0000000000374795
AUTHOR
J.j. Abellán
Bayesian model to detect phenotype-specific genes for copy number data
Abstract Background An important question in genetic studies is to determine those genetic variants, in particular CNVs, that are specific to different groups of individuals. This could help in elucidating differences in disease predisposition and response to pharmaceutical treatments. We propose a Bayesian model designed to analyze thousands of copy number variants (CNVs) where only few of them are expected to be associated with a specific phenotype. Results The model is illustrated by analyzing three major human groups belonging to HapMap data. We also show how the model can be used to determine specific CNVs related to response to treatment in patients diagnosed with ovarian cancer. The …
Microbial Succession in the Gut: Directional Trends of Taxonomic and Functional Change in a Birth Cohort of Spanish Infants
In spite of its major impact on life-long health, the process of microbial succession in the gut of infants remains poorly understood. Here, we analyze the patterns of taxonomic and functional change in the gut microbiota during the first year of life for a birth cohort of 13 infants. We detect that individual instances of gut colonization vary in the temporal dynamics of microbiota richness, diversity, and composition at both functional and taxonomic levels. Nevertheless, trends discernible in a majority of infants indicate that gut colonization occurs in two distinct phases of succession, separated by the introduction of solid foods to the diet. This change in resource availability causes…
Daily follow-up of bacterial communities in the human gut reveals stable composition and host-specific patterns of interaction
In the last decade, an extensive effort has been made to characterize the human intestinal microbiota by means of SSU rRNA gene sequence and metagenomic analysis. Relatively few studies have followed intestinal bacterial communities over time to assess their stability in the absence of perturbation. In this study, we have monitored the faecal bacteria of three healthy subjects during 15 consecutive days. The global community structure was analysed through SSU rRNA gene sequencing. In agreement with previous studies, we found that the between-subject variation in community structure was larger than within. The composition was fairly stable throughout, although daily fluctuations were detecte…
Metagenomics of human microbiome: beyond 16s rDNA.
Clin Microbiol Infect 2012; 18 (Suppl. 4): 4749 Abstract The gut microbiota presents a symbiotic relationship with the human host playing a beneficial role in human health. Since its establishment, the bacterial community is subjected to the influence of many different factors that shape its composition within each individual. However, an important convergence is observed at functional level in the gut microbiota. A metatranscriptomic study of healthy individuals showed homogeneity in the composition of the active microbiota that increased further at functional level.
Procesos puntuales como herramienta para el análisis de posibles fuentes de contaminación
El análisis de un patrón puntual engloba una serie de técnicas que permiten estudiar la distribución de un conjunto de eventos ocurridos sobre una región del plano. Este problema surge en epidemiología cuando se investiga una potencial fuente de contaminación ambiental alrededor de la cual se sospecha que surgen casos de una determinada enfermedad. En el presente trabajo, se explica brevemente en qué consiste el análisis de un patrón puntual y se ilustra con una aplicación a la determinación del origen medioambiental y al estudio de las zonas de mayor riesgo de incidencia en un brote de neumonía por Legionella ocurrido entre mediados de septiembre y principios de octubre en la ciudad de Alc…
Spatial analysis of the relationship between mortality from cardiovascular and cerebrovascular disease and drinking water hardness
Journal Article; Research Support, Non-U.S. Gov't; Reproduced with permission from Environmental Health Perspectives. Previously published scientific papers have reported a negative correlation between drinking water hardness and cardiovascular mortality. Some ecologic and case-control studies suggest the protective effect of calcium and magnesium concentration in drinking water. In this article we present an analysis of this protective relationship in 538 municipalities of Comunidad Valenciana (Spain) from 1991-1998. We used the Spanish version of the Rapid Inquiry Facility (RIF) developed under the European Environment and Health Information System (EUROHEIS) research project. The strateg…
Environmental distribution of prokaryotic taxa
14 pages, 5 figures, 1 table, 10 additional files avalaible [http://www.biomedcentral.com/content/supplementary/1471-2180-10- 85-S10.PDF ]
Analysis of the renal transplant waiting list in the País Valencià (Spain).
In this paper we analyse the renal transplant waiting list of the Pais Valencia in Spain, using Queueing theory. The customers of this queue are patients with end-stage renal failure waiting for a kidney transplant. We set up a simplified model to represent the flow of the customers through the system, and perform Bayesian inference to estimate parameters in the model. Finally, we consider several scenarios by tuning the estimations achieved and computationally simulate the behaviour of the queue under each one. The results indicate that the system could reach equilibrium at some point in the future and the model forecasts a slow decrease in the size of the waiting list in the short and mid…
Geographical Distribution of Cardiovascular Mortality in Comunidad Valenciana (Spain)
Comunidad Valenciana is one of the seventeen autonomous regions into which Spain is divided. It is located on the east coast of Spain, next to the Mediterranean sea, with an area of 23,255 km2 and with 4,009,329 inhabitants in 1996. From an administrative point of view there are three levels of aggregation: provinces (3 units), health areas (20 units) and municipalities (541 units).
Statistical relationship between hardness of drinking water and cerebrovascular mortality in Valencia: a comparison of spatiotemporal models
The statistical detection of environmental risk factors in public health studies is usually difficult due to the weakness of their effects and their confounding with other covariates. Small area geographical data bring the opportunity of observing health response in a wide variety of exposure values. Temporal sequences of these geographical datasets are crucial to gaining statistical power in detecting factors. The spatiotemporal models required to perform the statistical analysis have to allow for spatial and temporal correlations, which are more easily modelled via hierarchical structures of hidden random factors. These models have produced important research activity during the last deca…
Hepatitis C virus viral kinetics during α-2a or α-2b pegylated interferon plus ribavirin therapy in liver transplant recipients with different immunosuppression regimes
Abstract Background Predictors of sustained virological response (SVR) to antiviral therapy post-liver transplantation (LT) for chronic hepatitis C are needed. In non-transplanted patients, viral kinetics can predict SVR. Objectives To determine the early viral kinetics in LT recipients with different immunosuppression (tacrolimus – Tac- vs. cyclosporine – CsA-) during treatment with peg-IFN + RBV. Study design Prospective pilot study in HCV-1b infected patients: (LT CsA n = 8; Tac n = 8; non-LT n = 4), treated with IFN α-2a vs. α-2b (180 μg or 1.5 μg/kg, respectively) once weekly plus weight-based RBV. Median CsA or Tac baseline trough levels were 141 and 7.70 ng/mL, respectively. HCV-RNA …
Structural alterations of faecal and mucosa-associated bacterial communities in irritable bowel syndrome
Summary Irritable bowel syndrome (IBS) is the most common functional gastrointestinal disorder in western coun- tries. Previous studies on IBS, mostly based on faecal samples, suggest alterations in the intestinal micro- biota. However, no consensus has been reached regarding the association between specific bacteria and IBS. We explore the alterations of intestinal bac- terial communities in IBS using massive sequencing of amplified 16S rRNA genes. Mucosal biopsies of the ascending and descending colon and faeces from 16 IBS patients and 9 healthy controls were analysed. Strong inter-individual variation was observed in the composition of the bacterial communities in both patients and cont…
Source Detection in an Outbreak of Legionnaire’s Disease
Spatial statistics have broadly been applied, developed and demanded from the field of epidemiology. The point process theory is an appropriate framework to analyse the spatial variation of risk of disease from information at individual level.
Metatranscriptomic Approach to Analyze the Functional Human Gut Microbiota
The human gut is the natural habitat for a large and dynamic bacterial community that has a great relevance for health. Metagenomics is increasing our knowledge of gene content as well as of functional and genetic variability in this microbiome. However, little is known about the active bacteria and their function(s) in the gastrointestinal tract. We performed a metatranscriptomic study on ten healthy volunteers to elucidate the active members of the gut microbiome and their functionality under conditions of health. First, the microbial cDNAs obtained from each sample were sequenced using 454 technology. The analysis of 16S transcripts showed the phylogenetic structure of the active microbi…
Instability of the faecal microbiota in diarrhoea-predominant irritable bowel syndrome
The irritable bowel syndrome (IBS) is a functional gastrointestinal disorder with a largely unknown aetiology and a wide range of symptoms. Most cross-sectional studies carried out so far suggest subtle alterations in the structure of the intestinal microbiota that are barely reproduced, partly because of the high inter-subject variation in the community composition and disorder-specific features. We performed a longitudinal study to explore the within-subject variation in the faecal microbiota in two patients with IBS classified into the diarrhoea subtype and the healthy spouse of one of them. Faecal communities were monitored over 6-8 weeks and analysed through metagenomic and metatranscr…