 11 known single nucleotide polymorphisms were identified in the SCN1A gene and composed a putative disease-associated haplotype in patients with DS phenotype. One of the two patients with putative disease-associated haplotype in SCN1A had also one known single nucleotide polymorphism in the SCN1B gene. The sequencing analyses of the SCN1A gene revealed the presence of a putative disease-associated haplotype in two patients affected with Dravet syndrome.     

Polymorphisms of endothelial nitric oxide synthase gene in systolic heart failure: an haplotype analysis

BackgroundEndothelial nitric oxide synthase (eNOS) gene polymorphisms have been associated with the pathogenesis of cardiovascular diseases, but few studies have evaluated the role of eNOS haplotypes on the risk and prognosis of heart failure (HF). This prospective study was designed to analyze the impact of three eNOS polymorphisms (T-786C, VNTR4a/b and Glu298Asp) and their haplotypes on the susceptibility and clinical outcomes in HF outpatients with systolic dysfunction.Methods and resultsWe conducted a case-control and a cohort study in which 316 HF patients and 360 healthy controls were recruited from a tertiary care university hospital. DNA was extracted from peripheral blood and eNOS polymorphisms were detected by PCR or PCR-RFLP. Patients were predominantly men, had a mean left ventricular ejection fraction of 31% and were followed-up for a median of 41 months; there were 96 deaths, including 58 HF-related deaths. Genotype distribution of the eNOS T-786C, VNTR 4a/b and Glu298Asp was similar between HF patients and controls. Haplotype frequencies differed between HF patients and controls only in African–Brazilians (p = 0.043). African–Brazilian patients that carried the haplotype -786C/4b/Asp298 had a better prognosis than patients that carried other haplotypes (log rank p value = 0.016 for all-cause mortality). In a Cox proportional hazard model adjusted for clinical variables of risk, the -786C/4b/Asp298 haplotype remained as an independent genetic predictor of survival (adjusted HR = 0.11; 95% CI = 0.01–0.83; p = 0.03).ConclusionsThe -786C/4b/Asp298 eNOS haplotype had a significant impact on HF susceptibility and prognosis, particularly in African–Brazilian patients.     

Quantitative Analysis of Single Nucleotide Polymorphisms within Copy Number Variation

Background

Single nucleotide polymorphisms (SNPs) have been used extensively in genetics and epidemiology studies. Traditionally, SNPs that did not pass the Hardy-Weinberg equilibrium (HWE) test were excluded from these analyses. Many investigators have addressed possible causes for departure from HWE, including genotyping errors, population admixture and segmental duplication. Recent large-scale surveys have revealed abundant structural variations in the human genome, including copy number variations (CNVs). This suggests that a significant number of SNPs must be within these regions, which may cause deviation from HWE.

Results

We performed a Bayesian analysis on the potential effect of copy number variation, segmental duplication and genotyping errors on the behavior of SNPs. Our results suggest that copy number variation is a major factor of HWE violation for SNPs with a small minor allele frequency, when the sample size is large and the genotyping error rate is 0∼1%.

Conclusions

Our study provides the posterior probability that a SNP falls in a CNV or a segmental duplication, given the observed allele frequency of the SNP, sample size and the significance level of HWE testing.     

H-2 typing of mutants of thet 6 haplotype in the mouse

Mutantt haplotypes derived from thet ⁶ haplotype were typed forH-2. The mutantt ^h2 that arose fromt ⁶ due to crossing over in the region betweenT andtf had, as expected, lost theH-2 haplotype characteristic oft ⁶. The haplotypest ^h17,t ^h18, andt ^p1, which also arose by recombination, but which represent the complementary crossover products, including the distal part of thet ⁶ haplotype, carried the sameH-2 type ast ⁶. This suggests that crossing over betweentf andH-2 is suppressed int ^h17 andt ¹⁸. This in turn suggests that mutantt haplotypes suppress crossing over for that part of thet chromatin that they still retain.The origin oft ^h7, which apparently did not include any crossover distal toT, and which retains the crossover-suppressing property oft ⁶, retains thet ⁶ H-2 type. Unexpectedly, J ^h20 , which expressestf and was at first thought to have arisen due to crossing over, also retains theH-2 type oft ⁶. This provides part of the evidence thatt ^h20 arises fromt ⁶ not by crossing over, but by a small deletion, and hence that duplication and deletion are possible modes of origin of mutantt haplotypes.Abbreviations used in this paper are t haplotype mutant haplotype of the chromosome 17, often designated J allele - T Brachyury mutant - T/+ short-tailed mouse - T/T lethal during embryogenesis - T-int T interaction (characteristic oft haplotypes that interact in heterozygotes withT to produce a tailless mouse) - tf locus homozygotes showing waves of hair loss - Kb knobby, which produces a knobbly tailed heterozygote, homozygous lethal - titer reciprocal of serum dilution giving 50% kill     

Conserved haplotype blocks within the sheep MHC and low SNP heterozygosity in the Class IIa subregion

This report describes single-nucleotide polymorphisms (SNPs) in the sheep major histocompatibility complex (MHC) class II and class III regions and provides insights into the internal structure of this important genomic complex. MHC haplotypes were deduced from sheep family trios based on genotypes from 20 novel SNPs representative of the class II region and 10 previously described SNPs spanning the class III region. All 30 SNPs exhibited Hardy-Weinberg proportions in the sheep population studied. Recombination within an extended sire haplotype was observed within the class II region for 4 of 20 sheep chromosomes, thereby supporting the presence of separated IIa and IIb subregions similar to those present in cattle. SNP heterozygosity varied across the class II and III regions. One segment of the class IIa subregion manifested very low heterozygosity for several SNPs spanning approximately 120 Kbp. This feature corresponds to a subregion within the human MHC class II region previously described as a 'SNP desert' because of its paucity of SNPs. Linkage disequilibrium (LD) was reduced at the junction separating the putative class IIb and IIa subregions and also between the class IIa and the class III subregions. The latter observation is consistent with either an unmapped physical separation at this location or more likely a boundary characterized by more frequent recombination between two conserved subregions, each manifesting high within-block LD. These results identify internal blocks of loci in the sheep MHC, within which recombination is relatively rare.