The interleukin-10-1082 G/A polymorphism: allele frequency in different populations and functional significance.

Genotypic variation in the human interleukin-10 (IL-10) promoter may account for marked inter-individual variation in IL-10 production and may influence susceptibility to autoimmune diseases. The G/A polymorphism at position -1082 has been linked to high/low IL-10 producer status. We directly tested the functional significance of this polymorphism using DNA-binding assays and reporter gene assays, examined allele frequencies in two geographically distinct populations and assessed intra- and inter-individual variation in IL-10 production in vitro according to genotype. Functional analyses showed that the -1082 region contains a putative ETS-like transcription factor-binding site, and nuclear factors from a monocyte cell line bind to this region. Transient transfection studies in an Epstein-Barr virus-transformed B cell line indicated that the -1082 A allele confers a two fold increase in transcriptional activity of the IL-10 promoter compared to the G allele. There was marked inter-individual variation in IL-10 production by peripheral blood mononuclear cells in vitro, with no consistent effect of genotype.

Carotenoid discrimination by the avian embryo: a lesson from wild birds.

The concentrations (microg/g wet yolk) of total carotenoids in eggs of the common moorhen (Gallinula chloropus), American coot (Fulica americana) and lesser black-backed gull (Larus fuscus), collected in the wild, were 47.5, 131.0 and 71.6, respectively. In contrast to data for eggs of the domestic chicken, beta-carotene was a significant component in the yolks of these three wild species, forming 25-29% by wt. of the total carotenoids present. The concentration of total carotenoids in the livers of the newly-hatched chicks was 5-10 times higher than in the other tissues and beta-carotene was again a major component, forming 37-58% of the hepatic carotenoids. In the newly-hatched gull, the proportions of both lutein and zeaxanthin were very low in the liver but high in the heart and muscle when compared with the yolk. By contrast canthaxanthin, echinenone and beta-carotene were very minor constituents of heart and muscle when compared with their proportions in the yolk of the gull. The proportions of lutein and zeaxanthin in the liver of the newly-hatched coot and moorhen were also far lower than in the yolk whereas the liver was relatively enriched with beta-cryptoxanthin, beta-carotene and (in the moorhen) echinenone. The results indicate that avian embryos discriminate between different carotenoids during their distribution from the yolk to the various tissues.

Determination of cytokine regulatory haplotypes by induced heteroduplex analysis of DNA.

Multiple single nucleotide polymorphisms (SNP) in the promoter region of the human interleukin-10 (IL-10) gene and in the signal/leader sequence of the human transforming growth factor beta 1 (TGF-beta1) gene, have been associated with susceptibility, severity and clinical outcome for a number of diseases. One common explanation for this, is that different haplotypes of these SNPs regulate the expression of the respective cytokines. Therefore, accurate determination of haplotypes by physical linkage analysis represents an important tool in investigating the pathogenesis of such diseases. Here, we demonstrate that the use of induced heteroduplex generators (IHGs) may be used to identify haplotypes within target sequences in the IL-10 and TGF-beta1 genes. Four haplotypes were observed within the IL-10 promoter region, consisting of -1082, -851, -819 and -592 SNPs. For the TGF-beta1 signal/leader sequence, we observed three haplotypes of the T869C (Leu10Pro) and G915C (Arg25Pro) SNPs. In both cases, all combinations of these haplotypes could be resolved unequivocally with a single IHG reagent.

Identification of human TGF-beta1 signal (leader) sequence polymorphisms by PCR-RFLP.

Links between disease susceptibility and genetically determined variation in human cytokine expression have recently been described. This has led to a demand for simple methods of identifying cytokine gene polymorphisms of potential clinical relevance. Here, we describe a polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) method for identifying two human transforming growth factor beta1 (TGF-beta1) signal (leader) sequence polymorphisms, T869C (Leu10Pro) and G915C (Arg25Pro). This permits simple and robust identification of TGF-beta1 leader sequence genotypes and demonstrates the physical linkage in cis between T869C (Leu10Pro) and G915C (Arg25Pro). The method does not require previously genotyped standards. The efficacy of enzyme digestion is internally controlled by the presence of conserved restriction sites.

A novel polymorphism in the human interleukin-13 (IL-13) promoter.

Using PCR-SSCP and automated nucleotide sequencing we have identified a novel single nucleotide C --> T polymorphism in the human IL-13 promoter, at position -1055 relative to the transcription start site. Allele frequency analysis in a population of normal cord blood donors indicated frequencies of 0.833 (C) and 0. 167 (T).

Induced heteroduplex genotyping of TNF-alpha, IL-1beta, IL-6 and IL-10 polymorphisms associated with transcriptional regulation.

We describe the construction and use of 7 induced heteroduplex generators, reagents for the rapid and unequivocal genotyping of nucleotide sequence polymorphism in TNF-alpha, IL-1beta, IL-6 and IL-10. Polymorphisms detected are those previously associated with regulation of gene transcription: TNF-alpha positions -308 and -238; IL-1beta position +3953; IL-6 position -174; and IL-10 positions -1082, -819 and -592. The reagents were used for analysis of allele and haplotype frequencies in a population of healthy Caucasian volunteer blood donors.

Sequence variation at the phenylalanine hydroxylase gene in the British Isles.

Using mutation and haplotype analysis, we have examined the phenylalanine hydroxylase gene in the phenylketonuria populations of four geographical areas of the British Isles: the west of Scotland, southern Wales, and southwestern and southeastern England. The enormous genetic diversity of this locus within the British Isles is demonstrated in the large number of different mutations characterized and in the variety of genetic backgrounds on which individual mutations are found. Allele frequencies of the more common mutations exhibited significant nonrandom distribution in a north/south differentiation. Differences between the west of Scotland and southwestern England may be related to different events in the recent and past histories of their respective populations. Similarities between southern Wales and southeastern England are likely to reflect the heterogeneity that is seen in and around two large capital cities. Finally, comparison with more recently colonized areas of the world corroborates the genealogical origin by range expansion of several mutations.

Genetic diagnosis of factor V Leiden using heteroduplex technology.

A new genetic test has been developed for detection of the mutation known as factor V Leiden. The test employs heteroduplex technology and comprises a single PCR reaction followed immediately by PCR product analysis. It therefore represents the minimum practical route from blood/tissue sample to genetic result. A cohort of 100 patients with a history of thrombosis have been screened using both the new heteroduplex test and a previously described PCR-restriction endonuclease test. Results gave 100% correlation: normals 75 (75%), heterozygotes 24 (24%) and homozygotes 1 (1%). The heteroduplex test has been shown to give straightforward diagnosis in three different analytical systems: standard polyacrylamide gel electrophoresis (PAGE), mini-gel PAGE and capillary electrophoresis. The latter system is semiautomated, therefore rapid through-put of large sample numbers is now possible.

A rapid HLA-DRB1*04 subtyping method using PCR and DNA heteroduplex generators.

We describe here a rapid polymerase chain reaction (PCR)-based method for the identification of HLA-DRB1*0401-*0412 alleles. The method is based on the generation of specific DNA heteroduplex patterns between PCR products derived from selective group-specific amplification of the various DRB1*04 alleles and PCR products derived from two synthetic DNA heteroduplex generator (DHG) molecules following non-denaturing polyacrylamide minigel electrophoresis. One DHG was designed to detect DRB1*0401, *0405, *0407, *0408, and *0409 alleles, whilst the other was designed to detect DRB1*0402, *0403, *0404, *0406, *0410, *0411, and *0412 alleles. Characteristic heteroduplex patterns were obtained for all DRB1*04 alleles tested both in homozygous and heterozygous situations. Both DHG and PCR-SSP (sequence-specific primer) typing were performed on 41 DRB1*04 positive DNAs from Singaporean Chinese blood donors and complete concordance in results was obtained. HLA-DRB1*0403, *0405, and *0406 were found to account for 95% of the DRB1*04 alleles in the population studied. The DHG technique described is technically simple and rapid since it essentially involves only two PCR amplifications per individual subtyping. The technique is particularly useful for resolving DRB1*04 combinations which are indistinguishable by PCR-SSO (sequence-specific oligonucleotide) or PCR-SSP subtyping.

Discordant phenylketonuria phenotypes in one family: the relationship between genotype and clinical outcome is a function of multiple effects.

Four members spanning three generations of one family have phenylketonuria of varying degrees of severity. Two first cousins were screened in the neonatal period and have had dietary phenylalanine restriction since diagnosis, the older patient having been classified as having more severe PKU and the younger one as having mild PKU. Their mutual grandfather and his older brother also have a significant hyperphenylalaninaemia and are of normal intelligence despite never having had restricted phenylalanine intake. Mutation analysis of the phenylalanine hydroxylase (PAH) gene has established that there are four different mutations, two in exon 2 (F39L and L48S) and two in exon 3 (R111X and S67P), which give rise to PKU in this family. In order to establish their relative severity, we screened the PKU populations of western Scotland and the south west of England for these mutations. The exon 3 mutations are rare; however, F39L is relatively common in Scotland and L48S in England. A comparison of diagnostic blood phenylalanine concentrations in subjects carrying L48S/null or F39L/null mutations with those carrying two null mutations suggest that these exon 2 mutations are less deleterious. Thus, in this family, the different biochemical phenotypes can be explained, in part, by different genotypes at the PAH locus but our results show that the relationship between genotype and clinical outcome is more complex and is a function of multiple effects.

Detection of beta-thalassaemia mutations using DNA heteroduplex generator molecules.

In this report we describe a rapid polymerase chain reaction (PCR) based method for the detection of beta-thalassaemia (beta-thal) mutations. This method is based on the visualization of unique DNA heteroduplex banding patterns, following non-denaturing polyacrylamide gel electrophoresis, resulting from hybridization between mutant PCR products and synthetic DNA heteroduplex generator molecules. Using the Singaporean population, which consists of Chinese, Malay and Asian Indian ethnic groups, as a model, we have constructed and evaluated three DNA heteroduplex generator molecules for the detection of the common beta-thalassaemia mutations found in this population. The results show that these three molecules are capable of detecting approximately 95% of the mutations found in the Singaporean population. We propose that this technology may be applied as an alternative screening strategy for beta-thalassaemia mutations because it is technically simple, flexible, cost-effective, and requires only minimal laboratory resources.

HLA-DRB1*01 subtyping by heteroduplex analysis.

In this report we describe an alternative method for the identification of the four known HLA-DRB1*01 alleles, which is based on the generation of unique heteroduplex patterns between the different DRB*01 alleles and a synthetic DNA heteroduplex generator (DHG) molecule. The method is technically simple, rapid and cost-effective, as it essentially involves only a single polymerase chain reaction (PCR) followed by polyacrylamide gel electrophoresis. This technique allows the rapid discrimination of the various known HLA-DRB1*01 subtypes, both in homozygous and heterozygous situations. We propose that this technology can potentially be applied to most HLA class I and class II subtyping.

Mutation analysis of the phenylalanine hydroxylase gene using heteroduplex analysis with synthetic DNA constructs.

Using heteroduplex analysis generated with synthetic PCR-amplifiable DNA we have screened the PKU populations of southwest England and Wales, western Scotland, and southeast and central England for mutations in exons 3, 7 and 12 of the phenylalanine hydroxylase (PAH) gene. The technique characterized three mutations in exon 12, two in exon 3 and five in exon 7. Altogether over 370 PKU chromosomes were screened. In all geographical regions exon 12 mutations (R408W, IVS12nt1g- > a and Y414C) accounted for about 40% of mutant chromosomes. Exon 3 mutations (principally I65T) were found on between 9 and 12% of mutant alleles and exon 7 mutations accounted for a further 5-7%. Heteroduplex analysis is rapid, simple and safe and three constructs covering three exons can identify between 55 and 60% of mutations in various PKU populations of the UK.

HLA-DR/Dw matching by PCR fingerprinting: the origin of PCR fingerprints and further applications.

Polymerase chain reaction (PCR) fingerprinting, a new method for the rapid matching of HLA-Dr/Dw allotypes, involves the visual comparison of polymorphic HLA-DRB gene second exon PCR products, resolved in non-denaturing polyacrylamide gels (Bidwell & Hui, 1990). We show here that the satellite DNA bands within PCR fingerprints originate by heteroduplex formation between heterologous DNAs co-amplified by a common PCR primer set. We also present two further applications of the technique which permit discrimination between unrelated HLA-DR/Dw allotypes with similar PCR fingerprints.