New Single Nucleotide Polymorphism (new + single_nucleotide_polymorphism)

Distribution by Scientific Domains

Selected Abstracts

Polymorphism in the promoter region of the gene encoding human allograft inflammatory factor-1

D. M. Turner
Summary We have identified a new single nucleotide polymorphism within the promoter region of the human allograft inflammatory factor (AIF-1) gene. The polymorphism, defined by Genbank accession number AF097515, was characterized as a C/T single base pair substitution at position ,932. The T allele is associated with both HLA-DR2 and HLA-B7. Also, this allele creates the consensus binding site for the E-box that has high affinity for the basic helix-loop-helix (bHLH) family of transcription factors. [source]

Characterization of single nucleotide polymorphism markers for the green sea turtle (Chelonia mydas)

Abstract We present data on 29 new single nucleotide polymorphism assays for the green sea turtle, Chelonia mydas. DNA extracts from 39 green turtles were used for two methods of single nucleotide polymorphism discovery. The first approach employed an amplified fragment length polymorphism technique. The second technique screened a microsatellite library. Allele-specific amplification assays were developed for high-throughput single nucleotide polymorphism genotyping and tested on two Pacific C. mydas nesting populations. Observed heterozygosities ranged from 0 to 0.95 for a Hawaiian population and from 0 to 0.85 for a Galapagos population. Each of the populations had one locus out of Hardy,Weinberg equilibrium, SSCM2b and SSCM5 for Hawaii and Galapagos, respectively. No loci showed significant genotypic linkage disequilibrium across an expanded set of four Pacific nesting populations. However, two loci, SSCM4 and SSCM10b showed linkage disequilibrium across three populations indicating possible association. [source]

Single nucleotide polymorphisms in succinate dehydrogenase subunits and citrate synthase genes: association results for impaired spermatogenesis

Sandra Bonache
Abstract Evaluation of the possible implication of the SDHA, SDHB, SDHC, SDHD and CS genes in non-obstructive male infertility was performed on the basis that sperm concentration in the ejaculate has been previously correlated with nuclear-encoded mitochondrial enzyme activities (the four subunits of succinate dehydrogenase/complex II of the respiratory chain and citrate synthase). We performed an exhaustive analysis of the five genes for the presence of sequence variants that could be associated with impairment of sperm production. blastn searches in the genomic sequence NCBI database evidenced the presence of highly homologous sequences elsewhere on the genome that can interfere with polymerase chain reaction experiments. Therefore, a careful design of the analytical strategy to search for sequence variants was performed. In this report, we provide primer sequences that allowed selective amplification of coding and immediate flanking regions of the five genes. Fifty-five sequence variations in the five genes were identified in infertile and normozoospermic fertile individuals as controls and only one of them (SDHA c.456+32G>A) showed significant genotype association with impairment of sperm production. Moreover, new single nucleotide polymorphisms identified should be useful in future association studies for other human diseases related to nuclear-encoded genes, leading to mitochondrial respiratory chain activity impairment revealing the physiological role of these genes. [source]

Genotypes of varicella-zoster virus wild-type strains in Germany

A. Sauerbrei
Abstract Surveillance of varicella-zoster virus (VZV) genotypes is indicated in Germany after implementation of universal varicella vaccination. This article reports genotyping data of 77 VZV strains obtained from 54 patients with varicella, 1 newborn with congenital varicella syndrome, 2 fetuses with intrauterine VZV infection and 20 cases with zoster. Fragments of the open reading frames (ORF) 1, 21, 22, 37, 50, 54, and 60 were analyzed by sequencing. In addition, the PstI polymorphism of the ORF 38 was characterized. Thirty strains, 22 from varicella and 8 from zoster, had the genetic markers of genotype E2, 2 of them carried new single nucleotide polymorphisms (SNP). Twenty-nine VZV isolates, 17 from varicella, and 12 from zoster, could be analyzed as E1 strains, 6 of them as E1 variants containing individual SNPs. Finally, 17 strains taken from primary VZV infection were classified as genotype M1, 13 of which belonged to the M1 subtype 1, 3 to the M1 subtype 2, and 1 to the M1 subtype 3. One strain was regarded as potential E2/J recombinant. In conclusion, VZV genotypes E2, E1, and M1 can be found in nearly equal incidence in varicella in Germany. The most frequent group is attributed to the genotype E2. Genotype M1 strains can only be detected after primary VZV infection and not in zoster cases. The possible recombinant could not be classified definitely by the scattered SNP method used and, therefore, has to be confirmed by full-genome sequencing studies. J. Med. Virol. 80:1123,1130, 2008. 2008 Wiley-Liss, Inc. [source]