ArticleScientific data2022
Ultra-deep multi-oncopanel sequencing of benchmarking samples with a wide range of variant allele frequencies.
Article in Scientific data, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 3 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
3 citing papers in PubMed.
- Evaluation of false positive and false negative errors in targeted next generation sequencing.Genome biology · 2025Article
- Targeted DNA-seq and RNA-seq of Reference Samples with Short-read and Long-read Sequencing.Scientific data · 2024Article
- Towards accurate indel calling for oncopanel sequencing through an international pipeline competition at precisionFDA.Scientific reports · 2024Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
5 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The lack of suitable reference genomic material to enable a transparent cross-lab study of oncopanels inspired the SEQC2 Oncopanel Sequencing Working Group to develop four reference samples, sequenced with eight oncopanels at independent test laboratories with ultra-deep sequencing depth. This rich, publicly available dataset enabled performance assessment of the clinical applicability of oncopanels. In addition, this dataset present sample opportunities for developing specific and robust bioinformatics pipelines and fine-tuning parameters for more accurate variant calling, investigating ideal sequencing depth for variant calling of a given minimum VAF and variant type, and also recommending best use cases for Unique Molecular Identifier (UMI) technology.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.