Biology subjects

Emmanouil Dermitzakis

Publications and source records attributed to Emmanouil Dermitzakis.

3 recordsLinked to original sources

bioRxiv2016

A complete tool set for molecular QTL discovery and analysis

Population scale studies combining genetic information with molecular phenotypes (e.g. gene expression) become a standard to dissect the effects of genetic variants onto organismal. This kind of datasets requires powerful, fast and versatile methods able to discover molecular Quantitative Trait Loci (molQTL). Here we propose such a solution, QTLtools, a modular framework that contains multiple methods to prepare the data, to discover proximal and distal molQTLs and to finally integrate them with GWAS variants and functional annotations of the genome. We demonstrate its utility by performing a complete expression QTL study in a few and easy-to-perform steps. QTLtools is open source and available at https://gtltools.github.io/gtltools/

Bioinformatics↗

bioRxiv2016

Age-dependent changes in mean and variance of gene expression across tissues in a twin cohort

Gene expression changes with age have consequences for healthy aging and disease development. Here we investigate age-related changes in gene expression measured by RNA-seq in four tissues and the interplay between genotypes and age-related changes in expression. Using concurrently measured methylation array data from fat we also investigate the relationship between methylation, gene expression and age. We identified age-dependent changes in mean levels of gene expression in 5,631 genes and in splicing of 904 genes. Age related changes were widely shared across tissues, with up to 60% of age-related changes in expression and 47% on splicing in multi-exonic genes shared; amongst these we highlight effects on genes involved in diseases such as Alzheimer and cancer. We identified 137 genes with age-related changes in variance and 42 genes with age-dependent discordance between genetically identical individuals; implying the latter are driven by environmental effects. We also give four examples where genetic control of expression is affected by the aging process. Analysis of methylation observed a widespread and stronger effect of age on methylation than expression; however we did not find a strong relationship between age-related changes in both expression and methylation. In summary, we quantified aging affects in splicing, level and variance of gene expression, and show that these processes can be both environmentally and genetically influenced.

Genomics↗

bioRxiv2015

Fast and efficient QTL mapper for thousands of molecular phenotypes

MotivationIn order to discover quantitative trait loci (QTLs), multi-dimensional genomic data sets combining DNA-seq and ChiP-/RNA-seq require methods that rapidly correlate tens of thousands of molecular phenotypes with millions of genetic variants while appropriately controlling for multiple testing.\n\nResultsWe have developed FastQTL, a method that implements a popular cis-QTL mapping strategy in a user- and cluster-friendly tool. FastQTL also proposes an efficient permutation procedure to control for multiple testing. The outcome of permutations is modeled using beta distributions trained from a few permutations and from which adjusted p-values can be estimated at any level of significance with little computational cost. The Geuvadis & GTEx pilot data sets can be now easily analyzed an order of magnitude faster than previous approaches.\n\nAvailabilitySource code, binaries and comprehensive documentation of FastQTL are freely available to download at http://fastqtl.sourceforge.net/.\n\nContactolivier.delaneau@unige.ch

Bioinformatics↗