Journal ArticleDOI
Reproducibility of high-throughput mRNA and small RNA sequencing across laboratories
Peter A C 't Hoen,Marc R. Friedländer,Jonas Carlsson Almlöf,Michael Sammeth,Irina Pulyakhina,Seyed Yahya Anvar,Jeroen F.J. Laros,Jeroen F.J. Laros,Henk P. J. Buermans,Olof Karlberg,Mathias Brännvall,Johan T. den Dunnen,Johan T. den Dunnen,Gert-Jan B. van Ommen,Ivo Gut,Roderic Guigó,Xavier Estivill,Ann-Christine Syvänen,Emmanouil T. Dermitzakis,Emmanouil T. Dermitzakis,Tuuli Lappalainen,Tuuli Lappalainen +21 more
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TLDR
It is concluded that distributing RNA sequencing among different laboratories is feasible, given proper standardization and randomization procedures, and a set of quality measures and guidelines for assessing technical biases in RNA-seq data are provided.Abstract:
RNA sequencing is an increasingly popular technology for genome-wide analysis of transcript sequence and abundance. However, understanding of the sources of technical and interlaboratory variation is still limited. To address this, the GEUVADIS consortium sequenced mRNAs and small RNAs of lymphoblastoid cell lines of 465 individuals in seven sequencing centers, with a large number of replicates. The variation between laboratories appeared to be considerably smaller than the already limited biological variation. Laboratory effects were mainly seen in differences in insert size and GC content and could be adequately corrected for. In small-RNA sequencing, the microRNA (miRNA) content differed widely between samples owing to competitive sequencing of rRNA fragments. This did not affect relative quantification of miRNAs. We conclude that distributing RNA sequencing among different laboratories is feasible, given proper standardization and randomization procedures. We provide a set of quality measures and guidelines for assessing technical biases in RNA-seq data.read more
Citations
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Journal ArticleDOI
Salmon provides fast and bias-aware quantification of transcript expression
TL;DR: Salmon is the first transcriptome-wide quantifier to correct for fragment GC-content bias, which substantially improves the accuracy of abundance estimates and the sensitivity of subsequent differential expression analysis.
Journal ArticleDOI
Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype
TL;DR: This work presents a method named HISAT2 (hierarchical indexing for spliced alignment of transcripts 2) that can align both DNA and RNA sequences using a graph Ferragina Manzini index, and uses it to represent and search an expanded model of the human reference genome.
Journal ArticleDOI
Transcriptome and genome sequencing uncovers functional variation in humans
Tuuli Lappalainen,Michael Sammeth,Marc R. Friedländer,Peter A C 't Hoen,Jean Monlong,Manuel A. Rivas,Mar Gonzàlez-Porta,Natalja Kurbatova,Thasso Griebel,Pedro G. Ferreira,Matthias Barann,Thomas Wieland,Liliana Greger,Maarten van Iterson,Jonas Carlsson Almlöf,Paolo Ribeca,Irina Pulyakhina,Daniela Esser,Thomas Giger,Andrew Tikhonov,Marc Sultan,Gabrielle Bertier,Daniel G. MacArthur,Daniel G. MacArthur,Monkol Lek,Monkol Lek,Esther Lizano,Henk P. J. Buermans,Ismael Padioleau,Ismael Padioleau,Thomas Schwarzmayr,Olof Karlberg,Halit Ongen,Halit Ongen,Helena Kilpinen,Helena Kilpinen,Sergi Beltran,Marta Gut,Katja Kahlem,Vyacheslav Amstislavskiy,Oliver Stegle,Matti Pirinen,Stephen B. Montgomery,Stephen B. Montgomery,Peter Donnelly,Mark I. McCarthy,Mark I. McCarthy,Paul Flicek,Tim M. Strom,Hans Lehrach,Stefan Schreiber,Ralf Sudbrak,Angel Carracedo,Stylianos E. Antonarakis,Robert Häsler,Ann-Christine Syvänen,Gert-Jan B. van Ommen,Alvis Brazma,Thomas Meitinger,Philip Rosenstiel,Roderic Guigó,Ivo Gut,Xavier Estivill,Emmanouil T. Dermitzakis,Emmanouil T. Dermitzakis +64 more
TL;DR: Se sequencing and deep analysis of messenger RNA and microRNA from lymphoblastoid cell lines of 462 individuals from the 1000 Genomes Project—the first uniformly processed high-throughput RNA-sequencing data from multiple human populations with high-quality genome sequences discover extremely widespread genetic variation affecting the regulation of most genes.
Journal ArticleDOI
Normalization of RNA-seq data using factor analysis of control genes or samples
TL;DR: This work proposes a normalization strategy, called remove unwanted variation (RUV), that adjusts for nuisance technical effects by performing factor analysis on suitable sets of control genes or samples and leads to more accurate estimates of expression fold-changes and tests of differential expression compared to state-of-the-art normalization methods.
Journal ArticleDOI
The role of regulatory variation in complex traits and disease
Frank W. Albert,Leonid Kruglyak +1 more
TL;DR: Recent insights into the molecular nature of regulatory variants are reviewed and examples of complete chains of causality that link individual polymorphisms to changes in gene expression, which in turn result in physiological changes and, ultimately, disease risk are presented.
References
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