Background Previous phylogeographic studies of the lion (Panthera leo) have improved our insight into the distribution of genetic variation, as well as a revised taxonomy which now recognizes a... Show moreBackground Previous phylogeographic studies of the lion (Panthera leo) have improved our insight into the distribution of genetic variation, as well as a revised taxonomy which now recognizes a northern (Panthera leo leo) and a southern (Panthera leo melanochaita) subspecies. However, existing whole range phylogeographic studies on lions either consist of very limited numbers of samples, or are focused on mitochondrial DNA and/or a limited set of microsatellites. The geographic extent of genetic lineages and their phylogenetic relationships remain uncertain, clouded by massive sampling gaps, sex-biased dispersal and incomplete lineage sorting. Results In this study we present results of low depth whole genome sequencing and subsequent variant calling in ten lions sampled throughout the geographic range, resulting in the discovery of >150,000 Single Nucleotide Polymorphisms (SNPs). Phylogenetic analyses revealed the same basal split between northern and southern populations, as well as four population clusters on a more local scale. Further, we designed a SNP panel, including 125 autosomal and 14 mitochondrial SNPs, which was tested on >200 lions from across their range. Results allow us to assign individuals to one of these four major clades (West & Central Africa, India, East Africa, or Southern Africa) and delineate these clades in more detail. Conclusions The results presented here, particularly the validated SNP panel, have important applications, not only for studying populations on a local geographic scale, but also for tracing samples of unknown origin for forensic purposes, and for guiding conservation management of ex situ populations. Thus, these genomic resources not only contribute to our understanding of the evolutionary history of the lion, but may also play a crucial role in conservation efforts aimed at protecting the species in its full diversity. Show less
Aim: To determine the safety, feasibility, pharmacokinetics, and cost of UGT1A1 genotype-guided dosing of irinotecan.Patients and methods: In this prospective, multicentre, non-randomised study,... Show moreAim: To determine the safety, feasibility, pharmacokinetics, and cost of UGT1A1 genotype-guided dosing of irinotecan.Patients and methods: In this prospective, multicentre, non-randomised study, patients intended for treatment with irinotecan were pre-therapeutically genotyped for UGT1A1*28 and UGT1A1)93. Homozygous variant carriers (UGT1A1 poor metabolisers; PMs) received an initial 30% dose reduction. The primary endpoint was incidence of febrile neutropenia in the first two cycles of treatment. Toxicity in UGT1A1 PMs was compared to a historical cohort of UGT1A1 PMs treated with full dose therapy, and to UGT1A1 non-PMs treated with full dose therapy in the current study. Secondary endpoints were pharmacokinetics, feasi- bility, and costs.Results: Of the 350 evaluable patients, 31 (8.9%) patients were UGT1A1 PM and received a median 30% dose reduction. The incidence of febrile neutropenia in this group was 6.5% compared to 24% in historical UGT1A1 PMs (P = 0.04) and was comparable to the incidence in UGT1A1 non-PMs treated with full dose therapy. Systemic exposure of SN-38 of reduced dosing in UGT1A1 PMs was still slightly higher compared to a standard-dosed irinotecan patient cohort (difference: thorn 32%). Cost analysis showed that genotype-guided dosing was cost-saving with a cost reduction of V183 per patient.Conclusion: UGT1A1 genotype-guided dosing significantly reduces the incidence of febrile neutropenia in UGT1A1 PM patients treated with irinotecan, results in a therapeutically effec- tive systemic drug exposure, and is cost-saving. Therefore, UGT1A1 genotype-guided dosing of irinotecan should be considered standard of care in order to improve individual patient safety. (C) 2022 The Authors. Published by Elsevier Ltd. Show less
Claassens, D.M.F.; Gimbel, M.E.; Bergmeijer, T.O.; Vos, G.J.A.; Hermanides, R.S.; Harst, P. van der; ... ; Berg, J.M. ten 2021
Background: Patients with acute coronary syndrome (ACS) who are carrying CYP2C19 loss-of-function alleles derive less benefit from clopidogrel treatment. Despite this, in elderly patients,... Show moreBackground: Patients with acute coronary syndrome (ACS) who are carrying CYP2C19 loss-of-function alleles derive less benefit from clopidogrel treatment. Despite this, in elderly patients, clopidogrel might be preferred over more potent P2Y12 inhibitors due to a lower bleeding risk. Whether CYP2C19 genotype-guided antiplatelet treatment in the elderly could be of benefit has not been studied specifically.Methods: Patients aged 70 years and older with known CYP2C19*2 and *3 genotype were identified from the POPular Genetics and POPular Age trials. Noncarriers of loss-of-function alleles treated with clopidogrel were compared to patients, irrespective of CYP2C19 genotype, treated with ticagrelor and to clopidogrel treated carriers of loss-of-function alleles. We assessed net clinical benefit (all-cause death, myocardial infarction, stroke and Platelet Inhibition and Patient Outcomes (PLATO) major bleeding), atherothrombotic outcomes (cardiovascular death, myocardial infarction, stroke) and bleeding outcomes (PLATO major and minor bleeding).Results: A total of 991 patients were assessed. There was no significant difference in net clinical benefit (17.2% vs. 15.1%, adjusted hazard ratio (adjHR) 1.05, 95% confidence interval (CI) 0.77-1.44), atherothrombotic outcomes (9.7% vs. 9.2%, adjHR 1.00, 95%CI 0.66-1.50), and bleeding outcomes (17.7% vs. 19.8%, adjHR 0.80, 95%CI 0.62-1.12) between clopidogrel in noncarriers of loss-of-function alleles and ticagrelor respectively.Conclusion: In ACS patients aged 70 years and older, there was no significant difference in net clinical benefit and atherothrombotic outcomes between noncarriers of a loss-of-function allele treated with clopidogrel and pa-tients treated with ticagrelor. The bleeding rate was numerically; though not statistically significant, lower in pa-tients using clopidogrel.(c) 2021 Published by Elsevier B.V. Show less
The aim of the research described in this thesis was to obtain more insight in the risk factors of BK polyomavirus (BKPyV) infection after kidney transplantation (KTx), with special emphasis on... Show moreThe aim of the research described in this thesis was to obtain more insight in the risk factors of BK polyomavirus (BKPyV) infection after kidney transplantation (KTx), with special emphasis on pretransplantation related risk factors. Both donor and recipient as well as viral factors, were investigated. The ultimate goal was to identify reliable predictive markers of BKPyV infection after KTx, thereby providing opportunities to optimize and personalize the currently recommended BKPyV screening strategy. Chapter Two describes the correlation between pretransplantation donor-recipient pair seroreactivity against BKPyV and development of BKPyV viremia and BKPyVAN after KTx. In Chapter Three the stability of BKPyV seroreactivity in KTRs and healthy blood donors, and the correlation of BKPyV seroreactivity with preceding viremia in KTRs is described. In Chapter Four the reduced risk of BKPyV infection in HLA-B51 positive recipients after KTx is described. Chapter Five describes the development and evaluation of a Luminex bead-based multiplex immunoassay for BKPyV serotyping. In Chapter Six the application of the Luminex bead-based multiplex immunoassay for BKPyV serotyping is described in a cohort of KTx donor-recipient pairs. In the General Discussion implications for prediction of BKPyV infections in recipients after KTx, as well as suggestions for further research are described. Show less
Fluorescence bias in in signals from individual SNP arrays can be calibrated using linear models. Given the data, the system of equations is very large, so a specialized symbolic algorithm was... Show moreFluorescence bias in in signals from individual SNP arrays can be calibrated using linear models. Given the data, the system of equations is very large, so a specialized symbolic algorithm was developed. These models are also used to illustrate that genomic waves do not exist, but are merely an artifact of commonly used methods. Furthermore, a new semi-parametric, single array, approach to SNP genotyping is introduced and shown to be both effective and efficient. A refined algorithm for copy number estimation, using a zero-exponent norm is proposed, which performs well, as is illustrated by thorough comparisons with other methods. Indications that the signal calibration can improve (genotyping) results from lower quality samples are also discussed. A software suite that implements the above is described and illustrated. Show less
Out, A.A.; Wasielewski, M.; Huijts, P.E.A.; Minderhout, I.J.H.M. van; Houwing-Duistermaat, J.J.; Tops, C.M.J.; ... ; Devilee, P. 2012
Type 2 Diabetes (T2D) is a chronic disease, characterized by hyperglycaemia, caused by decreased insulin secretion by beta-cells and insulin resistance of target tissues of insulin. Several risk... Show moreType 2 Diabetes (T2D) is a chronic disease, characterized by hyperglycaemia, caused by decreased insulin secretion by beta-cells and insulin resistance of target tissues of insulin. Several risk factors are known, like decreased exercise, ageing and western diet. Also genetic variance can alter susceptibility to develop T2D. Until recently only four T2D susceptibility genes were identified (PPARG, KCNJ11, CAPN10 and TCF7L2). However, recent Genome Wide Association Studies (GWAS) have increased this number to at least 20. My thesis describes the search for additional T2D susceptibility genes. For this we used a classical candidate gene approach and we case/control studies from the Netherlands, Scandinavia and the UK. We selected 14 nuclear encoded candidate genes, all regarded essential for mitochondrial protein synthesis and biogenesis. Since mitochondrial function was shown to be associated with T2D, we hypothesized that genes in these pathways are good candidates. Tagging SNPs were selected, which should cover all known common variation (minor allele frequency (MAF) > 0.05) in the candidate genes. These tagging SNPs were measured in our first stage, comprising of the Dutch Hoorn study and significant associations were than taking forward for replication in our replication cohorts in the second stage of this study. However, after second stage genotyping non of the signals remained significant, indicating that the selected candidate genes do not play a major role in T2D susceptibility. Furthermore, nuclear encoded mitochondrial genes were not among the top hits of GWAS, which were made available online after completion of our study. Therefore, we conclude that nuclear encoded mitochondrial genes do not have a major contribution to the development of T2D. Next, we analyzed the association of mitochondrial DNA (mtDNA) content with T2D. First we estimated the heritability in Dutch twins and found a heritability of 35% (19%-48%). Next we analyzed the association with prevalent and incident T2D in a Dutch case control study and two prospective studies from the Netherlands and Finland. However, no associations were observed. Therefore, we conclude that mtDNA content does not play a major role in the development of T2D. Finally, we analyzed four known fasting plasma glucose (FPG) influencing genes (GCK, GCKR, G6PC2 and MTNR1B). In a Dutch population based sample we could replicate the association of these genes with FPG levels (except for GCKR). Furthermore, the combined risk alleles (ranging from 0 to 8 risk alleles) were strongly associated with FPG and HbA1C levels. This risk allele score was also associated with T2D susceptibility and age of diagnosis at T2D. We therefore conclude that the FPG influencing genes have a combined effect on FPG and are associated with T2D susceptibility and age at diagnosis of T2D. In conclusion, we could not find evidence that nuclear encoded mitochondrial proteins and mtDNA content are associated with T2D susceptibility. The four known FPG genes do not only influence FPG levels, but also have a combined effect on T2D susceptibility and age at diagnosis of T2D. Show less
This thesis starts with a general introduction and a description of the development of a detection and genotyping method for Betapapillomavirus types. This genotyping method is used in three... Show moreThis thesis starts with a general introduction and a description of the development of a detection and genotyping method for Betapapillomavirus types. This genotyping method is used in three chapters to acquire more knowledge on the natural history of Betapapillomavirus infection. Very little is known about this subject and more knowledge could support future studies into the clinical relevance of these viruses. Furthermore, three subsequent chapters focus on possible associations of betaPV infection with three different (pre)malignant diseases. A final chapter includes general discussion and conclusions. Show less
The aim of this thesis was to obtain insight into the epidemiology and molecular basis of multidrug resistance of Acinetobacter baumannii at the population level. To this aim a number of studies... Show moreThe aim of this thesis was to obtain insight into the epidemiology and molecular basis of multidrug resistance of Acinetobacter baumannii at the population level. To this aim a number of studies were performed on strains mainly from the Czech Republic (CR) which have shown in particular that (i) the vast majority of multidrug resistant (MDR) clinical isolates of A. baumannii from CR belong to clonal lineages termed EU clone I and II; (ii) these two clones have predominated among MDR hospital isolates in CR since at least 1991; (iii) recent emergence of A. baumannii resistance to carbapenems in CR was associated with the country-wide spread of a subclone of EU clone II; (iv) multidrug resistance is a general feature of strains of EU clones I and II, yet strains belonging to one clone may vary in the content of resistance genes; (v) upregulation of genes intrinsic to A. baumannii as well as horizontal acquisition of resistance genes can be sources of development of multidrug resistance and intraclonal diversification; (vi) the genes encoding the non-specific efflux system AdeABC are present in nearly all A. baumannii strains, yet the AdeABC overexpression is seen mostly in MDR strains harbouring additional resistance genes. Show less
Clostridium difficile was first discovered in 1935, but it was not until 1977 that this bacterium was found to be associated with pseudomembranous colitis. The disease was considered to be caused... Show moreClostridium difficile was first discovered in 1935, but it was not until 1977 that this bacterium was found to be associated with pseudomembranous colitis. The disease was considered to be caused by the production of two C. difficile toxins, toxins A and B (TcdA and TcdB). TcdA was shown to exhibit enterotoxic effects on the intestine, whereas TcdB was shown to be more cytotoxic. Strains of C. difficile that do not produce these toxins are known to be non-toxinogenic and therefore non-pathogenic. However, outbreaks and more severe infections due to strains producing only TcdB have been described. To diagnose C. difficile -associated disease, a method with a high sensitivity and specificity is necessary. This thesis describes the application of methods based on the molecular detection of the pathogen in comparison with conventional microbiological methods. After isolation of the pathogen, the epidemiology of C. difficile -associated disease can be studied using molecular typing methods on the isolates. These typing methods need to be highly discriminatory, depending on the epidemiological data to be studied, and methods need to be stable en reproducible, with the possibility to exchange data between different laboratories all over the world. Show less
