No description available.

Hereditär hemokromatos (HH) är en vanlig multigenetisk defekt som leder till ett onormalt förhöjt järnupptag i tarmen och ses framförallt hos kaukasisk befolkning. Sjukdomen har på senare år visats orsakats av mutationen c.845G>A men även mer ovanliga varianter som c.187C>G och c.193A>T, vilka alla finns belägna i genen HFE. HFE som finns lokaliserad intill Human Leukocyte Antigen (HLA)-genen på kromosom sex korta arm kodar för ett HFE-protein som har till uppgift att reglera kroppens järnmetabolism i interaktion med hormonet hepcidin. Vid HH avtar proteinets järnregulatoriska funktion och järnackumulation uppstår. Idag diagnostiseras HH främst via genotypning där ovanstående genvarianter påvisas. Beroende på genvariant löper individer olika hög risk för sjukdomsutveckling. I studien var syftet att verifiera det kommersiella kitet LightMix® in-vitro diagnostics kit HFE H63D S65C C282Y diagnostics kit för kvalitativ diagnostik av HFE-genotyper via Realtids-Polymerase Chain Reaction (PCR) via smältkurveanalys för eventuell införsel i rutindiagnostik. I studien kunde samtliga patientprover (n=49) ifrån Halmstad med misstänkt hemokromatos genotypas för genvarianterna i HFE-genen. Utifrån godkända resultat i prov-till-prov variation tillsammans med icke-frekventa skillnader i imprecisionstest samt 100 % samstämmighet gentemot referensmetoder på externa laboratorier, kunde slutsatsen dras att metoden är relevant för rutinverksamheten på Länssjukhuset Ryhov, Region Jönköpings Län. / Hereditary hemochromatosis (HH) is a common multi-genetic defect that results in abnormally elevated iron uptake mainly in Caucasian populations. The disease has recently been found to be caused by mutation c.845G>A, in addition to the unusual variants c.187C>G and c.193A>T, all of which are detected in the gene HFE. HFE is located adjacent to the Human Leukocyte Antigen (HLA)-gene on chromosome six’s short arm and encodes for a HFE-protein, responsible for the body's iron metabolism regulation in interaction with the hormone hepcidin. As HH decreases the protein's iron-regulatory function, the iron accumulation increases. Today HH is diagnosed primarily through genotyping where variants in the HFE-gene are detected. Depending on the variant, individuals are put at varying high risk of disease development. The aim of this study was to verify the commercial LightMix® in-vitro diagnostics kit HFE H63D S65C C282Y for qualitative diagnosis of HFE-genotypes through Real-time Polymerase Chain Reaction (PCR) and melting-curve analysis for possible introduction in routine diagnostics. In the study, all samples (n=49) from patients with suspicious hemochromatosis were genotyped for the gene variants in HFE-gene. Based on all accepted results with non-frequent differences in imprecision test and 100 % consistency against the reference methods at external laboratories conclusions could be drawn that the method is applicable for routine diagnostics at the County Hospital Ryhov in Region Jönköping.

No description available.

No description available.

The protozoan parasite Giardia duodenalis (syn. G. lamblia, G. intestinalis) can cause diarrhea in humans, cats, dogs and other animals. Giardia duodenalis consists of eight assemblages (A-H) that are morphologically identical but genetically distinct. Assemblages C-H are generally species-specific, while A and B infect people and animals and are considered potentially zoonotic. Most canine and feline isolates belong to their respective species-specific assemblages, but isolates of assemblages A and B (predominantly found in humans) have also been recovered from dogs and cats. Diagnosis of infection has historically been by morphologic techniques (observing trophozoites on direct fecal smears or cysts on centrifugal zinc sulfate fecal flotations), and it is currently recommended to use morphologic techniques in conjunction with a sensitive and specific antigen test. Diagnosis is important for management of clinical giardiasis in cats and dogs and also to identify the assemblage present to determine its zoonotic potential. In my dissertation research I evaluated diagnostic techniques in use for companion animals, including centrifugal zinc sulfate fecal flotation, antigen tests optimized for use in dogs and cats, direct immunofluorescent assay (IFA), and Polymerase Chain Reaction (PCR). I showed that when compared to the reference IFA the veterinary optimized antigen tests performed similarly and had no statistically significant differences in sensitivity or specificity when combined with a centrifugal zinc sulfate fecal flotation test. Sensitivity and specificity by comparison to IFA was ≥ 82% and ≥ 90%, respectively, for all diagnostic tests evaluated in dogs and cats. When analyzed via Bayesian analysis sensitivity and specificity for all diagnostic tests was ≥83% and ≥95%, respectively. The Bayesian analysis also showed that using the direct immunofluorescent assay (IFA) as the reference test was supported. I also evaluated PCR as a molecular diagnostic technique to detect Giardia infections in dogs with soft stool or diarrhea (mimicking clinical signs of infection). I utilized both conventional and real time PCR assays and compared the results to the recommended method of diagnosis, the zinc sulfate fecal flotation combined with an immunoassay test. I found that agreement between PCR and microscopy combined with an immunoassay was poor to fair and varied depending on the molecular parameters and size of the DNA target underscoring the complexity of test evaluation and molecular diagnostics for Giardia. I also evaluated cats from a varied population (owned, shelter, feral) in Virginia to determine to what extent (if any) they were infected with potentially zoonotic assemblages of Giardia. The species-specific assemblage F was detected in 57% of the samples and assemblage A, which is considered potentially zoonotic, was recovered from 32% of the sampleI. In 11% both assemblages F and A were detected. We showed for the first time that cats in Virginia are infected with potentially zoonotic assemblages of Giardia. / PHD

BACKGROUND:Cryptococcus gattii has been the cause of an ongoing outbreak starting in 1999 on Vancouver Island, British Columbia and spreading to mainland Canada and the US Pacific Northwest. In the course of the outbreak, C. gattii has been identified outside of its previously documented climate, habitat, and host disease. Genotyping of C. gattii is essential to understand the ecological and geographical expansion of this emerging pathogen.METHODS:We developed and validated a mismatch amplification mutation assay (MAMA) real-time PCR panel for genotyping C. gattii molecular types VGI-VGIV and VGII subtypes a,b,c. Subtype assays were designed based on whole-genome sequence of 20 C. gattii strains. Publically available multilocus sequence typing (MLST) data from a study of 202 strains was used for the molecular type (VGI-VGIV) assay design. All assays were validated across DNA from 112 strains of diverse international origin and sample types, including animal, environmental and human.RESULTS:Validation revealed each assay on the panel is 100% sensitive, specific and concordant with MLST. The assay panel can detect down to 0.5 picograms of template DNA.CONCLUSIONS:The (MAMA) real-time PCR panel for C. gattii accurately typed a collection of 112 diverse strains and demonstrated high sensitivity. This is a time and cost efficient method of genotyping C. gattii best suited for application in large-scale epidemiological studies.

Class of 2007 Abstract / Objectives: The objective of this study was to determine the cost-effectiveness of using the Invader® UGT1A1 Molecular Assay to identify patients at risk of experiencing neutropenia from irinotecan monotherapy and FOLFIRI. Methods: Publicly available search engines were used to search for literature reporting the rate, treatment, and cost of adverse events and the population rate of genotypes. Drug acquisition costs were determined using average wholesale prices. Additional costs were determined using the Physicians’ Fee and Coding Guide. Monte Carlo Simulations were performed to reveal average cost, average effectiveness, and 95% confidence intervals. Tornado diagrams were derived to identify variables most likely to affect the outcomes and sensitivity analyses. Results: Monte Carlo simulations of monotherapy revealed a mean cost of treatment with genotype assay information of $6,620 (SD: $3,235; 95% CI: $5,408 to $15, 258) and an effectiveness ratio of 0.877 (SD: 0.328; 95% CI: 0 to 1). Without the genotype assay information the mean cost of treatment was $7,358 (SD: $4,183; 95% CI: $5,083 to $14,883) and the effectiveness ratio was 0.764 (SD: 0.425; 95% CI: 0 to 1). Monte Carlo simulations of FOLFIRI data showed a mean cost of treatment with genotype assay information of $6,105 (SD: $3,438; 95% CI: $4,706 to $14,556) and an effectiveness ratio of 0.858 (SD: 0.349; 95% CI: 0 to 1). When genotype information was unknown, the mean cost of FOLFIRI was $6,833 (SD: $4,288; 95% CI: $4,331 to $14,181) and the effectiveness ratio was 0.746 (SD: 0.435; 95% CI: 0 to 1). Conclusions: Genotyping patients exposed to irinotecan monotherapy or FOLFIRI may be a cost-effective means of identifying at risk patients but the results from this study while favorable are not statistically significant.

Aphanomyces spp. are water moulds, eukaryotic fungus-like organisms, belonging to the class Oomycota. This genus contains primary pathogens of plants and animals as well as opportunistic and saprotrophic species. One of the animal parasites (A. astaci) is the causal agent of the crayfish plague, a disease listed by the World Organisation for Animal Health (OIE). It is believed that A. astaci was first introduced into Italy from the US in the late 19th century and rapidly spread in Europe causing the decline of native crayfish. It currently threatens to wipe out the UK native white-clawed crayfish (Austropotamobius pallipes). Random amplified polymorphic DNA (RAPD-PCR) on pure isolates of A. astaci distinguished five genotypes (A, B, C, D, and E). This distinction proved to be a useful tool for epidemiological studies aimed at understanding the history and spread of the disease in Europe; furthermore, there are differences in virulence among genotypes. No discriminatory morphological or physiological characters are available and widely used markers such as the internal transcribed spacer (ITS), the divergent domains regions (D1-D2) of nuclear large subunit (LSU) rDNA, and cytochrome c oxidase subunit I (COI) also fail to discriminate between A. astaci genotypes. There are some practical drawbacks to genotype by the currently available genotyping methods. Whole genome sequencing (WGS) was used to catalogue DNA single nucleotide variants and genotype-unique genomic regions that could be exploited as phylogenetic markers. These newly developed molecular markers were tested both on pure cultures and historical samples derived from outbreaks and carrier crayfish available in our laboratories, validating these genotyping methods, which represent new diagnostic tools aiding the detection and prevention of crayfish plague.

Thesis (M.Sc. (Medical Microbiology)) --University Limpopo, 2013 / Genotyping of TB is essential to investigate and confirm transmission of the multi-drug resistant tuberculosis and of great value in optimizing strategies for the determination of strains causing the increased mortality rates of TB outbreaks. Sputum samples (207) were collected from National Health Laboratory Services in Polokwane laboratory for determining mutations and genotypes of the Mycobacterium tuberculosis strains using GenoType®MTBDRplus (Hain LifeScience, Germany) and Real-Time PCR (Roche, South Africa) techniques. Of the 207 samples, 28 (13.5%) exhibited drug resistance. Thirteen of the 28 (46%) MDR-TB strains belonged to the non-Beijing family, with mutations at codons rpoB 516 and rpoB 526 for RIF and katG 315 and inhA 15 for INH resistance. The Non-Beijing strains 75% (21/28) were monoresistant to RIF 14% (3/21) at codons 516, 526, 531 of rpoB gene and INH 19% (4/21) at codon 315 of katG and codon 15 of inhA 5% (1/21). Of the eight Beijing strains, 3(8%) were INH- resistant at codon 315 for katG and codon 15 for inhA and 3(8%) were RIF-resistant with mutations at codons 516 and 526. Two samples were typed as MDR for the Beijing strains with codon 315 for INH and codons 526 and 531 for RIF. The sample with a co-infection for Beijing and non-Beijing was an MDR-TB strain with mutations in rpoB codons 526, 531, katG 315 and inhA 8, 15 and16. The study showed a high rate of drug resistance with the non-Beijing compared to Beijing strains and mutations in specific codons for RIF and INH are variable for the TB families.

The emerging field of personalized medicine and the prediction of side effects experienced due to pharmaceutical drugs is being studied intensively in the post genomic era. The molecular basis of inheritance and disease susceptibility is being unravelled, especially through the use of rapidly evolving new technologies. This in turn facilitates analyses of individual variations in the whole genome of both single subjects and large groups of subjects. Genetic variation is a common occurrence and although most genetic variations do not have any apparent effect on the gene product some do exhibit effects, such as an altered ability to detoxify xenobiotics. The human body has a highly effective detoxification system that detoxifies and excretes endogenous as well as exogenous toxins. Numerous studies have proved that specific genetic variations have an influence on the efficacy of the metabolism of pharmaceutical drugs and consequently the dosage administered. The primary aim of this project was the local implementation and assessment of two different genotyping approaches namely: the Applied Biosystems SNaPshot technique and Affymetrix DMET microarray. A secondary aim was to investigate if links could be found between the genetic data and the biochemical detoxification profile of participants. I investigated the approaches and gained insight into which method would be better for specific local applications, taking into consideration the robustness and ease of implementation as well as cost effectiveness in terms of data generated. The final study cohort comprised of 18 participants whose detoxification profiles were known. Genotyping was performed using the DMET microarray and SNaPshot techniques. The SNaPshot technique was used to genotype 11 SNPs relating to DNA repair and detoxification and was performed locally. Each DMET microarray delivers significantly more data in that it genotypes 1931 genetic markers relating to drug metabolism and transport. Due to the absence of a local service supplier, the DMET - microarrays were outsourced to DNALink in South Korea. DNALink generated raw data which was analysed locally. I experienced many problems with the implementation of the SNaPshot technique. Numerous avenues of troubleshooting were explored with varying degrees of success. I concluded that SNaPshot technology is not the best suited approach for genotyping. Data obtained from the DMET microarray was fed into the DMET console software to obtain genotypes and subsequently analysed with the help of the NWU statistical consultation services. Two approaches were followed: firstly, clustering the data and, secondly, a targeted gene approach. Neither of the two methods was able to establish a relationship between the DMET genotyping data and the detoxification profiling. For future studies to successfully correlate SNPs or SNP groups and a specific detoxification profile, two key issues should be addressed: i) The procedure for determining the detoxification profile following substrate loading should be further refined by more frequent sampling after substrate loading. ii) The number of participants should be increased to provide statistical power that will enable a true representation of the particular genetic markers in the specific population. The statistical analyses, such as latent class analyses to cluster the participants will also be of much more use for data analyses and interpretation if the study is not underpowered. / Thesis (M.Sc. (Biochemistry))--North-West University, Potchefstroom Campus, 2011.