All-in-one whole exome sequencing strategy with simultaneous copy number variant,single nucleotide variant and absence-of-heterozygosity analysis in fetuses with structural ultrasound anomalies: A 1-year experience

Objective

We performed a 1-year evaluation of a novel strategy of simultaneously analyzing single nucleotide variants (SNVs), copy number variants (CNVs) and copy-number-neutral Absence-of-Heterozygosity from Whole Exome Sequencing (WES) data for prenatal diagnosis of fetuses with ultrasound (US) anomalies and a non-causative QF-PCR result.

Methods

After invasive diagnostics, whole exome parent-offspring trio-sequencing with exome-wide CNV analysis was performed in pregnancies with fetal US anomalies and a non-causative QF-PCR result (WES-CNV). On request, additional SNV-analysis, restricted to (the) requested gene panel(s) only (with the option of whole exome SNV-analysis afterward) was performed simultaneously (WES-CNV/SNV) or as rapid SNV-re-analysis, following a normal CNV analysis.

Results

In total, 415 prenatal samples were included. Following a non-causative QF-PCR result, WES-CNV analysis was initially requested for 74.3% of the chorionic villus (CV) samples and 45% of the amniotic fluid (AF) samples. In case WES-CNV analysis did not reveal a causative aberration, SNV-re-analysis was requested in 41.7% of the CV samples and 17.5% of the AF samples. All initial analyses could be finished within 2 weeks after sampling. For SNV-re-analysis during pregnancy, turn-around-times (TATs) varied between one and 8 days.

Conclusion

We show a highly efficient all-in-one WES-based strategy, with short TATs, and the option of rapid SNV-re-analysis after a normal CNV result.     

Long-term consequences of non-intentional flows of substances: Modelling non-intentional flows of lead in the Dutch economic system and evaluating their environmental consequences

Substances may enter the economy and the environment through both intentional and non-intentional flows. These non-intentional flows, including the occurrence of substances as pollutants in mixed primary resources (metal ores, phosphate ores and fossil fuels) and their presence in re-used waste streams from intentional use may have environmental and economic consequences in terms of pollution and resource availability. On the one hand, these non-intentional flows may cause pollution problems. On the other hand, these flows have the potential to be a secondary source of substances.This article aims to quantify and model the non-intentional flows of lead, to evaluate their long-term environmental consequences, and compare these consequences to those of the intentional flows of lead. To meet this goal, the model combines all the sources of non-intentional flows of lead within one model, which also includes the intentional flows.Application of the model shows that the non-intentional flows of lead related to waste streams associated with intentional use are decreasing over time, due to the increased attention given to waste management. However, as contaminants in mixed primary resources application, lead flows are increasing as demand for these applications is increasing.     

Adaptation to the Impacts of Sea Level Rise in Egypt

Assessment of the vulnerability and expected socioeconomic losses over the Nile delta coast due to the impact of sea level rise is carried out in details. Impacts of sea level rise over the Governorates of Alexandria and Port Said in particular, are evaluated quantitatively. Analysis of the results at Alexandria Governorate indicate that, if no action is taken, an area of about 30% of the city will be lost due to inundation. Almost 2 million people will have to abandon their homeland; 195,000 jobs will be lost and an economic loss of over $3.5 Billion is expected over the next century. At Port Said Governorate results indicate that beach areas are most severely affected (hence tourism), followed by urban areas. The agriculture sector is the least affected sector. It is estimated that the economic loss is over $ 2.0 Billion for 0.50 m SLR and may exceed $ 4.4 Billion for 1.25 m SLR. Options and costs of adaptation are analyzed and presented. Multi-criteria and decision matrix approaches, based on questionnaire surveys are carried out to identify priorities for the two cases. Analysis of these techniques of two options; the current policy (hard protection measures on some vulnerable areas) and no action (stopping these activities) have the lowest scores. Beach nourishment and integrated coastal zone management (ICZM) have the highest scores, however ICZM has high cost measures. The most cost-effective option is the land-use change, however with relatively very high cost measure. It is recommended that an ICZM approach be adopted since it provides a reasonable trade off between costs and cost effectiveness.     

The fate of trace metals during the metamorphosis of chironomids (diptera, chironomidae)

The fate of the trace metals zinc, cadmium and copper during the metamorphosis of chironomids was studied under field and experimental conditions. Field observations demonstrated a significant decrease in the trace metal body burden of larvae and imagines of Stictochironomus histrio Fabricius. No such difference were noted between successive developmental stages of Chironomus anthracinus Zett. The exuviae of both species contained small amounts of trace metals. Experiments, in which larvae of S. histrio and C. riparius Meigen were individually exposed, showed that larvae of both species accumulated substantial amounts of zinc and cadmium. For these metals, a transfer to pupae and imagines occurred. However, pupae had a lower body burden than larvae, and imagines a lower body burden than the pupae. Copper was also accumulated in the larvae, but it was excreted almost completely before the pupal stage. Elimination pathways of the trace metals during metamorphosis and the ecotoxicological consequences of trace metal transfer are discussed.