Comprehensive prenatal diagnostics: Exome versus genome sequencing

Objective

This study aimed to assess the diagnostic yield of prenatal genetic testing using trio whole exome sequencing (WES) and trio whole genome sequencing (WGS) in pregnancies with fetal anomalies by comparing the results with conventional chromosomal microarray (CMA) analysis.

Methods

A total of 40 pregnancies with fetal anomalies or increased nuchal translucency (NT ≥ 5 mm) were included between the 12th and 21st week of gestation. Trio WES/WGS and CMA were performed in all cases.

Results

The trio WES/WGS analysis increased the diagnostic yield by 25% in cases with negative CMA results. Furthermore, all six chromosomal aberrations identified by CMA were independently detected by WES/WGS analysis. In total, 16 out of 40 cases obtained a genetic sequence variant, copy number variant, or aneuploidy explaining the phenotype, resulting in an overall WES/WGS diagnostic yield of 40%. WES analysis provided a more reliable identification of mosaic sequence variants than WGS because of its higher sequencing depth.

Conclusions

Prenatal WES/WGS proved to be powerful diagnostic tools for fetal anomalies, surpassing the diagnostic yield of CMA. They have the potential to serve as standalone methods for prenatal diagnosis. The study highlighted the limitations of WGS in accurately detecting mosaic variants, which is particularly relevant when analyzing chorionic villus samples.     

Levels and trends of persistent organic pollutants in ringed seals (Phoca hispida) from Central West Greenland, with particular focus on polybrominated diphenyl ethers (PBDEs)

Polybrominated diphenyl ethers (PBDEs) and the organochlorine compounds polychlorinated biphenyls (PCBs), DDTs, HCB, chlordane-related pesticides, HCH and toxaphene were analysed in blubber of juvenile ringed seals from Central West Greenland collected between 1982 and 2006. The longest time series could be established for PBDEs, partly based on archived material, while PCBs and DDTs covered a study period from 1994-2006. All organochlorines showed decreasing trends, most pronounced for DDT and HCH with an annual change of 8%. BDE-47 had a significantly increasing trend of 5% annually. It was the only BDE congener consistently above the detection limit, with annual median concentrations between 0.78 ng/g lw to 3.54 ng/g lw, i.e. about 10 times lower than values from East Greenland observed in a similar time trend study on ringed seal blubber [Rigét F, Vorkamp K, Dietz R, Rastogi SC. Temporal trend studies on polybrominated diphenyl ethers (PBDEs) and polychlorinated biphenyls (PCBs) in ringed seals from East Greenland. J Environ Monit 2006; 8: 1000-5]. A clear East>West difference was also found for PCBs and DDTs, but not for chlordanes, toxaphene or HCHs. Sigma 10-PCB, Sigma DDT and Sigma Chlordanes had similar annual median concentrations, typically exceeding SigmaPBDE by two orders of magnitude. The concentrations of HCH and toxaphene were in an intermediate group, with highest annual median concentrations of 135 ng/g lw and 20 ng/g lw, respectively. For most compound groups, the circumpolar trend previously established under for example the Arctic Monitoring and Assessment Programme was confirmed, but apparently, more data are needed for chlordane-related compounds and toxaphene. Statistical analyses of the compound patterns in the ringed seal samples revealed significantly greater differences between seals from East and West than between different sampling years. Higher proportions of PCBs and DDTs and lower proportions of chlordanes and HCHs were found in seals from East Greenland than in those from West Greenland. Based on principal component analysis of individual congener and compounds, seals from East Greenland were found to contain higher proportions of the higher chlorinated CB congeners. Varying patterns between sampling locations may be caused by different exposure situations related to contaminant emissions and transport, but different feeding habits may also affect the contaminant composition.     

State of the art in the analysis of brominated flame retardants in biota and sediment: insights from the characterisation of two new certified reference materials

Environmental Science and Pollution Research - The Joint Research Centre (JRC) of the European Commission has recently released two new Certified Reference Materials (CRMs) for the analysis of...     

Fate of the fungicide dodemorph during anaerobic digestion of biological waste

The aim of this study was to examine the stability and distribution of the fungicide dodemorph during anaerobic digestion of biological waste, including a short subsequent aerobic treatment. Three reactor experiments were conducted. The influences of pH and dissolved organic carbon (DOC) were further studied in batch experiments. The reactor experiments showed no decrease in the concentration of dodemorph, indicating stability of the fungicide. In connection with the results of the batch experiments, a clear pH-dependency of the partitioning of dodemorph between solid and water phase could be shown. At pH values below the pK(a) value of 7.8, protonated dodemorph molecules predominate. However, a release into the water phase was only observed at pH values of 5 and below. It can be assumed that in the pH range between 5 and 7.8 dodemorph forms bonds with carboxyl groups of organic matter. Dodemorph was not completely extractable from the solid waste matrix due to strong bonds with the organic matter. Solubilising effects by water ingredients of the process water were not apparent.     

The Application of Stable Isotopes for Assessing the Hydrological, Sulfur, and Iron Balances of Acidic Mining Lake ML 111 (Lusatia, Germany) as a Basis for Biotechnological Remediation

Stable isotope (¹⁸O–H₂O, ²H–H₂O ³⁴S–SO₄ ^2-) andhydrochemical data (SO₄ ^2-, Fe-concentrations) have beenused to estimate the annual groundwater inflow and outflow of mining lake ML 111 and to calculate the total amount of dissolvedsulfate and iron that is carried into the lake by groundwater. The hydrological balance suggests an annual groundwater inflow of 23 700 m³ and an annual groundwater outflow of 15 700 m³. The calculation of the sulfur and iron balances yielded an annual sulfate input of 37 800 kg and an annual iron input of 7000 kg with the groundwater inflow. Furthermore it was shown that significant fluxes of these elements go into the lake sediments which results in continuous release of acidity in the lake water.     

14C-Photosynthesis of Phytoplankton in an Oligotrophic Alpine Lake (Traunsee,Austria) and its Response to Turbidity Caused by Industrial Tailings

The influence of industrial tailings on the biological integrity of the phytoplankton was assessed from annual measurements of photosynthetic rates in the alpine lake Traunsee. The mean annual integral production of 21 mmol C m^-2 d^-1 corresponded to the oligotrophic nature of the lake. Effects of effluents were tested by comparing photosynthesis at a station close to the industrial outlet (EB) and at a reference site with a maximum depth of 190 m (VI). Between-site optical properties (vertical attenuation coefficient, euphotic depth) were statistically significant different. The euphotic zone at the impacted station was on average 2 m shallower than at the reference site, owing to turbidity emanating from the industrial plant. The adaptation to low light intensities by the algal community at this station was evident from a high maximum light utilisation coefficient (^* at low light saturation (E _K). Algae at the deep reference site were photosynthetically less efficient but adapted to high light intensities. Photosynthetic adaptation to different light climates in the euphotic zone without significant quantitative biomass alterations at the impacted site gave a clear signature of biological integrity of the phytoplankton in the oligotrophic Traunsee.     

Development and Evaluation of Bankfull Hydraulic Geometry Relationships for the Physiographic Regions of the United States

Bankfull hydraulic geometry relationships are used to estimate channel dimensions for streamflow simulation models, which require channel geometry data as input parameters. Often, one nationwide curve is used across the entire United States (U.S.) (e.g., in Soil and Water Assessment Tool), even though studies have shown that the use of regional curves can improve the reliability of predictions considerably. In this study, regional regression equations predicting bankfull width, depth, and cross‐sectional area as a function of drainage area are developed for the Physiographic Divisions and Provinces of the U.S. and compared to a nationwide equation. Results show that the regional curves at division level are more reliable than the nationwide curve. Reliability of the curves depends largely on the number of observations per region and how well the sample represents the population. Regional regression equations at province level yield even better results than the division‐level models, but because of small sample sizes, the development of meaningful regression models is not possible in some provinces. Results also show that drainage area is a less reliable predictor of bankfull channel dimensions than bankfull discharge. It is likely that the regional curves can be improved using multiple regression models to incorporate additional explanatory variables.     

A novel marine silk

The discovery of a novel silk production system in a marine amphipod provides insights into the wider potential of natural silks. The tube-building corophioid amphipod Crassicorophium bonellii produces from its legs fibrous, adhesive underwater threads that combine barnacle cement biology with aspects of spider silk thread extrusion spinning. We characterised the filamentous silk as a mixture of mucopolysaccharides and protein deriving from glands representing two distinct types. The carbohydrate and protein silk secretion is dominated by complex β-sheet structures and a high content of charged amino acid residues. The filamentous secretion product exits the gland through a pore near the tip of the secretory leg after having moved through a duct, which subdivides into several small ductules all terminating in a spindle-shaped chamber. This chamber communicates with the exterior and may be considered the silk reservoir and processing/mixing space, in which the silk is mechanically and potentially chemically altered and becomes fibrous. We assert that further study of this probably independently evolved, marine arthropod silk processing and secretion system can provide not only important insights into the more complex arachnid and insect silks but also into crustacean adhesion cements.     

Detecting general plant functional type responses in fragmented landscapes using spatially-explicit simulations

Habitat loss and increasing landscape fragmentation are known to be key forces driving the ongoing loss of plant species diversity. While the combined effects of increasing isolation and decreasing population size have been studied intensively; it is less understood how plant population performance in heterogeneous landscapes is affected by changes in fragmentation alone.