Design of experiments (DoE) is a valuable tool for the optimization of quantitative bioanalytical methods utilizing liquid chromatography coupled to tandem mass spectrometry (LC–MS/MS). Liquid ...chromatography mass spectrometry (LC–MS) is composed of several processes, including, liquid introduction and analyte ionization. The goal is to transfer analytes from atmospheric pressure to vacuum and maintain conditions that are compatible for both LC and MS. These processes involve many experimental factors which need to be simultaneously optimized to obtain maximum sensitivity and resolution at minimum retention time. In this tutorial, the basic concepts of DoE will be explained with focus on practical use of DoE. Three case studies optimized with DoE for liquid chromatography tandem mass spectrometry (LC–MS/MS) quantitative assays will then be presented.
Design of experiment (DoE) is a chemometric approach to study the influence of each experimental factor simultaneously at various levels with a predefined number of experiments, considering all ...possible interactions between the factors. In this tutorial special feature article, Margrét Thorsteinsdóttir and colleague provide an overview of the basic concepts of DoE and a strategy for implementation of DoE for the optimization of a quantitative LC‐MS/MS methods. Indeed, DoE is an excellent tool for the development and optimization of hyphenated techniques such as LC‐MS/MS, where several experimental factors need to be simultaneously optimized to obtain maximum sensitivity with adequate resolution between closely eluting peaks. The results are expressed as a mathematical function of the experimental conditions providing a mean to predict and estimate results at levels that were not directly studied. The data can be explored by use of counter plots and response surface plots to visualize how the response is affected by the factors studied and for finding a combination of factor settings that will result in optimum analytical conditions. With better designed experiments, flow of measurements to knowledge can proceed in the most cost‐effective way. Margrét Thorsteinsdóttir (PhD) is Professor at the Faculty of Pharmaceutical Science at the University of Iceland (Reykjavik, Iceland). Her main research interest is focused on the development of high‐performance separation science with applications in clinical MS.
•Relation between geological structures and geothermal resources.•Location of geothermal resources is controlled by fault interaction.•Integration between fieldwork and geophysical data.•Intersection ...of faults increases rock permeability.
The Krafla volcano-geothermal area is located in Northeast Iceland, within the active Northern Volcanic Zone sector of the axial rift and has experienced two eruptions in historical times. The Krafla system displays NNE-SSW oriented fissure swarm, a central volcano and associated geothermal manifestations (i.e. steam and gas emissions, hydrothermal alterations). However, during its exploration and exploitation, several geophysical indications have suggested the occurrence of WNW-ESE trending structures, i.e. near orthogonal with respect to the faults delimiting the axial rift. This paper describes the results of a structural survey carried out in a wide area in the NE-sector of Iceland along the Húsavík-Flatey shear zone and in the Krafla area, measuring fractures and alignments of geothermal manifestations and fissure swarms. The dataset highlights the occurrence of structures oriented in two main trends, i.e. NNW-SSE to NNE-SSW and WNW-ESE. At their intersection, geothermal manifestations and silica sinter deposits commonly occur. Both of these trends have been documented in the Krafla geothermal area and compared with borehole and geophysical data. Our conclusions support that the location of the high-temperature Krafla geothermal area is mainly controlled by the enhanced permeability at the intersection between structures of the axial rift zone and incipient transform faults crossing the Krafla area.
Objective: Familial hypercholesterolemia (FH) is traditionally defined as a monogenic disease characterized by severely elevated LDL-C (low-density lipoprotein cholesterol) levels. In practice, FH is ...commonly a clinical diagnosis without confirmation of a causative mutation. In this study, we sought to characterize and compare monogenic and clinically defined FH in a large sample of Icelanders.
Approach and Results: We whole-genome sequenced 49 962 Icelanders and imputed the identified variants into an overall sample of 166 281 chip-genotyped Icelanders. We identified 20 FH mutations in LDLR, APOB, and PCSK9 with combined prevalence of 1 in 836. Monogenic FH was associated with severely elevated LDL-C levels and increased risk of premature coronary disease, aortic valve stenosis, and high burden of coronary atherosclerosis. We used a modified version of the Dutch Lipid Clinic Network criteria to screen for the clinical FH phenotype among living adult participants (N=79 058). Clinical FH was found in 2.2% of participants, of whom only 5.2% had monogenic FH. Mutation-negative clinical FH has a strong polygenic basis. Both individuals with monogenic FH and individuals with mutation-negative clinical FH were markedly undertreated with cholesterol-lowering medications and only a minority attained an LDL-C target of <2.6 mmol/L (<100 mg/dL; 11.0% and 24.9%, respectively) or <1.8 mmol/L (<70 mg/dL; 0.0% and 5.2%, respectively), as recommended for primary prevention by European Society of Cardiology/European Atherosclerosis Society cholesterol guidelines.
Conclusions: Clinically defined FH is a relatively common phenotype that is explained by monogenic FH in only a minority of cases. Both monogenic and clinical FH confer high cardiovascular risk but are markedly undertreated.
Iron is essential for many biological functions and iron deficiency and overload have major health implications. We performed a meta-analysis of three genome-wide association studies from Iceland, ...the UK and Denmark of blood levels of ferritin (N = 246,139), total iron binding capacity (N = 135,430), iron (N = 163,511) and transferrin saturation (N = 131,471). We found 62 independent sequence variants associating with iron homeostasis parameters at 56 loci, including 46 novel loci. Variants at DUOX2, F5, SLC11A2 and TMPRSS6 associate with iron deficiency anemia, while variants at TF, HFE, TFR2 and TMPRSS6 associate with iron overload. A HBS1L-MYB intergenic region variant associates both with increased risk of iron overload and reduced risk of iron deficiency anemia. The DUOX2 missense variant is present in 14% of the population, associates with all iron homeostasis biomarkers, and increases the risk of iron deficiency anemia by 29%. The associations implicate proteins contributing to the main physiological processes involved in iron homeostasis: iron sensing and storage, inflammation, absorption of iron from the gut, iron recycling, erythropoiesis and bleeding/menstruation.
Multiple myeloma (MM) is characterized by an uninhibited, clonal growth of plasma cells. While first-degree relatives of patients with MM show an increased risk of MM, the genetic basis of inherited ...MM susceptibility is incompletely understood. Here we report a genome-wide association study in the Nordic region identifying a novel MM risk locus at ELL2 (rs56219066T; odds ratio (OR)=1.25; P=9.6 × 10(-10)). This gene encodes a stoichiometrically limiting component of the super-elongation complex that drives secretory-specific immunoglobulin mRNA production and transcriptional regulation in plasma cells. We find that the MM risk allele harbours a Thr298Ala missense variant in an ELL2 domain required for transcription elongation. Consistent with a hypomorphic effect, we find that the MM risk allele also associates with reduced levels of immunoglobulin A (IgA) and G (IgG) in healthy subjects (P=8.6 × 10(-9) and P=6.4 × 10(-3), respectively) and, potentially, with an increased risk of bacterial meningitis (OR=1.30; P=0.0024).
The nature of nurture: Effects of parental genotypes Kong, Augustine; Thorleifsson, Gudmar; Frigge, Michael L ...
Science (American Association for the Advancement of Science),
2018-Jan-26, 2018-01-26, 20180126, Letnik:
359, Številka:
6374
Journal Article
Recenzirano
Odprti dostop
Sequence variants in the parental genomes that are not transmitted to a child (the proband) are often ignored in genetic studies. Here we show that nontransmitted alleles can affect a child through ...their impacts on the parents and other relatives, a phenomenon we call "genetic nurture." Using results from a meta-analysis of educational attainment, we find that the polygenic score computed for the nontransmitted alleles of 21,637 probands with at least one parent genotyped has an estimated effect on the educational attainment of the proband that is 29.9% (
= 1.6 × 10
) of that of the transmitted polygenic score. Genetic nurturing effects of this polygenic score extend to other traits. Paternal and maternal polygenic scores have similar effects on educational attainment, but mothers contribute more than fathers to nutrition- and heath-related traits.
The limited ability of common variants to account for the genetic contribution to complex disease has prompted searches for rare variants of large effect, to partly explain the 'missing ...heritability'. Analyses of genome-wide genotyping data have identified genomic structural variants (GSVs) as a source of such rare causal variants. Recent studies have reported multiple GSV loci associated with risk of obesity. We attempted to replicate these associations by similar analysis of two familial-obesity case-control cohorts and a population cohort, and detected GSVs at 11 out of 18 loci, at frequencies similar to those previously reported. Based on their reported frequencies and effect sizes (OR≥25), we had sufficient statistical power to detect the large majority (80%) of genuine associations at these loci. However, only one obesity association was replicated. Deletion of a 220 kb region on chromosome 16p11.2 has a carrier population frequency of 2×10(-4) (95% confidence interval 9.6×10(-5)-3.1×10(-4)); accounts overall for 0.5% 0.19%-0.82% of severe childhood obesity cases (P = 3.8×10(-10); odds ratio = 25.0 9.9-60.6); and results in a mean body mass index (BMI) increase of 5.8 kg.m(-2) 1.8-10.3 in adults from the general population. We also attempted replication using BMI as a quantitative trait in our population cohort; associations with BMI at or near nominal significance were detected at two further loci near KIF2B and within FOXP2, but these did not survive correction for multiple testing. These findings emphasise several issues of importance when conducting rare GSV association, including the need for careful cohort selection and replication strategy, accurate GSV identification, and appropriate correction for multiple testing and/or control of false discovery rate. Moreover, they highlight the potential difficulty in replicating rare CNV associations across different populations. Nevertheless, we show that such studies are potentially valuable for the identification of variants making an appreciable contribution to complex disease.
Celotno besedilo
Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
Genetic diversity arises from recombination and de novo mutation (DNM). Using a combination of microarray genotype and whole-genome sequence data on parent-child pairs, we identified 4,531,535 ...crossover recombinations and 200,435 DNMs. The resulting genetic map has a resolution of 682 base pairs. Crossovers exhibit a mutagenic effect, with overrepresentation of DNMs within 1 kilobase of crossovers in males and females. In females, a higher mutation rate is observed up to 40 kilobases from crossovers, particularly for complex crossovers, which increase with maternal age. We identified 35 loci associated with the recombination rate or the location of crossovers, demonstrating extensive genetic control of meiotic recombination, and our results highlight genes linked to the formation of the synaptonemal complex as determinants of crossovers.
PDF
