ArticleNature communications2024
A real-world multi-center RNA-seq benchmarking study using the Quartet and MAQC reference materials.
Article in Nature communications, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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Who cites it
18 citing papers in PubMed.
- Article
- Benchmarking RNA-seq with the Quartet and MAQC reference materials to establish best practices for accurate alternative splicing analysis.Nature communications · 2026Article
- Article
- Tumor-educated platelets in cancer diagnostics and prognostics: A critical appraisal and roadmap for clinical translation.International journal of cancer · 2026Review
- Identification of key genes associated with T cell exhaustion in HIV infection based on transcriptomic data.Virology journal · 2026Article
- Genomic characterization and pathogenicity validation of Mycoplasma ovipneumoniae strains from diseased sheep: insights into potential pathogenic mechanisms of GSWW364.Veterinary research · 2026Article
- Benchmarking Q40 sequencing for sensitive and efficient detection of rare genomic variants.Genome biology · 2026Article
- A metrological foundation for absolute transcriptomics using International System of Units-anchored calibrators.Nature communications · 2026Article
- Protein-level batch-effect correction enhances robustness in MS-based proteomics.Nature communications · 2025Article
- Aging-related signature stratifies LUAD prognosis and uncovers senescence-induced chemoresistance via NF-κB/RELA activation.Respiratory research · 2025Article
- fastp 1.0: An ultra-fast all-round tool for FASTQ data quality control and preprocessing.iMeta · 2025Article
- Construction of RNA reference materials for improving the quantification of transcriptomic data.Nature protocols · 2025Review
- Spreading depolarization triggers pro- and anti-inflammatory signalling: a potential link to headache.Brain : a journal of neurology · 2025Article
- Current Bioinformatics Tools in Precision Oncology.MedComm · 2025Review
- Clinical validation of RNA sequencing for Mendelian disorder diagnostics.American journal of human genetics · 2025Article
- Enhancing skin lesion classification: a CNN approach with human baseline comparison.PeerJ. Computer science · 2025Article
- A real-world multi-center RNA-seq benchmarking study using the Quartet and MAQC reference materials.Nature communications · 2024Article
- Gabapentin's effect on human dorsal root ganglia: Donor-specific electrophysiological and transcriptomic profiles.Molecular painArticle
Corrections and comments
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Authors and funding
15 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Translating RNA-seq into clinical diagnostics requires ensuring the reliability and cross-laboratory consistency of detecting clinically relevant subtle differential expressions, such as those between different disease subtypes or stages. As part of the Quartet project, we present an RNA-seq benchmarking study across 45 laboratories using the Quartet and MAQC reference samples spiked with ERCC controls. Based on multiple types of 'ground truth', we systematically assess the real-world RNA-seq performance and investigate the influencing factors involved in 26 experimental processes and 140 bioinformatics pipelines. Here we show greater inter-laboratory variations in detecting subtle differential expressions among the Quartet samples. Experimental factors including mRNA enrichment and strandedness, and each bioinformatics step, emerge as primary sources of variations in gene expression. We underscore the profound influence of experimental execution, and provide best practice recommendations for experimental designs, strategies for filtering low-expression genes, and the optimal gene annotation and analysis pipelines. In summary, this study lays the foundation for developing and quality control of RNA-seq for clinical diagnostic purposes.
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