Early circulating tumour DNA kinetics measured by ultra-deep next-generation sequencing during radical radiotherapy for non-small cell lung cancer: a feasibility study.

BACKGROUND: The evaluation of circulating tumour DNA (ctDNA) from clinical blood samples, liquid biopsy, offers several diagnostic advantages compared with traditional tissue biopsy, such as shorter processing time, reduced patient risk and the opportunity to assess tumour heterogeneity. The historically poor sensitivity of ctDNA testing, has restricted its integration into routine clinical practice for non-metastatic disease. The early kinetics of ctDNA during radical radiotherapy for localised NSCLC have not been described with ultra-deep next generation sequencing previously. MATERIALS AND METHODS: Patients with CT/PET-staged locally advanced, NSCLC prospectively consented to undergo serial venepuncture during the first week of radical radiotherapy alone. All patients received 55Gy in 20 fractions. Plasma samples were processed using the commercially available Roche AVENIO Expanded kit (Roche Sequencing Solutions, Pleasanton, CA, US) which targets 77 genes. RESULTS: Tumour-specific mutations were found in all patients (1 in 3 patients; 2 in 1 patient, and 3 in 1 patient). The variant allele frequency of these mutations ranged from 0.05-3.35%. In 2 patients there was a transient increase in ctDNA levels at the 72 h timepoint compared to baseline. In all patients there was a non-significant decrease in ctDNA levels at the 7-day timepoint in comparison to baseline (p = 0.4627). CONCLUSION: This study demonstrates the feasibility of applying ctDNA-optimised NGS protocols through specified time-points in a small homogenous cohort of patients with localised lung cancer treated with radiotherapy. Studies are required to assess ctDNA kinetics as a predictive biomarker in radiotherapy. Priming tumours for liquid biopsy using radiation warrants further exploration.

Descriptive epidemiology of clubfoot in Romania: a clinic-based study.

OBJECTIVE: Congenital clubfoot affects 1 per 1000 live births per year in Romania. To date, no epidemiological studies have been conducted in this country to assess risk factors associated with the deformity. The aim of this study was to evaluate specific environmental and socio-demographic factors that may increase the risk of an infant to be born with clubfoot. PATIENTS AND METHODS: A descriptive clinic-based study over a twelve-week period was conducted using structured questionnaires given to biological parents of clinically confirmed clubfoot and control subjects. 62 parents of probands and 66 parents of control patients were enrolled for risk factor questionnaires. Phenotypic data from clubfoot children was also collected. RESULTS: We found that males were twice as likely to have clubfoot and half of clubfoot subjects were affected bilaterally. There was no significant difference in the rate of left versus right clubfoot. Infant and maternal characteristics showing a strong association with clubfoot included breech presentation and old maternal age at conception. CONCLUSIONS: Our results support reported literature data that males are two times as likely to have clubfoot which indicates a genetic influence. Previous reports suggest clubfoot babies are born to young mothers but in Romania advanced maternal age (≥ 35 years) was an indicator which may suggest genetic influence. This clinic-based study does not support previously recorded data of a positive association for maternal or household smoking. Data from this Romanian population also does not support previous data suggesting strong associations with maternal diabetes.

Managing agricultural emissions to the atmosphere: state of the science, fate and mitigation, and identifying research gaps.

The impact of agriculture on regional air quality creates significant challenges to sustainability of food supplies and to the quality of national resources. Agricultural emissions to the atmosphere can lead to many nuisances, such as smog, haze, or offensive odors. They can also create more serious effects on human or environmental health, such as those posed by pesticides and other toxic industrial pollutants. It is recognized that deterioration of the atmosphere is undesirable, but the short- and long-term impacts of specific agricultural activities on air quality are not well known or understood. These concerns led to the organization of the 2009 American Chemical Society Symposium titled . An outcome of this symposium is this special collection of 14 research papers focusing on various issues associated with production agriculture and its effect on air quality. Topics included emissions from animal feeding operations, odors, volatile organic compounds, pesticides, mitigation, modeling, and risk assessment. These papers provide new research insights, identify gaps in current knowledge, and recommend important future research directions. As the scientific community gains a better understanding of the relationships between anthropogenic activities and their effects on environmental systems, technological advances should enable a reduction in adverse consequences on the environment.

Fate of dietary perchlorate in lactating dairy cows: Relevance to animal health and levels in the milk supply.

Perchlorate is a goitrogenic anion that competitively inhibits the sodium iodide transporter and has been detected in forages and in commercial milk throughout the U.S. The fate of perchlorate and its effect on animal health were studied in lactating cows, ruminally infused with perchlorate for 5 weeks. Milk perchlorate levels were highly correlated with perchlorate intake, but milk iodine was unaffected, and there were no demonstrable health effects. We provide evidence that up to 80% of dietary perchlorate was metabolized, most likely in the rumen, which would provide cattle with a degree of refractoriness to perchlorate. Data presented are important for assessing the environmental impact on perchlorate concentrations in milk and potential for relevance to human health.

Acetylcholinesterase activity in grass shrimp and aqueous pesticide levels from South Florida drainage canals.

Freshwater drainage canals in South Florida are utilized to manage water in agricultural, urban, and water conservation areas and, as a result, collect urban and agricultural storm runoff that is discharged into the Atlantic Ocean and Gulf of Mexico. Pesticides in this runoff may be toxic to the biota inhabiting these waters. This study evaluated the effects of contaminants in South Florida canals draining into Biscayne Bay on the estuarine grass shrimp (Palaemonetes intermedius), a representative invertebrate species. Results of surface water analysis for pesticides indicated that eight pesticides out of 52 analyzed were detected. The herbicide metolachlor was found at all nine sites in the five canals sampled at concentrations up to 119 ng/L. Atrazine was detected at seven sites at concentrations up to 29 ng/L. Three organophosphate insecticides (chlorpyrifos, malathion, diazinon) were detected at three sites in two canals (Military and North). Grass shrimp from these three sites showed significantly reduced levels of the acetylcholinesterase enzyme as compared to control shrimp. These two canals are similar in the land use areas drained--urban and suburban and agriculture. The results suggest that monitoring organisms for AChE levels can be a means of detecting exposure to organophosphorus pesticide contamination.

Thermodynamic, spectroscopic, and computational evidence for the irreversible conversion of beta- to alpha-endosulfan.

Previous studies have provided unequivocal evidence for the symmetry of beta-endosulfan and the corresponding asymmetry of alpha-endosulfan; the conversion of beta-endosulfan to alpha-endosulfan was identified. In this study, evidence from differential scanning calorimetry (DSC) and nuclear magnetic resonance (NMR) experiments combined with computational chemistry calculations was used to propose a molecular mechanism for the corresponding conformational changes that occur in this process. DSC and NMR data of mixtures indicated that both isomers can influence the conformer populations in the solid, solution, and vapor phase. Computational chemistry demonstrated that the relative S==O configuration between alpha- and beta-isomers can be the intermediate state through which the conformations of alpha- and beta-isomers affect each other. Furthermore, calculations for mixtures indicated that the asymmetrical conformation of the sulfite in alpha-endosulfan can induce asymmetry in beta-endosulfan, and conversion to alpha-endosulfan occurs from this transition state.

Runoff loss of pesticides and soil: a comparison between vegetative mulch and plastic mulch in vegetable production systems.

Current vegetable production systems use polyethylene (plastic) mulch and require multiple applications of agrochemicals. During rain events, runoff from vegetable production is enhanced because 50 to 75% of the field is covered with an impervious surface. This study was conducted to quantify off-site movement of soil and pesticides with runoff from tomato (Lycopersicon esculentum Mill.) plots containing polyethylene mulch and a vegetative mulch, hairy vetch (Vicia villosa Roth). Side-by-side field plots were instrumented with automated flow meters and samplers to measure and collect runoff, which was filtered, extracted, and analyzed to determine soil and pesticide loss. Seasonal losses of two to four times more water and at least three times as much sediment were observed from plots with polyethvlene mulch (55.4 to 146 L m(-2) and 247 to 535 g m(-2), respectively) versus plots with hairy vetch residue (13.7 to 75.7 L m(-2) and 32.8 to 118 g m(-2), respectively). Geometric means (+/-standard deviation) of total pesticide loads for chlorothalonil (tetrachloroisophthalonitrile) and alpha-and beta-endosulfan (6,7,8,9,10,10-hexachloro-1,5,5a,6,9,9a-hexahydro6,9-methano-2,4,3-benzodioxathiepin 3-oxide) for a runoff event were 19, 6, and 9 times greater from polyethylene (800+/-4.6, 17.6+/-3.9, and 39.1+/-4.9 microg m(-2), respectively) than from hairy vetch mulch plots (42+/-6.0, 2.8+/-5.0, and 4.3+/-4.6 microg m(-2), respectively) due to greater concentrations and larger runoff volumes. The increased runoff volume, soil loss, and off-site loading of pesticides measured in runoff from the polyethylene mulch suggests that this management practice is less sustainable and may have a harmful effect on the environment.

Hydrolysis of chlorpyrifos in natural waters of the Chesapeake Bay.

Chlorpyrifos is the most widely used insecticide in the Chesapeake Bay region. Recent studies show that this organophospate chemical is consistently present in the air, rain and surface waters of the Chesapeake Bay region, suggesting a long environmental half-life. Hydrolytic degradation of chlorpyrifos is likely a dominant removal process, but existing hydrolysis data do not reflect conditions in the Chesapeake Bay. In this project, hydrolysis rates of chlorpyrifos were measured in sterilized, ambient water from the mouth of four Chesapeake Bay tributaries ranging in salinity from 0 to 17 ppt. The measured hydrolysis half-lives varied from 24 d in the Patuxent River to 126 d in the Susquehanna River. These results indicate that pH alone cannot be used as a single parameter to predict hydrolysis under field conditions. The influence of copper concentration, and other water constituents, need to be further evaluated as they may emerge as independent predictors to assess the fate of pesticides in natural systems.

Pesticides and amphibian population declines in California, USA.

Several species of anuran amphibians have undergone drastic population declines in the western United States over the last 10 to 15 years. In California, the most severe declines are in the Sierra Mountains east of the Central Valley and downwind of the intensely agricultural San Joaquin Valley. In contrast, coastal and more northern populations across from the less agrarian Sacramento Valley are stable or declining less precipitously. In this article, we provide evidence that pesticides are instrumental in declines of these species. Using Hyla regilla as a sentinel species, we found that cholinesterase (ChE) activity in tadpoles was depressed in mountainous areas east of the Central Valley compared with sites along the coast or north of the Valley. Cholinesterase was also lower in areas where ranid population status was poor or moderate compared with areas with good ranid status. Up to 50% of the sampled population in areas with reduced ChE had detectable organophosphorus residues, with concentrations as high as 190 ppb wet weight. In addition, up to 86% of some populations had measurable endosulfan concentrations and 40% had detectable 4,4'-dichlorodiphenyldichloroethylene, 4,4'-DDT, and 2,4'-DDT residues.

Pesticides are involved with population declines of amphibians in the California Sierra Nevadas.

Several species of frogs and toads are in serious decline in the Sierra Nevada Mountains of California. These species include the threatened red-legged frog ( Rana aurora ), foothill yellow-legged frog ( R. boylii ), mountain yellow-legged frog ( R. muscosa ), Cascades frog ( Rana cascadae ), western toad ( Bufo boreas ) and Yosemite toad ( B. canorus ). For many of these species current distributions are down to 10% of historical ranges. Several factors including introduced predators, habitat loss, and ultraviolet radiation have been suggested as causes of these declines. Another probable cause is air-borne pesticides from the Central Valley of California. The Central Valley, especially the San Joaquin Valley, is a major agricultural region where millions of pounds of active ingredient pesticides are applied each year (http://www.cdpr.ca.gov/dprdatabase.htm). Prevailing westerly winds from the Pacific Coast transport these pesticides into the into the Sierras.

Genetic testing and Alzheimer disease: recommendations of the Stanford Program in Genomics, Ethics, and Society.

Several genes associated with Alzheimer disease (AD) have been localized and cloned; two genetic tests are already commercially available, and new tests are being developed. Genetic testing for AD--either for disease prediction or for diagnosis--raises critical ethical concerns. The multidisciplinary Alzheimer Disease Working Group of the Stanford Program in Genomics, Ethics, and Society (PGES) presents comprehensive recommendations on genetic testing for AD. The Group concludes that under current conditions, genetic testing for AD prediction or diagnosis is only rarely appropriate. Criteria for judging the readiness of a test for introduction into routine clinical practice typically rely heavily on evaluation of technical efficacy. PGES recommends a broader and more comprehensive approach, considering: 1) the unique social and historical meanings of AD; 2) the availability of procedures to promote good surrogate decision making for incompetent patients and to safeguard confidentiality; 3) access to sophisticated genetic counselors able to communicate complex risk information and effectively convey the social costs and psychological burdens of testing, such as unintentional disclosure of predictive genetic information to family members; 4) protection from inappropriate advertising and marketing of genetic tests; and 5) recognition of the need for public education about the meaning and usefulness of predictive and diagnostic tests for AD. In this special issue of Genetic Testing, the PGES recommendations are published along with comprehensive background papers authored by Working Group members.

Understanding genetic testing for Alzheimer disease: medical and epidemiological background.

To assess the potential benefits and risks of genetic testing for Alzheimer disease (AD), patients and families, health care providers, and policymakers must understand the medical and epidemiologic aspects of the disease. This paper provides a brief overview of the symptoms, progression, and etiology of AD, as well as of the prevalence and incidence of the disease. The established and the controversial risk factors thought to be associated with the development of AD are described. Current methods for diagnosing and treating AD are also reviewed.

The genetics of Alzheimer disease and the application of molecular tests.

Two general classes of genes are associated with the development of Alzheimer disease (AD). The first group consists of genes that appear to cause AD when mutated, and the second category is composed of genes that are statistically associated with AD, depending on the inheritance of specific alleles. This paper reviews the current state of knowledge about the genetics of AD, and we then discuss the two molecular tests that are currently commercially available. These include a genetic test for mutations in the presenilin 1 (PS1) gene that can diagnose or predict a subset of early onset familial AD with a high degree of certainty. The value of the genetic test for the apolipoprotein (APOE) allele status is far less clear. Inheritance of the epsilon 4 allele is associated with an increased risk of AD at a population level, but APOE genotyping is inappropriate for prediction of future disease in an individual and offers only a marginal increase in diagnostic certainty when symptomatic individuals are tested. In the future, genetic tests may become more broadly applicable to the diagnosis and prediction of AD. However, the utility of such tests is currently limited to a small subset of individuals because in the vast majority of AD cases no clear genetic or environmental cause has been defined.

Evaluation of genetic tests: APOE genotyping for the diagnosis of Alzheimer disease.

Many studies have now confirmed the association between inheritance of the epsilon 4 allele of the apolipoprotein E (APOE) gene and Alzheimer disease (AD). However, although the medical community holds the near-unanimous opinion that APOE genotyping should not be used for prediction in asymptomatic individuals, controversy remains about whether it should be used for diagnosis in patients who show signs of dementia. We assessed critically the recent clinical studies, on the basis of four criteria recommended to ensure safety and effectiveness of genetic tests. We also developed a formal framework for evaluating the usefulness of APOE genotyping using decision-theoretic principles. We conclude that neither the presence nor absence of an epsilon 4 allele provides diagnostic certainty, and the proper interpretation of either result in heterogeneous populations requires further investigation. The appropriate role of APOE genotyping among elements of a traditional assessment for AD has not been determined. Whether APOE genotyping provides sufficient information to change patient management decisions has not been determined. APOE genotyping presents foreseeable, significant psychosocial consequences for family members that must be weighed against any psychosocial benefits. Therefore, the diagnostic use of APOE genotyping outside research settings is premature until such testing is shown to be of practical value.

The application of medical decision analysis to genetic testing: an introduction.

The availability of genetic tests to diagnose or predict Alzheimer disease (AD) causes a shift in the way people think about the condition and how they assess the options available to them. Decision analysis in a quantitative approach for dealing with the uncertainties inherent in many medical decisions, including decisions about genetic testing. Decision analysis does not guarantee a good outcome, but aims to yield better overall average results by providing a framework for people to evaluate their options and minimize cognitive biases. We provide an overview of the decision analysis process, including the terms and tools commonly associated with it. We also use a recent example to demonstrate one way decision analysis has been applied to genetics in the medical literature. This paper is an introduction to subsequent papers that explore the specific question of whether decision analysis is a helpful tool for understanding the uncertainty inherent in probabilistic information about genetic risk for AD.

Small intestinal ulceration secondary to carcinoid tumour arising in a Meckel's diverticulum.

A solitary small intestinal ulcer associated with a carcinoid tumour in a nearby Meckel's diverticulum was found in a 77 year old man presenting with massive rectal bleeding. Angiography and a radioisotope study localised the bleeding to the ileum. At operation, the Meckel's diverticulum was identified, with bleeding from an ulcer just distal to it. Pathological examination revealed a small carcinoid tumour confined to the Meckel's diverticulum. Close to the opening of the diverticulum, within the ileum, a well demarcated ulcer was present. Histology showed a non-specific ulcer which eroded a large blood vessel. This is the first documented occurrence of solitary small intestinal ulceration in association with a carcinoid tumour. Carcinoid tumour should be added to the list of possible causes of small intestinal ulceration. The ulceration may be secondary to release of cytokines by the tumour.