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A comprehensive assessment of RNA-seq accuracy, reproducibility and information content by the Sequencing Quality Control Consortium
A comprehensive assessment of RNA-seq accuracy, reproducibility and information content by the Sequencing Quality Control Consortium
- Source :
- Nature biotechnology, Nature Biotechnology, 32(9), 903-914. Nature Publishing Group
- Publication Year :
- 2014
-
Abstract
- We present primary results from the Sequencing Quality Control (SEQC) project, coordinated by the US Food and Drug Administration. Examining Illumina HiSeq, Life Technologies SOLiD and Roche 454 platforms at multiple laboratory sites using reference RNA samples with built-in controls, we assess RNA sequencing (RNA-seq) performance for junction discovery and differential expression profiling and compare it to microarray and quantitative PCR (qPCR) data using complementary metrics. At all sequencing depths, we discover unannotated exon-exon junctions, with >80% validated by qPCR. We find that measurements of relative expression are accurate and reproducible across sites and platforms if specific-filters are used. In contrast, RNA-seq and microarrays do not provide accurate absolute measurements, and gene-specific biases are observed for all examined platforms, including qPCR. Measurement performance depends on the platform and data analysis pipeline, and variation is large for transcript-level profiling. The complete SEQC data sets, comprising >100 billion reads (10Tb), provide unique resources for evaluating RNA-seq analyses for clinical and regulatory settings.
- Subjects :
- Profiling (computer programming)
Genetics
0303 health sciences
Microarray
Sequence analysis
Sequence Analysis, RNA
Biomedical Engineering
Reproducibility of Results
Bioengineering
RNA-Seq
Genome project
Computational biology
Biology
Applied Microbiology and Biotechnology
Polymerase Chain Reaction
Article
Transcriptome
03 medical and health sciences
0302 clinical medicine
Molecular Medicine
Human genome
DNA microarray
030217 neurology & neurosurgery
030304 developmental biology
Biotechnology
Subjects
Details
- Language :
- English
- ISSN :
- 10870156
- Volume :
- 32
- Issue :
- 9
- Database :
- OpenAIRE
- Journal :
- Nature Biotechnology
- Accession number :
- edsair.doi.dedup.....f574fbd57cb9cc567146ad9815046e12
- Full Text :
- https://doi.org/10.1038/nbt.2957