9 research outputs found
Do objective neighbourhood characteristics relate to residents’ preferences for certain sports locations? A cross-sectional study using a discrete choice modelling approach
Calling genotypes from public RNA-sequencing data enables identification of genetic variants that affect gene-expression levels
Background: RNA-sequencing (RNA-seq) is a powerful technique for the identification of genetic variants that affect gene-expression levels, either through expression quantitative trait locus (eQTL) mapping or through allele-specific expression (ASE) analysis. Given increasing numbers of RNA-seq samples in the public domain, we here studied to what extent eQTLs and ASE effects can be identified when using public RNA-seq data while deriving the genotypes from the RNA-sequencing reads themselves. Methods: We downloaded the raw reads for all available human RNA-seq datasets. Using these reads we performed gene expression quantification. All samples were jointly normalized and subjected to a strict quality control. We also derived genotypes using the RNA-seq reads and used imputation to infer non-coding variants. This allowed us to perform eQTL mapping and ASE analyses jointly on all samples that passed quality control. Our results were validated using samples for which DNA-seq genotypes were available. Results: 4,978 public human RNA-seq runs, representing many different tissues and cell-types, passed quality control. Even though these data originated from many different laboratories, samples reflecting the same cell type clustered together, suggesting that technical biases due to different sequencing protocols are limited. In a joint analysis on the 1,262 samples with high quality genotypes, we identified cis-eQTLs effects for 8,034 unique genes (at a false discovery rate Conclusions: By deriving and imputing genotypes from RNA-seq data, it is possible to identify both eQTLs and ASE effects. Given the exponential growth of the number of publicly available RNA-seq samples, we expect this approach will become especially relevant for studying the effects of tissue-specific and rare pathogenic genetic variants to aid clinical interpretation of exome and genome sequencing
Comparative Service Consumption in six Countries
DEMPATEM project reportThe study presents cross-country comparativr workon shifts in houdsehold expenditure patterns during the 1980s and 1990s in France Germany, the netherlands, Spain, the United Kingdom and the United States
Resolving variants of unknown significance through reanalysis of 4,978 public RNA-seq samples
<p>Presentation given at the European Society of Human Genetics (ESHG) 2014 conference.</p