Absence Of Single Nucleotide Polymorphisms Research Articles

Combination Therapy for Mycoplasma genitalium, and New Insights Into the Utility of parC Mutant Detection to Improve Cure.

Mycoplasma genitalium (MG) infection is challenging to cure because of rising antimicrobial resistance and limited treatment options. This was a prospective evaluation of the efficacy and tolerability of resistance-guided combination antimicrobial therapy for MG treatment at Melbourne Sexual Health Centre (August 2019-December 2020). All patients received 7 days of doxycycline before combination therapy based on the macrolide-resistant profile. Macrolide-susceptible infections received combination doxycycline + azithromycin (1g, day 1; 500mg, days 2-4) and macrolide-resistant infections combination doxycycline + moxifloxacin (400mg daily for 7 days). Adherence and adverse effects were recorded at test-of-cure, recommended 14-28 days after antimicrobial completion. Sequencing was performed to determine the prevalence of single nucleotide polymorphisms (SNPs) in the parC gene and their association with moxifloxacin treatment outcomes in macrolide-resistant infections. Of 100 patients with macrolide-susceptible MG treated with doxycycline + azithromycin, 93 were cured (93.0%; 95% confidence interval [CI], 86.1-97.1). Of 247 patients with macrolide-resistant MG receiving doxycycline + moxifloxacin, 210 were cured (85.0%; 95% CI, 80.0-89.2). parC sequencing was available for 164 (66%) macrolide-resistant infections; 29% had SNPs at parC S83 or D87 (23% S83I). The absence of SNPs at parC S83/D87 was associated with 98.3% cure (95% CI, 93.9-99.8) following doxycycline + moxifloxacin. The presence of the parC S83I-SNP was associated with failure in 62.5% (95% CI, 45.8-77.3). Side effects were common (40%-46%) and predominantly mild and gastrointestinal. Combination doxycycline + azithromycin achieved high cure for macrolide-susceptible infections. However, in the context of a high prevalence of the parC S83I mutation (23%) in macrolide-resistant infections, doxycycline + moxifloxacin cured only 85%. Infections that were wild-type for S83/D87 experienced high cure following doxycycline + moxifloxacin, supporting the use of a parC-resistance/susceptibility testing strategy in clinical care.

Absence of single nucleotide polymorphisms (SNPs) in the open reading frame (ORF) of the prion protein gene (PRNP) in a large sampling of various chicken breeds

BackgroundPrion diseases are zoonotic diseases with a broad infection spectrum among mammalian hosts and are caused by the misfolded prion protein (PrPSc) derived from the normal prion protein (PrPC), which encodes the prion protein gene (PRNP). Currently, although several prion disease-resistant animals have been reported, a high dose of prion agent inoculation triggers prion disease infection in these disease-resistant animals. However, in chickens, natural prion disease-infected cases have not been reported, and experimental challenges with prion agents have failed to cause infection. Unlike other prion disease-resistant animals, chickens have shown perfect resistance to prion disease thus far. Thus, investigation of the chicken PRNP gene could improve for understanding the mechanism of perfect prion-disease resistance. Here, we investigated the genetic characteristics of the open reading frame (ORF) of the chicken PRNP gene in a large sampling of various chicken breeds.ResultsWe found only tandem repeat deletion polymorphisms of the chicken PRNP ORF in the 4 chicken breeds including 106 Dekalb White, 100 Ross, 98 Ogolgye and 100 Korean native chickens. In addition, the distribution of chicken insertion/deletion polymorphisms was significantly different among the 4 chicken breeds. Finally, we found significant differences in the number of PRNP SNPs between prion disease-susceptible species and prion disease-resistant species. Notably, chickens lack SNPs in the ORF of the prion protein.ConclusionIn this study, we found that the absence of SNPs in the chicken PRNP ORF is a notable feature of animals with perfect resistant to prion disease.

O034 Whole genome sequencing to predictNeisseria gonorrhoeaeantibiotic susceptibility: toward tailored antimicrobial therapy

Background/introduction Absence of genotypic resistance-associated markers in Neisseria gonorrhoeae (NG) may predict antibiotic phenotypic susceptibility (APS). NG Whole genome sequencing (NG-WGS) on nucleic acid amplification test (NAAT) positive samples may allow for the avoidance and preservation of first line treatments such as ceftriaxone. However, NG-WGS predictive accuracy for APS should first be established. Aim(s)/objectives To evaluate NG-WGS “wild-type” predictive value for tetracycline, ciprofloxacin and azithromycin APS. Methods NG-WGS was performed on prospectively collected NG isolates from a London clinic in 2013, using Illumina MiSeq. Presence of 31 known single nucleotide polymorphisms (SNPs) and other resistance markers for tetracycline, ciprofloxacin, and azithromycin, were compared against a wild-type reference NG strain (FA1090). Results Of 57 samples, APS to tetracycline, ciprofloxacin, and azithromycin was 14%, 72% and 87% respectively. Genotypic susceptibility ( GeSu ) was defined as absence of SNPs and other resistance-associated markers. For tetracyclines, ciprofloxacin and azithromycin, GeSu-Tet , GeSu-Cip and GeSu-Azi , accurately predicted APS in 7/8 (87.5%; 95% CI 52.9%–97.8%), 40/41 (97.6%; 95% CI 87.4%–99.6%) and 25/25 (100%; 95% CI 86.7%–100%) respectively. One phenotypically resistant GeSu-Tet isolate had “Intermediate” resistance. Of seven isolates, both genotypically and phenotypically susceptible to tetracyclines, all were also susceptible to ciprofloxacin, 24/25 isolates susceptible to azithromycin were also susceptible to ciprofloxacin. Discussion/conclusion NG-WGS accurately predicted ciprofloxacin and azithromycin but not tetracycline APS. If validated on NG NAAT positive samples, this may allow for new precision ceftriaxone-sparing or ceftriaxone-adjunctive treatment combinations, for a substantial proportion of patients.

Direct to Consumer Genetic Testing: Uncertain Benefit

Dr Hamid has disclosed no financial relationship relevant to this commentary. This commentary does not contain a discussion of an unapproved/investigative use of a commercial product/device. Direct-to-consumer (DTC) genetic tests, sold directly to the public without input from a health care provider, typically scan the DNA of an individual to determine the presence or absence of single nucleotide polymorphisms (SNP). DTC companies claim that testing will allow consumers to make more informed health care decisions and better lifestyle choices. Consumers have shown considerable interest in knowing genetic risk information …

An analysis of sequence variability in eight genes putatively involved in drought response in sunflower (Helianthus annuus L.)

With the aim to study variability in genes involved in ecological adaptations, we have analysed sequence polymorphisms of eight unique genes putatively involved in drought response by isolation and analysis of allelic sequences in eight inbred lines of sunflower of different origin and phenotypic characters and showing different drought response in terms of leaf relative water content (RWC). First, gene sequences were amplified by PCR on genomic DNA from a highly inbred line and their products were directly sequenced. In the absence of single nucleotide polymorphisms, the gene was considered as unique. Then, the same PCR reaction was performed on genomic DNAs of eight inbred lines to isolate allelic variants to be compared. The eight selected genes encode a dehydrin, a heat shock protein, a non-specific lipid transfer protein, a z-carotene desaturase, a drought-responsive-element-binding protein, a NAC-domain transcription regulator, an auxin-binding protein, and an ABA responsive-C5 protein. Nucleotide diversity per synonymous and non-synonymous sites was calculated for each gene sequence. The π (a)/π (s) ratio range was usually very low, indicating strong purifying selection, though with locus-to-locus differences. As far as non-coding regions, the intron showed a larger variability than the other regions only in the case of the dehydrin gene. In the other genes tested, in which one or more introns occur, variability in the introns was similar or even lower than in the other regions. On the contrary, 3'-UTRs were usually more variable than the coding regions. Linkage disequilibrium in the selected genes decayed on average within 1,000bp, with large variation among genes. A pairwise comparison between genetic distances calculated on the eight genes and the difference in RWC showed a significant correlation in the first phases of drought stress. The results are discussed in relation to the function of analysed genes, i.e. involved in gene regulation and signal transduction, or encoding enzymes and defence proteins.

The Estimation of GC Repeats in Promoter P1 of IGF-1 Gene and Their Influence on IGF-1 Plasma Levels in Stable Angina Patients

Increased plasma levels of insulin-like growth factor 1 (IGF-1) are observed in advanced arteriosclerosis, but the reasons for these elevated levels remain unknown. One possibility to explain them is variation in the sequences that control IGF-1 gene expression. The goal of this study was to determine the effect of molecular variants of the IGF-1 P1 promoter on IGF-1 serum levels and to determine the impact of IGF-1 levels on the severity of coronary atherosclerosis. Methods: Blood samples were collected from 101 consecutive patients undergoing routine angiography. Genomic DNA was isolated from the nucleated cells of the blood plasma as described (2). Based on the presence of conformational differences in the DNA strand and on the absence of single nucleotide polymorphisms, the DNA from 38 patients was further analyzed by the “allelic ladder” method to determine the number of repeated GC dinucleotides in the P1 promoter of the IGF-1 gene. In addition, we analyzed serum growth hormone levels in order to examine the effect on systemic IGF-1 synthesis. Results: Conformational differences in the P1 promoter of the IGF-1 gene were observed in 38 out of the 101 patients. Several genotypes, depending on the number of GC repeats, were observed (11/19,17/19,18/19,18/21,19/19,19/20,19/21). Interestingly, a family history of coronary artery disease was seen less often among individuals heterozygous for the GC repeats. A lower IGF-1 levels were seen in non-variant carriers (homozygous genotypes for 19 or 21 repeats of GC, or heterozygous genotype 19/21) when compared to the variant group (other heterozygous genotypes then 19/21) (181.6 ± 47.9 ng/mL vs. 227.7 ± 73.7, p = 0.026). A correlation between IGF-1, IGF-binding protein number 3, and growth hormone levels (p = ns) was not observed, and there were no significant differences in the growth hormone levels in the studied group of patients (p = ns).

A High-Density Whole-Genome Association Study Reveals That APOE Is the Major Susceptibility Gene for Sporadic Late-Onset Alzheimer's Disease

While the apolipoprotein E (APOE) epsilon allele is a well-established risk factor for late-onset Alzheimer's disease (AD), initial genome scans using microsatellite markers in late-onset AD failed to identify this locus on chromosome 19. Recently developed methods for the simultaneous assessment of hundreds of thousands of single nucleotide polymorphisms (SNPs) promise to help more precisely identify loci that contribute to the risk of AD and other common multigenic conditions. We sought here to demonstrate that more precise identification of loci that are associated with complex, multi-genic genetic disorders can be achieved using ultra-high-density whole-genome associations by demonstrating their ability to identify the APOE locus as a major susceptibility gene for late-onset AD, despite the absence of SNPs within the APOE locus itself, as well as to refine odds ratios (ORs) based on gold-standard phenotyping of the study population. An individualized genome-wide association study using 502,627 SNPs was performed in 1086 his-topathologically verified AD cases and controls to determine the OR associated with genes predisposing to Alzheimer's disease. As predicted, ultra-high-density SNP genotyping, in contrast to traditional microsatellite-based genome screening approaches, precisely identified the APOE locus as having a significant association with late-onset AD. SNP rs4420638 on chromosome 19, located 14 kilobase pairs distal to the APOE epsilon variant, significantly distinguished between AD cases and controls (Bonferroni corrected p value = 5.30 x 10(-34), OR = 4.01) and was far more strongly associated with the risk of AD than any other SNP of the 502,627 tested. This study provides empirical support for the suggestion that the APOE locus is the major susceptibility gene for late-onset AD in the human genome, with an OR significantly greater than any other locus in the human genome. It also supports the feasibility of the ultra-high-density whole-genome association approach to the study of AD and other heritable phenotypes. These whole-genome association studies show great promise to identify additional genes that contribute to the risk of AD.

Studies of Human Herpes Virus-8 in Thailand

Thailand has experienced a major epidemic of HIV/AIDS since 1988. Currently over 650,000 persons are HIVinfected and 400,000 have died of AIDS in Thailand. However, Kaposi's Sarcoma (KS) is very rare. Among the 101,945 adults AIDS cases reported between 1994 and 1998 only 0.2% had KS. We have ruled out the possibility that HHV-8 infections are rare; in a study of 992 persons at risk or positive for HIV we found an HHV-8 antibody prevalence of 24.2%. Another hypothesis to explain the rarity of KS is that endothelial cells in Thai's are relatively resistant to HHV-8 infection. We obtained umbilical cord endothelial cell cultures from 10 Thai women who were HIV negative and analyzed their DNA for novel single nucleotide polymorphisms (SNPs) in the coding region for the promoter and 3' UTR region of the DC-SIGN gene. These results were compared to other Asian (11), Caucasian (n = 120), and African (n = 206) samples. No novel SNPs were found in the Thai samples, however some haplotypes that differed from the Caucasian samples were found. Three Thai samples were homozygous for a complete absence of SNPs in the UTR and reduced diversity in the promoter. This was not seen in the Caucasian samples. Additional analysis of linkage disequilibrium and HHV-8 infectivity analysis of these cell cultures are in progress. It is possible that genetic differences in the endothelial cell receptors for HHV-8 or resistance of cells to HHV-8 among Thai's could partially explain the rarity of AIDSrelated KS among Asians. from 2005 International Meeting of The Institute of Human Virology Baltimore, USA, 29 August – 2 September 2005