P2RX7 genotype association in severe sepsis identified by a novel Multi-Individual Array for rapid screening and replication of risk SNPs.

BACKGROUND: Functional single nucleotide polymorphisms (SNPs) are relevant to individual therapeutic approaches and may play a role in disease susceptibility. Genome-wide scans, which are now widely applied to detect disease-associated SNPs, provide only limited evidence about SNP associations. Their usefulness as disease markers requires appropriate phenotype analysis and retesting of the gene providing SNP information. Larger data sets of thousands of samples are necessary to confirm the suggested SNPs. METHODS: We applied a newly established microarray-based technology that significantly accelerates and simplifies such studies. A tailor-made microarray surface chemistry, sample/probe immobilization and a primer extension reaction are central to the multi-individual array (MIA) platform, which simultaneously identifies the same variable nucleotide in thousands of samples. The set of SNPs to be typed for is highly flexible and can be adapted to the demands of defined clinical questions. RESULTS: A MIA-SNP analysis of functional SNPs in the P2RX7 calcium channel is presented. One risk genotype has been verified by functional analysis using patch clamping. Two clinically relevant genotypes composed of 5 functional SNPs in the P2RX7 gene have been identified in patients with severe sepsis and septic shock, whereas no significant association has been found in patient suffering from hemophagocytic syndromes. CONCLUSIONS: These results support a functional SNP genotyping of the P2RX7 gene in patients at risk of severe sepsis following surgical trauma.

Allelic variation at a hypervariable compound microsatellite locus in the ascomycete Ascochyta rabiei.

The genome of the fungal chickpea pathogen Ascochyta rabiei was screened for polymorphisms by microsatellite-primed PCR. While ethidium-bromide staining of electrophoretically separated amplification products showed only limited polymorphism among 24 Tunisian A. rabiei isolates, Southern hybridization of purified PCR fragments to restriction digests of fungal DNA revealed polymorphic DNA fingerprints. One particular probe that gave rise to a hypervariable single-locus hybridization signal was cloned from the Syrian isolate AA6 and sequenced. It contained a large compound microsatellite harbouring the penta- and decameric repeat units (CATTT)n, (CATTA)n, (CATATC-ATTT)n and (TATTT)n. We call this locus ArMS1 (Ascochyta rabiei microsatellite 1). Unique flanking sequences were used to design primer pairs for locus-specific microsatellite amplification and direct sequencing of additional ArMS1 alleles from Tunisian and Pakistani isolates. A high level of sequence variation was observed, suggesting that multiple mutational mechanisms have contribute to polymorphism. Hybridization and PCR analyses were performed on the parents and 62 monoascosporic F1 progeny derived from a cross between two different mating types of the fungus. Progeny alleles could be traced back to the parents, with one notable exception, where a longer than expected fragment was observed. Direct sequencing of this new length allele revealed an alteration in the copy number of the TATTT repeat [(TATTT)53 to (TATTT)65], while the remainder of the sequence was unchanged.

Oligonucleotide fingerprinting detects genetic diversity among Ascochyta rabiei isolates from a single chickpea field in Tunisia.

Fifty isolates of Ascochyta rabiei (Pass.) Labr. were hierarchically sampled from four well-separated locations of a single chickpea field in Beja (Tunisia), and single-spored. DNA was isolated from in-vitro-grown mycelia, digested with HinfI or RsaI, and hybridized to a set of synthetic oligonucleotides complementary to simple repetitive sequences. According to the fingerprint patterns derived from the probes (CA)8, (CAA)5, (CAT)5 and (GATA)4, 12 different fungal haplotypes were found at various frequencies within the investigated field. Seven haplotypes were confined to one location only, four occurred at two, one at three, and none at all four locations. Most of the genetic variability originated from diversity within, rather than between, locations. In some cases, more than one haplotype was isolated from the same lesion of a single host plant. Genetic distances between isolates, as calculated from band-sharing data, varied between 0.05 and 0.22. Relatedness between the different haplotypes was evaluated by cluster analysis using UPGMA.