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A comprehensive assessment of RNA-seq accuracy, reproducibility and information content by the Sequencing Quality Control Consortium
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(2014) A comprehensive assessment of RNA-seq accuracy, reproducibility and information content by the Sequencing Quality Control Consortium. Nature Biotechnology , Volume 32 (Number 9). pp. 903-914. doi:10.1038/nbt.2957 ISSN 1087-0156.
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Official URL: http://dx.doi.org/10.1038/nbt.2957
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.
Item Type: | Journal Article | ||||||||||
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Divisions: | Faculty of Science, Engineering and Medicine > Science > Centre for Scientific Computing | ||||||||||
Journal or Publication Title: | Nature Biotechnology | ||||||||||
Publisher: | Nature Publishing Group | ||||||||||
ISSN: | 1087-0156 | ||||||||||
Official Date: | 9 September 2014 | ||||||||||
Dates: |
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Volume: | Volume 32 | ||||||||||
Number: | Number 9 | ||||||||||
Page Range: | pp. 903-914 | ||||||||||
DOI: | 10.1038/nbt.2957 | ||||||||||
Status: | Peer Reviewed | ||||||||||
Publication Status: | Published | ||||||||||
Access rights to Published version: | Restricted or Subscription Access |
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