Assessment of Digital PCR as a Primary Reference Measurement Procedure to Support Advances in Precision Medicine.

BACKGROUND: Genetic testing of tumor tissue and circulating cell-free DNA for somatic variants guides patient treatment of many cancers. Such measurements will be fundamental in the future support of precision medicine. However, there are currently no primary reference measurement procedures available for nucleic acid quantification that would support translation of tests for circulating tumor DNA into routine use. METHODS: We assessed the accuracy of digital PCR (dPCR) for copy number quantification of a frequently occurring single-nucleotide variant in colorectal cancer (KRAS c.35G>A, p.Gly12Asp, from hereon termed G12D) by evaluating potential sources of uncertainty that influence dPCR measurement. RESULTS: Concentration values for samples of KRAS G12D and wild-type plasmid templates varied by <1.2-fold when measured using 5 different assays with varying detection chemistry (hydrolysis, scorpion probes, and intercalating dyes) and <1.3-fold with 4 commercial dPCR platforms. Measurement trueness of a selected dPCR assay and platform was validated by comparison with an orthogonal method (inductively coupled plasma mass spectrometry). The candidate dPCR reference measurement procedure showed linear quantification over a wide range of copies per reaction and high repeatability and interlaboratory reproducibility (CV, 2%-8% and 5%-10%, respectively). CONCLUSIONS: This work validates dPCR as an SI-traceable reference measurement procedure based on enumeration and demonstrates how it can be applied for assignment of copy number concentration and fractional abundance values to DNA reference materials in an aqueous solution. High-accuracy measurements using dPCR will support the implementation and traceable standardization of molecular diagnostic procedures needed for advancements in precision medicine.

Arsenic partitioning among particle-size fractions of mine wastes and stream sediments from cinnabar mining districts.

Tailings from abandoned mercury mines represent an important pollution source by metals and metalloids. Mercury mining in Asturias (north-western Spain) has been carried out since Roman times until the 1970s. Specific and non-specific arsenic minerals are present in the paragenesis of the Hg ore deposit. As a result of intensive mining operations, waste materials contain high concentrations of As, which can be geochemically dispersed throughout surrounding areas. Arsenic accumulation, mobility and availability in soils and sediments are strongly affected by the association of As with solid phases and granular size composition. The objective of this study was to examine phase associations of As in the fine grain size subsamples of mine wastes (La Soterraña mine site) and stream sediments heavily affected by acid mine drainage (Los Rueldos mine site). An arsenic-selective sequential procedure, which categorizes As content into seven phase associations, was applied. In spite of a higher As accumulation in the finest particle-size subsamples, As fractionation did not seem to depend on grain size since similar distribution profiles were obtained for the studied granulometric fractions. The presence of As was relatively low in the most mobile forms in both sites. As was predominantly linked to short-range ordered Fe oxyhydroxides, coprecipitated with Fe and partially with Al oxyhydroxides and associated with structural material in mine waste samples. As incorporated into short-range ordered Fe oxyhydroxides was the predominant fraction at sediment samples, representing more than 80% of total As.

Comparison of three sequential extraction procedures for fractionation of arsenic from highly polluted mining sediments.

Three sequential extraction procedures were evaluated for the study of fractionation of arsenic in environmental solid samples. The procedures considered were as follows: i) the standardized and widely recognised BCR procedure, conceived for the study of the partitioning of heavy metals; ii) the procedure developed by Manful, who adapted a phosphorus scheme for arsenic fractionation; and iii) a novel sequential extraction scheme especially devised for arsenic. The efficiency and suitability of these methods and the corresponding extraction steps for partitioning arsenic obtained from the most important solid forms were tested by application of the methods to real sediment samples heavily polluted by mining activity. Results showed the BCR scheme was inappropriate for arsenic fractionation. The procedure could, nevertheless, be a first approach for the assessment of arsenic partitioning, because its first extraction step can be regarded as adequate for the estimation of the most easily mobilizable arsenic. Although the Manful scheme results in a more differentiated arsenic pattern, some drawbacks arise from the lack of selectivity of some of the reagents used, for example overlapping of specific target phases, overestimation of adsorbed arsenate because of inadequate coprecipitation processes, and the inability to discriminate among amorphous and crystalline oxyhydroxides which are mainly responsible for arsenic retention. The novel procedure achieves the most suitable arsenic fractionation, because the main phases retaining arsenic are selectively targeted according to mobilization potential. In addition, the simplicity of its extraction steps would enable automation in a continuous flow scheme.

Arsenic contamination and speciation in surrounding waters of three old cinnabar mines.

The impact of arsenic pollution in waters from the surroundings of three abandoned Hg mines in Northern Spain, as well as reaching the Caudal River, was evaluated. For assessing the factors controlling arsenic release, an extensive study based on the physicochemical characterization and multivariate statistical analysis of waters upstream and downstream each mine site was performed. Waters downstream of the La Soterraña mine present the highest arsenic concentrations, up to 38.8 mg L(-1), coming mainly from the solubilisation of calcium, magnesium and strontium arsenates at a pH close to neutral. Although arsenic concentrations downstream of La Peña are markedly lower, these values remain too high, indicating that the encapsulation carried out in this spoil heap is insufficient. In addition, the high water flow in this point involves an extremely high input of arsenic to the surroundings (0.3 g s(-1)). Waters close to tailings from Los Rueldos suffer from acid mine drainage, provoking an important solubilisation of arsenic and heavy metals, a situation which is rapidly softened with distance. The study of arsenic speciation reveals the omnipresence of As(v) in waters from the three mines, whereas in La Peña low amounts of As(iii) were also detected. Different preservation methods for As speciation were compared, such as the addition of HCl, EDTA and the storage of samples without any additive, and no alteration of samples in any case up to nine months after the collection was observed. A study of seasonal variations of As and the main parameters affecting its concentration and speciation was completed throughout a year, showing no remarkable dependency with rainfall for any studied variable.

The ichthyology collection at the Natural History Museum of El Salvador (MUHNES): Species checklist and new country records.

The ichthyology collection at the Natural History Museum of El Salvador (MUHNES) was established in 1970. Herein, we provide the first quantitative and qualitative description of the collection; and the first public record of the specimens and taxa therein represented. The MUHNES fish collection is the largest and most important of El Salvador, hosting 3791 specimens in 1005 lots representing 26 orders, 75 families, 159 genera and 248 species from both marine and freshwater environments, including larval, juvenile and mainly adult specimens. MUHNES specimens include 39% of the 587 species reported in the official national checklist of fishes of El Salvador, and support the inclusion of 47 additional species for a new total of 634. Furthermore, MUHNES specimens support (1) the occurrence of Cathorops fuerthii along the coast of El Salvador, extending its distribution from northern Costa Rica; (2) the occurrence of Atherinella starksi in El Salvador, reducing a gap for records between Nicaragua and México and (3) the extension in the distribution range of Profundulus kreiseri to Morazán, El Salvador. This study represents an advance on the understanding of diversity and distribution of the national ichthyofauna.

A methodological approach to evaluate arsenic speciation and bioaccumulation in different plant species from two highly polluted mining areas.

Arsenic accumulation and speciation in different plant species growing in two polluted sites were examined, in addition to arsenic transfer from soils to plants. The studied areas were two abandoned mercury mines in Northern Spain, La Soterraña and Los Rueldos. Plants accumulated extremely high amounts of arsenic in their tissues. Accumulation rates depend on both the grade of pollution of the site and on the plant species itself. Total arsenic concentrations varied depending on the part of the plant, with roots accumulating the most arsenic in all the studied plants (up to 1400 mg · kg(-1)). A suitable extraction method for arsenic speciation in the studied samples was developed and optimized using 0.3M orthophosphoric acid as the extracting agent in a graphite block digestion system at 90 °C for 1h. Extraction efficiencies were above 80% and speciation was not altered, since recoveries of the spiked arsenic species (As(III), As(V), DMA (dimethylarsonic acid) and MMA (monomethylarsonic acid)) were between 94 and 102%. Speciation studies were performed on the parts of each plant species by means of HPLC-ICP-MS with the results indicating no significant differences in the speciation between parts of the plants. As(V) was always the predominant species, although a non-negligible amount of As(III) was found for all samples. Little amounts of MMA and DMA occurred in certain samples. Arsenic uptake by plants depends on the plant available arsenic fraction in soils, here considered as the sum of water-soluble and phosphate-extractable fractions. Although soils from La Soterraña were less polluted, arsenic bioavailability was much higher than in Los Rueldos. Soil-to-plant transfer factors, based on total and available arsenic in soils, were evaluated for the studied plants. Dryopteris filix-mas and Calluna vulgaris (L.) Hull, from La Soterraña and Los Rueldos respectively, were the plants with the highest abilities to extract arsenic from their corresponding soils.

Arsenic pollution and fractionation in sediments and mine waste samples from different mine sites.

A characterization of arsenic pollution and its associations with solid mineral phases in sediments and spoil heap samples from four different abandoned mines in Spain is performed. Three of them were mercury mines located in the same mining district, in the province of Asturias, and the other one, devoted to arsenic mining, is in the province of León. A sequential extraction procedure, especially developed for arsenic, was applied for the study of arsenic partitioning. Very high total arsenic concentrations ranging 300-67,000 mg·kg(-1) were found. Arsenic fractionation in each mine is broadly in accordance with the mineralogy of the area and the extent of the mine workings. In almost all the studied samples, arsenic appeared predominantly associated with iron oxyhydroxides, especially in the amorphous form. Sediments from cinnabar roasted piles showed a higher arsenic mobility as a consequence of an intense ore treatment, posing an evident risk of arsenic spread to the surroundings. Samples belonging to waste piles where the mining activity was less intense presented a higher proportion of arsenic associated with structural minerals. Nevertheless, it represents a long-term source of arsenic to the environment.

Treating patients with fibromyalgia in primary care settings under routine medical practice: a claim database cost and burden of illness study.

INTRODUCTION: The objective of this study was to analyze health care and non-health care resource utilization under routine medical practice in a primary care setting claims database and to estimate the incremental average cost per patient per year of fibromyalgia syndrome (FMS) compared with a reference population. METHODS: A 12-month cross-sectional and retrospective study was completed using computerized medical records from a health provider database. Analyses were conducted from the perspective of the provider and from the viewpoint of society. Health care and non-health care resource utilization included drugs, complementary tests, all types of medical visits, referrals, hospitalizations, sick leave, and early retirement because of disability due to FMS. Patients with a diagnosis of FMS in accordance with ICD-10 (International Statistical Classification of Diseases and Related Health Problems, 10th revision) criteria were included in the analysis if they had at least one claim for FMS during the 12 months prior to the end of May 2007. A non-FMS comparison group was also created with the remaining subjects. RESULTS: Of the 63,526 patients recruited for the study, 1,081 (1.7%) (96.7% of whom were women, 54.2 [10.1] years old) met the criteria for FMS. After an adjustment for age and gender, FMS subjects used significantly more health care resources than the reference population and had more sick leave and the percentage of subjects with premature retirement was also significantly higher (P < 0.001 in all cases). As a result, FMS subjects showed an incremental adjusted per-patient per-year total cost of 5,010 euro (95% confidence interval [CI] 3,494 to 6,076, +153%, P < 0.001) on average compared with non-FMS subjects. Significantly higher differences were observed in both health care and non-health care adjusted costs: 614 euro (404 to 823, +66%) and 4,394 euro (3,373 to 5,420, +189%), respectively (P < 0.001 in both cases). Annual drug expenditure per patient on average was considerably higher in FMS patients, 230 euro (124 to 335, +64%, P < 0.001), than the reference group. CONCLUSIONS: Under routine medical practice, patients with FMS were associated with considerably higher annual total costs in the primary care setting compared with the reference population.