Assessing environmental exposure to viruses in wastewater treatment plant and swine farm scenarios with next-generation sequencing and occupational risk approaches.

Occupational exposure to pathogens can pose health risks. This study investigates the viral exposure of workers in a wastewater treatment plant (WWTP) and a swine farm by analyzing aerosol and surfaces samples. Viral contamination was evaluated using quantitative polymerase chain reaction (qPCR) assays, and target enrichment sequencing (TES) was performed to identify the vertebrate viruses to which workers might be exposed. Additionally, Quantitative Microbial Risk Assessment (QMRA) was conducted to estimate the occupational risk associated with viral exposure for WWTP workers, choosing Human Adenovirus (HAdV) as the reference pathogen. In the swine farm, QMRA was performed as an extrapolation, considering a hypothetical zoonotic virus with characteristics similar to Porcine Adenovirus (PAdV). The modelled exposure routes included aerosol inhalation and oral ingestion through contaminated surfaces and hand-to-mouth contact. HAdV and PAdV were widespread viruses in the WWTP and the swine farm, respectively, by qPCR assays. TES identified human and other vertebrate viruses WWTP samples, including viruses from families such as Adenoviridae, Circoviridae, Orthoherpesviridae, Papillomaviridae, and Parvoviridae. In the swine farm, most of the identified vertebrate viruses were porcine viruses belonging to Adenoviridae, Astroviridae, Circoviridae, Herpesviridae, Papillomaviridae, Parvoviridae, Picornaviridae, and Retroviridae. QMRA analysis revealed noteworthy risks of viral infections for WWTP workers if safety measures are not taken. The probability of illness due to HAdV inhalation was higher in summer compared to winter, while the greatest risk from oral ingestion was observed in workspaces during winter. Swine farm QMRA simulation suggested a potential occupational risk in the case of exposure to a hypothetical zoonotic virus. This study provides valuable insights into WWTP and swine farm worker's occupational exposure to human and other vertebrate viruses. QMRA and NGS analyses conducted in this study will assist managers in making evidence-based decisions, facilitating the implementation of protection measures, and risk mitigation practices for workers.

A fast non-parametric test of association for multiple traits.

The increasing availability of multidimensional phenotypic data in large cohorts of genotyped individuals requires efficient methods to identify genetic effects on multiple traits. Permutational multivariate analysis of variance (PERMANOVA) offers a powerful non-parametric approach. However, it relies on permutations to assess significance, which hinders the analysis of large datasets. Here, we derive the limiting null distribution of the PERMANOVA test statistic, providing a framework for the fast computation of asymptotic p values. Our asymptotic test presents controlled type I error and high power, often outperforming parametric approaches. We illustrate its applicability in the context of QTL mapping and GWAS.

The landscape of expression and alternative splicing variation across human traits.

Understanding the consequences of individual transcriptome variation is fundamental to deciphering human biology and disease. We implement a statistical framework to quantify the contributions of 21 individual traits as drivers of gene expression and alternative splicing variation across 46 human tissues and 781 individuals from the Genotype-Tissue Expression project. We demonstrate that ancestry, sex, age, and BMI make additive and tissue-specific contributions to expression variability, whereas interactions are rare. Variation in splicing is dominated by ancestry and is under genetic control in most tissues, with ribosomal proteins showing a strong enrichment of tissue-shared splicing events. Our analyses reveal a systemic contribution of types 1 and 2 diabetes to tissue transcriptome variation with the strongest signal in the nerve, where histopathology image analysis identifies novel genes related to diabetic neuropathy. Our multi-tissue and multi-trait approach provides an extensive characterization of the main drivers of human transcriptome variation in health and disease.

Evaluation of pathogen disinfection efficiency of electrochemical advanced oxidation to become a sustainable technology for water reuse.

Water treatment and reuse is gaining acceptance as a strategy to fight against water contamination and scarcity, but it usually requires complex treatments to ensure safety. Consequently, the electrochemical advanced processes have emerged as an effective alternative for water remediation. The main objective here is to perform a systematic study that quantifies the efficiency of a laboratory-scale electrochemical system to inactivate bacteria, bacterial spores, protozoa, bacteriophages and viruses in synthetic water, as well as in urban wastewater once treated in a wetland for reuse in irrigation. A Ti|RuO2-based plate and Si|BDD thin-film were comparatively employed as the anode, which was combined with a stainless-steel cathode in an undivided cell operating at 12 V. Despite the low resulting current density (<15 mA/cm2), both anodes demonstrated the production of oxidants in wetland effluent water. The disinfection efficiency was high for the bacteriophage MS2 (T99 in less than 7.1 min) and bacteria (T99 in about 30 min as maximum), but limited for CBV5 and TuV, spores and amoebas (T99 in more than 300 min). MS2 presented a rapid exponential inactivation regardless of the anode and bacteria showed similar sigmoidal curves, whereas human viruses, spores and amoebas resulted in linear profiles. Due the different sensitivity of microorganisms, different models must be considered to predict their inactivation kinetics. On this basis, it can be concluded that evaluating the viral inactivation from inactivation profiles determined for bacteria or some bacteriophages may be misleading. Therefore, neither bacteria nor bacteriophages are suitable models for the disinfection of water containing enteric viruses. The electrochemical treatment added as a final disinfection step enhances the inactivation of microorganisms, which could contribute to safe water reuse for irrigation. Considering the calculated low energy consumption, decentralized water treatment units powered by photovoltaic modules might be a near reality.

Evaluation of a virus concentration method based on ultrafiltration and wet foam elution for studying viruses from large-volume water samples.

Assessing the presence of viruses in large-volume samples involves cumbersome methods that require specialized training and laboratory equipment. In this study, a large volume concentration (LVC) method, based on dead-end ultrafiltration (DEUF) and Wet Foam Elution™ technology, was evaluated in different type of waters and different microorganisms. Its recovery efficiency was evaluated through different techniques (infectivity assays and molecular detection) by spiking different viral surrogates (bacteriophages PhiX174 and MS2 and Coxsackie virus B5 (CVB5) and Escherichia coli (E. coli). Furthermore, the application of a secondary concentration step was evaluated and compared with skimmed milk flocculation. Viruses present in river water, seawater and groundwater samples were concentrated by applying LVC method and a centrifugal ultrafiltration device (CeUF), as a secondary concentration step and quantified with specific qPCR Human adenoviruses (HAdV) and noroviruses (NoVs). MS2 was used as process control, obtaining a mean viral recovery of 22.0 ± 12.47%. The presence of other viruses was also characterized by applying two different next-generation sequencing approaches. LVC coupled to a secondary concentration step based on CeUF allowed to detect naturally occurring viruses such as HAdV and NoVs in different water matrices. Using HAdV as a human fecal indicator, the highest viral pollution was found in river water samples (100% of positive samples), followed by seawater (83.33%) and groundwater samples (66.67%). The LVC method has also proven to be useful as a virus concentration method in the filed since HAdV and NoVs were detected in the river water and groundwater samples concentrated in the field. All in all, LVC method presents high concentration factor and a low limit of detection and provides viral concentrates useful for subsequent molecular analysis such as PCR and massive sequencing.

Identification and analysis of splicing quantitative trait loci across multiple tissues in the human genome.

Alternative splicing (AS) is a fundamental step in eukaryotic mRNA biogenesis. Here, we develop an efficient and reproducible pipeline for the discovery of genetic variants that affect AS (splicing QTLs, sQTLs). We use it to analyze the GTEx dataset, generating a comprehensive catalog of sQTLs in the human genome. Downstream analysis of this catalog provides insight into the mechanisms underlying splicing regulation. We report that a core set of sQTLs is shared across multiple tissues. sQTLs often target the global splicing pattern of genes, rather than individual splicing events. Many also affect the expression of the same or other genes, uncovering regulatory loci that act through different mechanisms. sQTLs tend to be located in post-transcriptionally spliced introns, which would function as hotspots for splicing regulation. While many variants affect splicing patterns by altering the sequence of splice sites, many more modify the binding sites of RNA-binding proteins. Genetic variants affecting splicing can have a stronger phenotypic impact than those affecting gene expression.

Microbiological contamination of conventional and reclaimed irrigation water: Evaluation and management measures.

The wide diversity of irrigation water sources (i.e., drinking water, groundwater, reservoir water, river water) includes reclaimed water as a requested measure for increasing water availability, but it is also a challenge as pathogen exposure may increase. This study evaluates the level of microbial contamination in different irrigation waters to improve the knowledge and analyses management measures for safety irrigation. Over a one-year period, the occurrence of a set of viruses, bacteria and protozoa, was quantified and the performance of a wetland system, producing reclaimed water intended for irrigation, was characterized. Human fecal pollution (HAdV) was found in most of the irrigation water types analysed. Hepatitis E virus (HEV), an emerging zoonotic pathogen, was present in groundwater where porcine contamination was identified (PAdV). The skin-carcinoma associated Merkel cell polyomavirus (MCPyV), was found occasionally in river water. Noroviruses were detected, as expected, in winter, in river water and reclaimed water. Groundwater, river water and reservoir water also harboured potential bacterial pathogens, like Helicobacter pylori, Legionella spp. and Aeromonas spp. that could be internalized and viable inside amoebas like Acanthamoeba castellanii, which was also detected. Neither Giardia cysts, nor any Cryptosporidium oocysts were detected. The wetland system removed 3 Log10 of viruses and 5 Log10 of bacteria, which resembled the river water quality. Irrigation waters were prone to variable contamination levels and according to the European guidance documents, the E. coli (EC) levels were not always acceptable. Sporadic detection of viral pathogens as NoV GII and HAdV was identified in water samples presenting lower EC than the established limit (100MNP/100 mL). When dealing with reclaimed water as a source of irrigation the analysis of some viral parameters, like HAdV during the peak irrigation period (summer and spring) or NoV during the coldest months, could complement existing water management tools based on bacterial indicators.

Correlation of mRNA-PCA3 urine levels with the new grading system in prostate cancer / Correlación de mRNA-PCA3 en orina con el nuevo sistema de gradación de cáncer de próstata

Purpose: To evaluate the PCA3 (Prostate Cancer 3 gene) as a tool to improve prostate cancer (PCa) screening and its capability to predict PCa aggressiveness. Patients and methods: A retrospective study with data from consecutive patients with suspected PCa seen in the urology department between November 2009 and April 2016 and who were candidates for prostate biopsy. A total of 1038 urine samples were tested in our laboratory with a kit that generated a PCA3 score (s-PCA3). A prostate biopsy was recommended only in those patients with s-PCA3≥35. Associations between variables were analyzed using the R software. Results: In patients with a positive s-PCA3 (44.5%), a subsequent biopsy was recommended. Of a total of 151 biopsies studied, 56.3% yielded a diagnosis of PCa. The probability of a positive biopsy increased as the s-PCA3 increased (p=0.041). The percentage of affected cylinders increased as the s-PCA3 increased (p=0.015). A statistically significant relationship was observed between s-PCA3 and both the Gleason score and the Grade Group (p=0.001 and 0.008, respectively). The best log-linear models and a logistic model confirmed the relationships shown previously with Fisher's exact tests. Conclusions: S-PCA3 may serve as an additional marker to reduce the indication for biopsies and avoid overdiagnosis and overtreatment of patients with suspected PCa. The prognostic significance of s-PCA3 was confirmed, as it was associated with tumor volume and Gleason score. Importantly, to our knowledge this is the first time that an association has been demonstrated between s-PCA3 and the new Grade Group

Objetivo: Evaluar el estudio de PCA3 (gen Prostate Cancer 3) en orina como test complementario para mejorar el cribado de cáncer de próstata (CaP), así como su capacidad de predecir la agresividad tumoral antes de la biopsia. Pacientes y métodos: En este estudio retrospectivo se incluyeron pacientes consecutivos con sospecha de CaP y candidatos a biopsia, que se presentaron en la consulta del urólogo entre noviembre de 2009 y abril de 2016. Se testaron en nuestro laboratorio un total de 1.038 muestras de orina con un kit que generó un PCA3 score (s-PCA3). Se recomendó la biopsia en aquellos pacientes con s-PCA3≥35. Las asociaciones entre variables se analizaron con el software R. Resultados: En los pacientes con s-PCA3 positivo (44,5%) se recomendó la realización de una biopsia. Se estudiaron un total de 151 biopsias de las que un 56,3% fueron diagnosticadas de CaP. La probabilidad de obtener una biopsia positiva aumentó a medida que lo hacia el s-PCA3 (p=0,041). El porcentaje de cilindros afectados aumentó a medida que lo hacía el s-PCA3 (p=0,015). El s-PCA3 presentó una relación estadísticamente significativa con el grado de Gleason (p=0,001) y el grado grupo (p=0,008). El mejor modelo Log-lineal, así como el modelo logístico confirmaron las relaciones observadas previamente con las pruebas exactas de Fisher. Conclusiones: El s-PCA3 es una herramienta complementaria que permite reducir la indicación de biopsias y evitar el sobrediagnóstico y sobretratamiento de pacientes con sospecha de CaP. La significación pronóstica del s-PCA3 fue confirmada al demostrarse su asociación con el volumen tumoral y el grado de Gleason. Según la información de la que disponemos, este es el primer estudio en el que se demuestra la asociación entre el s-PCA3 y el nuevo sistema de gradación del CaP

Quantitative risk assessment of norovirus and adenovirus for the use of reclaimed water to irrigate lettuce in Catalonia.

Wastewater is an important resource in water-scarce regions of the world, and its use in agriculture requires the guarantee of acceptable public health risks. The use of fecal indicator bacteria to evaluate safety does not represent viruses, the main potential health hazards. Viral pathogens could complement the use of fecal indicator bacteria in the evaluation of water quality. In this study, we characterized the concentration and removal of human adenovirus (HAdV) and norovirus genogroup II (NoV GII), highly abundant and important viral pathogens found in wastewater, in two wastewater treatment plants (WWTPs) that use different tertiary treatments (constructed wetland vs conventional UV, chlorination and Actiflo® treatments) for a year in Catalonia. The main objective of this study was to develop a Quantitative Microbial Risk Assessment for viral gastroenteritis caused by norovirus GII and adenovirus, associated with the ingestion of lettuce irrigated with tertiary effluents from these WWTPs. The results show that the disease burden of NoV GII and HAdV for the consumption of lettuce irrigated with tertiary effluent from either WWTP was higher than the WHO recommendation of 10-6 DALYs for both viruses. The WWTP with constructed wetland showed a higher viral reduction on average (3.9 and 2.8 logs for NoV GII and HAdV, respectively) than conventional treatment (1.9 and 2.5 logs) but a higher variability than the conventional WWTP. Sensitivity analysis demonstrated that the input parameters used to estimate the viral reduction by treatment and viral concentrations accounted for much of the model output variability. The estimated reductions required to reach the WHO recommended levels in tertiary effluent are influenced by the characteristics of the treatments developed in the WWTPs, and additional average reductions are necessary (in WWTP with a constructed wetland: A total of 6.7 and 5.1 logs for NoV GII and HAdV, respectively; and in the more conventional treatment: 7 and 5.6 logs). This recommendation would be achieved with an average quantification of 0.5 genome copies per 100 mL in reclaimed water for both viruses. The results suggest that the analyzed reclaimed water would require additional treatments to achieve acceptable risk in the irrigation of vegetables with reclaimed water.

Correlation of mRNA-PCA3 urine levels with the new grading system in prostate cancer.

PURPOSE: To evaluate the PCA3 (Prostate Cancer 3 gene) as a tool to improve prostate cancer (PCa) screening and its capability to predict PCa aggressiveness. PATIENTS AND METHODS: A retrospective study with data from consecutive patients with suspected PCa seen in the urology department between November 2009 and April 2016 and who were candidates for prostate biopsy. A total of 1038 urine samples were tested in our laboratory with a kit that generated a PCA3 score (s-PCA3). A prostate biopsy was recommended only in those patients with s-PCA3≥35. Associations between variables were analyzed using the R software. RESULTS: In patients with a positive s-PCA3 (44.5%), a subsequent biopsy was recommended. Of a total of 151 biopsies studied, 56.3% yielded a diagnosis of PCa. The probability of a positive biopsy increased as the s-PCA3 increased (p=0.041). The percentage of affected cylinders increased as the s-PCA3 increased (p=0.015). A statistically significant relationship was observed between s-PCA3 and both the Gleason score and the Grade Group (p=0.001 and 0.008, respectively). The best log-linear models and a logistic model confirmed the relationships shown previously with Fisher's exact tests. CONCLUSIONS: S-PCA3 may serve as an additional marker to reduce the indication for biopsies and avoid overdiagnosis and overtreatment of patients with suspected PCa. The prognostic significance of s-PCA3 was confirmed, as it was associated with tumor volume and Gleason score. Importantly, to our knowledge this is the first time that an association has been demonstrated between s-PCA3 and the new Grade Group.

Characterization of the efficiency and uncertainty of skimmed milk flocculation for the simultaneous concentration and quantification of water-borne viruses, bacteria and protozoa.

In this study, the use of skimmed milk flocculation (SMF) to simultaneously concentrate viruses, bacteria and protozoa was evaluated. We selected strains of faecal indicator bacteria and pathogens, such as Escherichia coli and Helicobacter pylori. The viruses selected were adenovirus (HAdV 35), rotavirus (RoV SA-11), the bacteriophage MS2 and bovine viral diarrhoea virus (BVDV). The protozoa tested were Acanthamoeba, Giardia and Cryptosporidium. The mean recoveries with q(RT)PCR were 66% (HAdV 35), 24% (MS2), 28% (RoV SA-11), 15% (BVDV), 60% (E. coli), 30% (H. pylori) and 21% (Acanthamoeba castellanii). When testing the infectivity, the mean recoveries were 59% (HAdV 35), 12% (MS2), 26% (RoV SA-11) and 0.7% (BVDV). The protozoa Giardia lamblia and Cryptosporidium parvum were studied by immunofluorescence with recoveries of 18% and 13%, respectively. Although q(RT)PCR consistently showed higher quantification values (as expected), q(RT)PCR and the infectivity assays showed similar recoveries for HAdV 35 and RoV SA-11. Additionally, we investigated modelling the variability and uncertainty of the recovery with this method to extrapolate the quantification obtained by q(RT)PCR and estimate the real concentration. The 95% prediction intervals of the real concentration of the microorganisms inoculated were calculated using a general non-parametric bootstrap procedure adapted in our context to estimate the technical error of the measurements. SMF shows recoveries with a low variability that permits the use of a mathematical approximation to predict the concentration of the pathogen and indicator with acceptable low intervals. The values of uncertainty may be used for a quantitative microbial risk analysis or diagnostic purposes.

EGFR mutations in lung cancer / Mutaciones de EGFR en cancer de pulmón

The study of epidermal growth factor receptor mutations has become essential for the treatment of lung cancer. The aim of this study was to find a correlation between morphological changes and EGFR mutational status using both immunohistochemistry and molecular techniques. We also analyzed the cross-reaction of the L858R mutation-specific monoclonal antibody in cases with HER2 amplification described previously in breast and gastric cancer. A series of 100 primary lung adenocarcinomas were examined. Exon 19 E746_A750del and exon 21 L858R mutations were studied using immunohistochemistry with two specific monoclonal antibodies. Gene mutational status was determined using real-time PCR or Sanger sequencing followed by real-time PCR when negative. EGFR mutations were detected in 22 cases (22%) by molecular techniques, being significantly more frequent in women, low grade carcinoma and lepidic subtype, (p-value <0.05 in all cases). In addition, in our series presence of tumoral necrosis correlated with absence of mutations. The anti-E746_A750del antibody achieved a 100% positive predictive value and a negative predictive value of 97.7% which could restrict the use of molecular techniques to the 7% of cases with an equivocal result. The antibody for L858R mutation showed inconsistent results compared to molecular techniques, giving false positive result in two adenocarcinomas with HER2 amplification. However, its negative predictive value was very high (98.9%). The use of real-time PCR identifies mutations not detected by the other two techniques. These new antibodies could be useful as a screening tool prior to EGFR molecular techniques (AU)

El estudio de las mutaciones de EGFR ha resultado ser esencial en el tratamiento del cáncer de pulmón. La finalidad de este trabajo ha sido estudiar la correlación entre los cambios morfológicos y el estado mutacional de EGFR utilizando técnicas de inmunohistoquímica y moleculares. Asimismo se analizó la reacción cruzada del anticuerpo anti-L858R en casos con amplificación de HER2 descrita previamente en cáncer de mama y gástrico. La serie consta de 100 adenocarcinomas pulmonares primarios. Las mutaciones E746_A750del exón-19 y L858R exón-21 se estudiaron por inmunohistoquímica con dos anticuerpos monoclonales específicos. El estado mutacional del gen se determinó mediante PCR en tiempo-real o secuenciación por Sanger seguida de PCR en tiempo-real cuando resultó negativa. Se detectaron mutaciones de EGFR en 22 casos (22%) por técnicas moleculares, siendo significativamente más frecuente en mujeres, carcinoma de bajo grado y subtipo lepídico, (p-valor<0,05 en todos los casos). Además, en nuestra serie la presencia de necrosis tumoral se correlaciona con ausencia de mutaciones. El anticuerpo anti-E746_A750del presentó un valor-predictivo-positivo del 100% y un valor-predictivo-negativo del 97,7%, lo que podría restringir el uso de técnicas moleculares al 7% de casos no-concluyentes. El anticuerpo anti-L858R mostró resultados inconsistentes en comparación con las técnicas moleculares, dando resultado falso-positivo en dos adenocarcinomas con amplificación de HER2. Sin embargo, su valor-predictivo-negativo es muy alto (98,9%). El uso de PCR en tiempo-real rescata mutaciones no detectadas por las otras dos técnicas. Estos nuevos anticuerpos podrían ser útiles como herramienta de cribado previo al estudio de EGFR mediante técnicas moleculares (AU)

Human genomics. The human transcriptome across tissues and individuals.

Transcriptional regulation and posttranscriptional processing underlie many cellular and organismal phenotypes. We used RNA sequence data generated by Genotype-Tissue Expression (GTEx) project to investigate the patterns of transcriptome variation across individuals and tissues. Tissues exhibit characteristic transcriptional signatures that show stability in postmortem samples. These signatures are dominated by a relatively small number of genes­which is most clearly seen in blood­though few are exclusive to a particular tissue and vary more across tissues than individuals. Genes exhibiting high interindividual expression variation include disease candidates associated with sex, ethnicity, and age. Primary transcription is the major driver of cellular specificity, with splicing playing mostly a complementary role; except for the brain, which exhibits a more divergent splicing program. Variation in splicing, despite its stochasticity, may play in contrast a comparatively greater role in defining individual phenotypes.

Prospective validation of the microsatellite instability prediction models: RERtest6 and RERtest8

El estudio de la inestabilidad de microsatélites (MSI) es altamente recomendable en todos los carcinomas colorrectales, tanto como una primera aproximación para identificar posibles pacientes con síndrome de Lynch, como debido a su valor pronóstico y a su asociación con una mala respuesta a los regímenes basados en 5-fluorouracilo. A pesar de estas evidencias, la aplicación del estudio de MSI en la práctica general es bastante limitada. Este hecho pone de relieve la necesidad de herramientas de cribado para facilitar la implementación del estudio de MSI. Este trabajo presenta la validación de dos modelos de predicción previamente publicados, RERtest6 y RERtest8, basados en parámetros clínico-patológicos y dirigidos a una población no seleccionada por edad. La serie incluye 206 tumores colorrectales primarios de 199 pacientes, a los que se les aplicaron los modelos de predicción que contienen 6 ó 8 parámetros, respectivamente, antes de la evaluación del estado de MSI con el panel NCI consenso o el kit de MSI Promega. Se detectó alta inestabilidad de microsatélites (MSI-H) en 21 casos (10,1%). Ambos modelos han confirmado su robustez y fueron capaces de mantener valores predictivos negativos cercanos al 95%, lo que permite la reducción del número de casos que requieren un estudio molecular al 10%. Asimismo, la naturaleza de los parámetros incluidos en los modelos, que en su mayoría ya forman parte de un examen histopatológico de rutina, los convierten en una herramienta útil y de fácil aplicación en la práctica clínica (AU)

Determining microsatellite instability status (MSI) is now highly recommended for all diagnosed colorectal carcinomas, both as a first approach to identify putative Lynch syndrome patients, and as a valuable prognostic indicator as it is associated with a poor response to 5-fluorouracil-based regimes. However, generally the implementation of MSI testing is still quite limited, suggesting the need for screening tools which would simplify MSI testing. This study presents the validation of two previously published prediction models, RERtest6 and RERtest8, based on clinicopathological features and without age restriction. The series includes 206 primary colorectal tumors from 199 patients, to which the models containing 6 or 8 parameters were applied before the assessment of MSI status, using the consensus NCI panel or the MSI Promega kit. High-level microsatellite instability (MSI-H) was detected in 21 cases (10.1%). Both models confirmed their reliability and were able to maintain negative predictive values close to 95%, reducing the number of cases to be tested by molecular methods to 10%. Furthermore, the nature of the parameters included in the models, mostly already part of a routine histopathological examination, makes them a useful tool that can be easily implemented into routine practice (AU)

Chlorine inactivation of hepatitis E virus and human adenovirus 2 in water.

Hepatitis E virus (HEV) is transmitted via the fecal-oral route and has been recognized as a common source of large waterborne outbreaks involving contaminated water in developing countries. Thus, there is the need to produce experimental data on the disinfection kinetics of HEV by chlorine in water samples with diverse levels of fecal contamination. Here, the inactivation of HEV and human adenovirus C serotype 2 (HAdV2), used as a reference virus, was monitored using immunofluorescence and quantitative reverse transcription polymerase chain reaction (RT-qPCR) assays. HEV has been shown to be susceptible to chlorine disinfection and presented equivalent kinetics to human adenoviruses. The C(t) values observed for a 2-log reduction of HEV were 0.41 in buffered demand-free water and 11.21 mg/L × min in the presence of 1% sewage. The results indicate that the inactivation kinetics of HEV and HAdV2 are equivalent and support the use of chlorine disinfection as an effective strategy to control HEV waterborne transmission.

Identification of genetic variants associated with alternative splicing using sQTLseekeR.

Identification of genetic variants affecting splicing in RNA sequencing population studies is still in its infancy. Splicing phenotype is more complex than gene expression and ought to be treated as a multivariate phenotype to be recapitulated completely. Here we represent the splicing pattern of a gene as the distribution of the relative abundances of a gene's alternative transcript isoforms. We develop a statistical framework that uses a distance-based approach to compute the variability of splicing ratios across observations, and a non-parametric analogue to multivariate analysis of variance. We implement this approach in the R package sQTLseekeR and use it to analyze RNA-Seq data from the Geuvadis project in 465 individuals. We identify hundreds of single nucleotide polymorphisms (SNPs) as splicing QTLs (sQTLs), including some falling in genome-wide association study SNPs. By developing the appropriate metrics, we show that sQTLseekeR compares favorably with existing methods that rely on univariate approaches, predicting variants that behave as expected from mutations affecting splicing.

Adenovirus and Norovirus Contaminants in Commercially Distributed Shellfish.

Shellfish complying with European Regulations based on quantification of fecal bacterial indicators (FIB) are introduced into markets; however, information on viruses, more stable than FIB, is not available in the literature. To assess the presence of noroviruses (NoVs) GI and GII and human adenoviruses (HAdV) in domestic and imported mussels and clams (n = 151) their presence was analyzed during winter seasons (2004-2008) in north-west Spanish markets through a routine surveillance system. All samples tested negative for NoV GI and 13 % were positive for NoV GII. The role of HAdV as viral indicator was evaluated in 20 negative and 10 positive NoV GII samples showing an estimated sensitivity and specificity of HAdV to predict the presence of NoV GII of 100 and 74 % (cut-off 0.5). The levels of HAdV and NoVs and the efficiency of decontamination in shellfish depuration plants (SDP) were evaluated analyzing pre- and post-depurated mussels collected in May-June 2010 from three different SDP. There were no statistically significant differences in the prevalence and quantification of HAdV between pre- and post-depurated shellfish and between seawater entering and leaving the depuration systems. Moreover, infectious HAdV were detected in depurated mussels. These results confirm previous studies showing that current controls and depuration treatments limiting the number of FIB do not guarantee the absence of viruses in shellfish.

ERG expression and prostatic adenocarcinoma.

ERG gene rearrangement has been identified as a highly specific alteration that is present in 40-50 % of prostate carcinomas. The standardization of an immunohistochemical assay with a novel anti-ERG antibody recently described would have significant diagnostic value. The aims of this study were to identify the incidence of this rearrangement in a Spanish population and to test the specificity of immunohistochemical ERG evaluation for prostate carcinomas. Three prostate tissue microarrays were constructed using radical prostatectomy specimens and related to grade, local invasion, and regional invasion. In addition to samples from malignant cases (160), specimens of prostatic hyperplasia (26) and high-grade prostatic intraepithelial neoplasia (10) were included. Tissue microarrays of 270 samples from most common malignant tumors (breast, colon, lung, and bladder) were also tested. All were analyzed by immunohistochemistry. Seventy-five out of 154 evaluable cases (49 %) of prostate carcinoma showed ERG expression; 52/75 showed strong staining. No ERG expression was observed in any of the high-grade prostatic intraepithelial neoplasia. ERG expression was independent of Gleason score (p = 0.160), extent of invasion (p = 0.517), and regional lymph node involvement (p = 0.816). No ERG expression was found in any other type of tumor, with the exception of one bladder cancer sample that showed focal and weak expression. The frequency of ERG detected in our study correlated with the results published for other Caucasian populations. Strong ERG protein expression was exclusively detected in prostate carcinomas, corroborating the specificity of ERG rearrangements for these tumors. Thus, detecting ERG using immunohistochemistry may be useful in routine practice in pathology departments.