Controlling bias and inflation in epigenome- and transcriptome-wide association studies using the empirical null distribution

We show that epigenome- and transcriptome-wide association studies (EWAS and TWAS) are prone to significant inflation and bias of test statistics, an unrecognized phenomenon introducing spurious findings if left unaddressed. Neither GWAS-based methodology nor state-of-the-art confounder adjustment methods completely remove bias and inflation. We propose a Bayesian method to control bias and inflation in EWAS and TWAS based on estimation of the empirical null distribution. Using simulations and real data, we demonstrate that our method maximizes power while properly controlling the false positive rate. We illustrate the utility of our method in large-scale EWAS and TWAS meta-analyses of age and smoking

Skewed X-inactivation is common in the general female population

X-inactivation is a well-established dosage compensation mechanism ensuring that X-chromosomal genes are expressed at comparable levels in males and females. Skewed X-inactivation is often explained by negative selection of one of the alleles. We demonstrate that imbalanced expression of the paternal and maternal X-chromosomes is common in the general population and that the random nature of the X-inactivation mechanism can be sufficient to explain the imbalance. To this end, we analyzed blood-derived RNA and whole-genome sequencing data from 79 female children and their parents from the Genome of the Netherlands project. We calculated the median ratio of the paternal over total counts at all X-chromosomal heterozygous single-nucleotide variants with coverage ≥10. We identified two individuals where the same X-chromosome was inactivated in all cells. Imbalanced expression of the two X-chromosomes (ratios ≤0.35 or ≥0.65) was observed in nearly 50% of the population. The empirically observed skewing is explained by a theoretical model where X-inactivation takes place in an embryonic stage in which eight cells give rise to the hematopoietic compartment. Genes escaping X-inactivation are expressed from both alleles and therefore demonstrate less skewing than inactivated genes. Using this characteristic, we identified three novel escapee genes (SSR4, REPS2, and SEPT6), but did not find support for many previously reported escapee genes in blood. Our collective data suggest that skewed X-inactivation is common in the general population. This may contribute to manifestation of symptoms in carriers of recessive X-linked disorders. We recommend that X-inactivation results should not be used lightly in the interpretation of X-linked variants

Locus for elevated apolipoprotein B levels on chromosome 1p31 in families with familial combined hyperlipidemia

Department of Human Genetics, Gonda Genetics Research Center, University of California, Los Angeles 90095, USA. [email protected] Familial combined hyperlipidemia (FCH), a common cause of premature coronary artery disease, is genetically complex and poorly understood. Recently, a major locus on chromosome 1q21-23 exhibiting highly significant linkage was identified in Finnish FCH families by use of a parametric analysis. We now report highly significant evidence of linkage (maximum LOD score 3.8, recombination fraction 0) of an important FCH phenotype, elevated apolipoprotein B (apoB) levels, to a distinctly separate locus on chromosome 1p31 in Dutch pedigrees. ApoB is the major protein on very low density and low density lipoproteins, and elevated apoB levels have been used as a surrogate trait for FCH. Additional microsatellite markers in the 1p31 region were genotyped, and evidence of linkage improved (maximum LOD score 4.7) in a multipoint analysis of two markers in the peak region. The leptin receptor gene resides within this locus and is involved in obesity and insulin/glucose homeostasis. However, there was no evidence of an association between leptin receptor and apoB levels, raising the possibility that another gene on this chromosomal region contributes to elevated apoB levels in this Dutch population. This is one of the first loci identified for apoB levels in humans and is the second major locus implicated in the genetic etiology of FCH

Genome scan for adiposity in Dutch dyslipidemic families reveals novel quantitative trait loci for leptin, body mass index and soluble tumor necrosis factor receptor superfamily 1A

OBJECTIVE: To search for novel genes contributing to adiposity in familial combined hyperlipidemia (FCH), a disorder characterized by abdominal obesity, hyperlipidemia and insulin resistance, using a 10 cM genome-wide scan. DESIGN: Plasma leptin and soluble tumor necrosis factor receptor superfamily members 1A and 1B (sTNFRSF1A and sTNFRSF1B, also known as sTNFR1 and sTNFR2) were analyzed as unadjusted and adjusted quantitative phenotypes of adiposity, in addition to body mass index (BMI), in multipoint and single-point analyses. In the second stage of analysis, an important chromosome 1 positional candidate gene, the leptin receptor (LEPR), was studied. SUBJECTS: Eighteen Dutch pedigrees with familial combined hyperlipidemia (FCH) (n=198) were analyzed to search for chromosomal regions harboring genes contributing to adiposity. RESULTS: Multipoint analysis of the genome scan data identified linkage (log of odds, LOD, 3.4) of leptin levels to a chromosomal region defined by D1S3728 and D1S1665, flanking the leptin receptor (LEPR) gene by approximately 9 and 3 cM, respectively, The LOD score decreased to 1.8 with age- and gender-adjusted leptin levels. Notably, BMI also mapped to this region with an LOD score of 1.2 (adjusted BMI: LOD 0.5). Two polymorphic DNA markers in LEPR and their haplotypes revealed linkage to unadjusted and adjusted BMI and leptin, and an association with leptin levels was found as well. In addition, the marker D8S1110 showed linkage (LOD 2.8) with unadjusted plasma concentrations of soluble TNFRSF1A. BMI gave a LOD score of 0.6. Moreover, a chromosome 10 q-ter locus, AFM198ZB, showed linkage with adjusted BMI (LOD 3.3), CONCLUSION: These data provide evidence that a human chromosome 1 locus, harboring the LEPR gene, contributes to plasma leptin concentrations, adiposity and body weight in humans affected with this insulin resistant dyslipidemic syndrome, Navel loci on chromosome 8 and 10 qter need further study

Association Between Arterial Stiffness and Skin Microvascular Function: The SUVIMAX2 Study and The Maastricht Study

BACKGROUND: It has been hypothesized that arterial stiffness leads to generalized microvascular dysfunction and that individuals with type 2 diabetes mellitus (T2DM) are particularly prone to the detrimental effects of arterial stiffness. However, evidence for an association between stiffness and markers of generalized microvascular dysfunction is lacking. We therefore investigated the association between arterial stiffness and skin microvascular function in individuals without and with T2DM. METHODS: Cross-sectional data were used of The Supplementation en Vitamines et Mineraux Antioxydants 2 (SUVIMAX2) Study (n = 284/62.2 years/48.6% women/0% T2DM (by design)) and The Maastricht Study (n = 737/59.7 years/45.2% women/28.8% T2DM (by design)). Arterial stiffness was determined by carotid-femoral pulse wave velocity (cfPWV). Skin capillaroscopy was used to determine capillary density at baseline, and during reactive hyperemia and venous congestion. Laser Doppler flowmetry was used to assess acetylcholine- and local heating-induced vasoreactivity, and skin flowmotion. RESULTS: In The SUVIMAX2 Study, cfPWV (per +1 SD) was not associated with baseline capillary density (regression coefficient: -0.48 (95% confidence interval: 2.37; 1.41)) or capillary recruitment during venous congestion (0.54% (-0.74; 1.81%)). In addition, cfPWV was not associated with acetylcholine (-0.02% (-0.14; 0.10%)) or local heating-induced vasoreactivity (0.03% (-0.07; 0.12%)). In The Maastricht Study, in individuals without T2DM, cfPWV was not associated with baseline capillary density (-1.20 (-3.17; 0.77)), and capillary recruitment during reactive hyperemia (1.22% (-0.41; 2.84%)) or venous congestion (1.50% (-0.25; 3.25%)). In addition, cfPWV was not associated with flowmotion (-0.01 (-0.07; 0.06)). Results were adjusted for age and sex. Additional adjustments for confounders did not materially change these results. Results were qualitatively similar in individuals with T2DM. CONCLUSIONS: Arterial stiffness is not associated with skin microvascular function, irrespective of the presence of T2DM

LIFE The Green Link: restoring degraded areas with the cocoon ecotechnology

Trabajo presentado en TERRAenVISION Environmental Issues Today: Scientific Solutions for Societal Issues, celebrado en Barcelona (España) del 27 de enero al 2 de febrero de 2018The impacts of climate change in the Mediterranean area are becoming increasingly perceptible. Many semi-arid regions are suffering significant declines in water availability. This led to faster desertification and to increase forest fires occurrence. Therefore, implementing adaptation and mitigation measures is needed to reduce the vulnerability of these Mediterranean ecosystems and strengthening their resilience. The Green Link is a collaborative LIFE project (LIFE15 CCA/ES/000125) that aims to demonstrate the environmental and economic benefits of an innovative tree growing method. This consists of replacing traditional planting techniques with the ¿Cocoon¿, a low-cost and biodegradable device that improves water supply to seedlings during the first months. To prove the viability of the Cocoon technology and demonstrate its potential, the project has planted a variety of woody species on different soil types located in areas on a climate gradient from semi-dry to extremely dry across the Mediterranean basin and the Canary Islands. As a whole, 7 experimental areas located in Italy, Greece and Spain, covering more than 70 ha and 30 plant species (4 subspecies). The main expected results of the project are: 1. Demonstrate that the Cocoon technology allows planting woody species in dry climates and poor soils to combat desertification phenomena. 2. Offer a competitive market solution to plant trees without the need of irrigation, using the Cocoon device. 3. Improve long-term soil quality through microorganisms and mycorrhiza facilitation that will enhance the association among roots and soil. 4. Improve ecosystem services, mainly by increasing biodiversity and soil carbon stock over time. First characterization of the seedlings, planted autumn-winter 2016-17, was conducted in May-June 2017, according to a monitoring protocol. Despite the measurements were previous to the summer drought, important survival differences were detected between controls and Cocoon treatments. Globally, 9% of the seedlings were classified as dead trees, but referring to the controls this percentage increased to 30% while in Cocoons group the mortality ratio was only 3%.Peer reviewe

LIFE The Green Link: restaurando areas degradadas con la ecotecnología cocoon

Trabajo presentado en la IV Reunión conjunta del Grupo de Trabajo de Repoblaciones Forestales de la SECF y el Grupo de Trabajo de Restauración Ecológica de la AEET, celebrada en Alcázar de San Juan (Ciudad Real, España) del 17 al 19 de octubre de 2018Los impactos del cambio climático cada vez son más perceptibles en el área mediterránea, reduciendo de forma significativa la disponibilidad de agua y aumentado la recurrencia e intensidad de los períodos de sequía. En este contexto, los proyectos de restauración ambiental (forestal i/o agrícola) que incluyen la plantación de especies leñosas, ven cómo cada vez se incrementan más las marras y se dificulta el establecimiento de los plantones. The Green Link es un proyecto LIFE colaborativo (LIFE15 CCA/ES/000125) que tiene como objetivo demostrar los beneficios ambientales y económicos de un método de plantación innovador. Éste método consiste en reemplazar los procedimientos de plantación tradicionales por el “Cocoon”, un dispositivo biodegradable de bajo coste que suministra agua a los plantones durante los primeros meses. Con el objetivo de demostrar la viabilidad y potencialidad del Cocoon, los socios del proyecto han plantado una variedad de especies forestales en distintos tipos de suelos de la cuenca mediterránea y las Islas Canarias, con un gradiente que va desde climas semiáridos hasta los extremadamente áridos. En total, 7 áreas experimentales localizadas en Italia, Grecia, la Península Ibérica y las Islas Canarias, dónde se han plantado 73 ha con 30 especies de árboles y arbustos (forestales y agrícolas). En algunos casos se han acompañado de siembras para favorecer cubiertas verdes que protejan al suelo de la erosión e incrementen su fertilidad. Los principales resultados que se esperan del proyecto son: 1. Demostrar que el Cocoon permite plantar especies leñosas en climas secos y suelos pobres, con índices de supervivencia y establecimiento más altos que las técnicas tradicionales 2. Ofrecer una solución de mercado competitiva para plantar sin necesidad de riego 3. Mejorar la calidad del suelo a largo plazo mediante el uso de micorrizas y microorganismos facilitadores introducidos mediante las labores de siembra y plantación 4. Mejorar los servicios ecosistémicos de las áreas restauradas fomentando la economía verde, ayudando a la creación de empleo, y en definitiva fomentando la fijación de población en las zonas rurales Los resultados preliminares de la campaña de seguimiento realizada en mayo de 2018 muestran tasas de supervivencia y establecimiento de los plantones cercanas al 70%, aunque en algunos casos la supervivencia llega al 100% y en otros es inferior al 50%. En general, la percepción de los propietarios agrícolas y forestales, y de las administraciones involucradas es muy positiva, y las acciones de replicación del proyecto están superando las expectativas.Peer reviewe

The Green Link Project: Restore desertified areas with an innovative tree growing method across the mediterranean basin to increase resilience

Trabajo presentado en el 1st World Conference on Soil and Water Conservation under Global Change (CONSOWA), celebrado en Lleida del 12 al 16 de junio de 2017Desertification is defined as “land degradation in arid, semiarid and sub-humid areas resulting from various factors, including climatic variations and human activities” (UNCCD, 2013). In this sense, soil degradation is one of the most threatening consequences of climate change. Approximately 45% of soils in Europe are in a vulnerable state and 15% even being considered extremely vulnerable. Some southern parts of the EU, including Spain, Greece, Portugal, Italy and France (Corsica) are significantly affected (EEA, 2008). Soil degradation problems not only have environmental implications: more and more agricultural land are degrading and their cultivation becoming unprofitable, adding serious economic problems to rural areas already weakened by depopulation. This project aims to compensate impacts of climate change and contribute to increase resilience of Mediterranean ecosystems, specifically in Spain, Greece and Italy. There is a huge number of studies on the potential impacts of climate change on water resources which involve many different approaches. A common element is the reduction of water availability for forest ecosystems and for irrigation purposes across all regions (EEA, 2012). Reforestation and afforestation efforts in the Mediterranean region cannot be called cost-efficient currently, since the percentages of growth failure and seedling mortality rates are extremely high, mainly when broadleaved resprouting species (e.g. Quercus species) where planted (Vallejo et al 2012).This project is funded by the LIFE program (LIFE15 CCA/ES/000125).Peer reviewe