The Cost-Effectiveness of Germline BReast CAncer Gene Testing in Metastatic Prostate Cancer Followed by Cascade Testing of First-Degree Relatives of Mutation Carriers.

Objectives: Patients with metastatic prostate cancer (mPCa) with BReast CAncer gene (BRCA) mutations benefit from targeted treatments (eg, olaparib). In addition, family members of affected patients have increased risk of hereditary cancers and benefit from early detection and prevention. International guidelines recommend genetic testing in mPCa; however, the value for money of testing patients with mPCa and cascade testing of blood-related family members has not been assessed.

Evaluation of Endobronchial Ultrasound-Guided Transbronchial Needle Aspiration (EBUS-TBNA) Samples from Advanced Non-Small Cell Lung Cancer for Whole Genome, Whole Exome and Comprehensive Panel Sequencing.

Endobronchial ultrasound-guided transbronchial needle aspiration (EBUS-TBNA) is often the only source of tumor tissue from patients with advanced, inoperable lung cancer. EBUS-TBNA aspirates are used for the diagnosis, staging, and genomic testing to inform therapy options. Here we extracted DNA and RNA from 220 EBUS-TBNA aspirates to evaluate their suitability for whole genome (WGS), whole exome (WES), and comprehensive panel sequencing.

Discrepancies in tumor mutation burden reporting from sequential endobronchial ultrasound transbronchial needle aspiration samples within single lymph node stations - brief report.

Introduction: Tumour Mutation Burden (TMB) is a potential biomarker for immune cancer therapies. Here we investigated parameters that might affect TMB using duplicate cytology smears obtained from endobronchial ultrasound transbronchial needle aspiration (EBUS TBNA)-sampled malignant lymph nodes.

Methods: Individual Diff-Quik cytology smears were prepared for each needle pass.

Whole Genome Sequencing in Advanced Lung Cancer can be Performed Using Diff-Quik Cytology Smears Derived from Endobronchial Ultrasound, Transbronchial Needle Aspiration (EBUS TBNA).

Introduction: Maximising alternative sample types for genomics in advanced lung cancer is important because bronchoscopic samples may sometimes be insufficient for this purpose. Further, the clinical applications of comprehensive molecular analysis such as whole genome sequencing (WGS) are rapidly developing. Diff-Quik cytology smears from EBUS TBNA is an alternative source of DNA, but its feasibility for WGS has not been previously demonstrated.

Guidelines for genetic testing in prostate cancer: a scoping review.

Background: Genetic testing, to identify pathogenic or likely pathogenic variants in prostate cancer, is valuable in guiding treatment decisions for men with prostate cancer and to inform cancer prevention and early detection options for their immediate blood relatives. There are various guidelines and consensus statements for genetic testing in prostate cancer. Our aim is to review genetic testing recommendations across current guidelines and consensus statements and the level of evidence supporting those recommendations.

Evaluating Diff-Quik cytology smears for large-panel mutation testing in lung cancer-Predicting DNA content and success with low-malignant-cellularity samples.

Background: Cytology smears are commonly collected during endobronchial ultrasound-guided transbronchial needle aspiration (EBUS TBNA) procedures but are rarely used for molecular testing. Studies are needed to demonstrate their great potential, in particular for the prediction of malignant cell DNA content and for utility in molecular diagnostics using large gene panels.

Methods: A prospective study was performed on samples from 66 patients with malignant lymph nodes who underwent EBUS TBNA.

Iron-enhanced sand filters: Multi-year urban runoff (stormwater) quality performance.

Untreated urban runoff (stormwater) is a major pathway for contaminants, e.g., nutrients and metals, to receiving waters.

Using the Daphnia magna Transcriptome to Distinguish Water Source: Wetland and Stormwater Case Studies.

A major challenge in ecotoxicology is accurately and sufficiently measuring chemical exposures and biological effects given the presence of complex and dynamic contaminant mixtures in surface waters. It is impractical to quantify all chemicals in such matrices over space and time, and even if it were practical, concomitant biological effects would not be elucidated. Our study examined the performance of the Daphnia magna transcriptome to detect distinct responses across three water sources in Minnesota: laboratory (well) waters, wetland waters, and storm waters.

A Combined Quantitative Evaluation Model for the Capability of Hyperspectral Imagery for Mineral Mapping.

To analyze the influence factors of hyperspectral remote sensing data processing, and quantitatively evaluate the application capability of hyperspectral data, a combined evaluation model based on the physical process of imaging and statistical analysis was proposed. The normalized average distance between different classes of ground cover is selected as the evaluation index. The proposed model considers the influence factors of the full radiation transmission process and processing algorithms.

Contaminants of emerging concern in urban stormwater: Spatiotemporal patterns and removal by iron-enhanced sand filters (IESFs).

Numerous contaminants of emerging concern (CECs) typically occur in urban rivers. Wastewater effluents are a major source of many CECs. Urban runoff (stormwater) is a major urban water budget component and may constitute another major CEC pathway.

Demonstration of a novel Xp22.2 microdeletion as the cause of familial extreme skewing of X-inactivation utilizing case-parent trio SNP microarray analysis.

Background: We report a kindred referred for molecular investigation of severe hemophilia A in a young female in which extremely skewed X-inactivation was observed in both the proband and her clinically normal mother.

Methods: Bidirectional Sanger sequencing of all F8 gene coding regions and exon/intron boundaries was undertaken. Methylation-sensitive restriction enzymes were utilized to investigate skewed X-inactivation using both a classical human androgen receptor (HUMARA) assay, and a novel method targeting differential methylation patterns in multiple informative X-chromosome SNPs.

Sources and transport of contaminants of emerging concern: A two-year study of occurrence and spatiotemporal variation in a mixed land use watershed.

The occurrence and spatiotemporal variation of 26 contaminants of emerging concern (CECs) were evaluated in 68 water samples in 2011-2012 in the Zumbro River watershed, Minnesota, U.S.A.

Contaminants of Emerging Concern: Mass Balance and Comparison of Wastewater Effluent and Upstream Sources in a Mixed-Use Watershed.

Understanding the sources, transport, and spatiotemporal variability of contaminants of emerging concern (CECs) is important for understanding risks and developing monitoring and mitigation strategies. This study used mass balances to compare wastewater treatment plant (WWTP) and upstream sources of 16 CECs to a mixed-use watershed in Minnesota, under different seasonal and hydrological conditions. Three distinct CEC groups emerged with respect to their source proportionality and instream behavior.

Sediment-water distribution of contaminants of emerging concern in a mixed use watershed.

This study evaluated the occurrence and distribution of 15 contaminants of emerging concern (CECs) in stream water and sediments in the Zumbro River watershed in Minnesota and compared these with sub-watershed land uses. Sixty pairs of sediment and water samples were collected across all seasons from four stream sites for over two years and analyzed for selected personal care products, pesticides, human and veterinary medications, and phytoestrogens. Spatial and temporal analyses indicate that pharmaceuticals and personal care products (urban/residential CECs) are significantly elevated in water and/or sediment at sites with greater population density (>100 people/km(2)) and percentage of developed land use (>8% of subwatershed area) than those with less population density and land area under development.

Identifying sources of emerging organic contaminants in a mixed use watershed using principal components analysis.

Principal components analysis (PCA) was used to identify sources of emerging organic contaminants in the Zumbro River watershed in Southeastern Minnesota. Two main principal components (PCs) were identified, which together explained more than 50% of the variance in the data. Principal Component 1 (PC1) was attributed to urban wastewater-derived sources, including municipal wastewater and residential septic tank effluents, while Principal Component 2 (PC2) was attributed to agricultural sources.

A novel mutation of the erythropoietin receptor gene associated with primary familial and congenital polycythaemia.

Primary familial and congenital polycythaemia (PFCP) is a rare form of inherited erythrocytosis caused by heterozygous mutations in the erythropoietin receptor gene (EPOR). We present a novel mutation in the EPOR in a 15-year-old male who was referred to our clinic for investigation of a persistently elevated haemoglobin level. A significant family history of unexplained erythrocytosis spanning four generations of the patient's family was established.

Host-delivered RNAi: an effective strategy to silence genes in plant parasitic nematodes.

Root-knot nematodes (Meloidogyne spp.) are obligate, sedentary endoparasites that infect many plant species causing large economic losses worldwide. Available nematicides are being banned due to their toxicity or ozone-depleting properties and alternative control strategies are urgently required.

PineappleDB: an online pineapple bioinformatics resource.

Background: A world first pineapple EST sequencing program has been undertaken to investigate genes expressed during non-climacteric fruit ripening and the nematode-plant interaction during root infection. Very little is known of how non-climacteric fruit ripening is controlled or of the molecular basis of the nematode-plant interaction. PineappleDB was developed to provide the research community with access to a curated bioinformatics resource housing the fruit, root and nematode infected gall expressed sequences.

Developing pineapple fruit has a small transcriptome dominated by metallothionein.

In a first step toward understanding the molecular basis of pineapple fruit development, a sequencing project was initiated to survey a range of expressed sequences from green unripe and yellow ripe fruit tissue. A highly abundant metallothionein transcript was identified during library construction, and was estimated to account for up to 50% of all EST library clones. Library clones with metallothionein subtracted were sequenced, and 408 unripe green and 1140 ripe yellow edited EST clone sequences were retrieved.

Altered shoot/root Na+ distribution and bifurcating salt sensitivity in Arabidopsis by genetic disruption of the Na+ transporter AtHKT1.

Sodium (Na+) is toxic to most plants, but the molecular mechanisms of plant Na+ uptake and distribution remain largely unknown. Here we analyze Arabidopsis lines disrupted in the Na+ transporter AtHKT1. AtHKT1 is expressed in the root stele and leaf vasculature.