ArticleScientific reports2018
Sample-Index Misassignment Impacts Tumour Exome Sequencing.
Article in Scientific reports, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 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.
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Who cites it
9 citing papers in PubMed.
- ERIC recommendations for TP53 mutation analysis in chronic lymphocytic leukemia-2024 update.Leukemia · 2024Review
- A cost-effective sequencing method for genetic studies combining high-depth whole exome and low-depth whole genome.NPJ genomic medicine · 2024Article
- Strategies for sample labelling and library preparation in DNA metabarcoding studies.Molecular ecology resources · 2022Review
- Low-complexity and highly robust barcodes for error-rich single molecular sequencing.3 Biotech · 2021Article
- Proximity Extension Assay in Combination with Next-Generation Sequencing for High-throughput Proteome-wide Analysis.Molecular & cellular proteomics : MCP · 2021Article
- A novel high-throughput molecular counting method with single base-pair resolution enables accurate single-gene NIPT.Scientific reports · 2019Article
- Reliable multiplex sequencing with rare index mis-assignment on DNB-based NGS platform.BMC genomics · 2019Article
- Allele balance bias identifies systematic genotyping errors and false disease associations.Human mutation · 2019Article
- Characterization and remediation of sample index swaps by non-redundant dual indexing on massively parallel sequencing platforms.BMC genomics · 2018Article
Corrections and comments
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Authors and funding
9 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Sample pooling enabled by dedicated indexes is a common strategy for cost-effective and robust high-throughput sequencing. Index misassignment leading to mutual contamination between pooled samples has however been described as a general problem of the latest Illumina sequencing instruments utilizing exclusion amplification. Using real-life data from multiple tumour sequencing projects, we demonstrate that index misassignment can induce artefactual variant calls closely resembling true, high-quality somatic variants. These artefactual calls potentially impact cancer applications utilizing low allelic frequencies, such as in clonal analysis of tumours. We discuss the available countermeasures with an emphasis on improved library indexing methods, and provide software that can assist in the identification of variants that may be consequences of index misassignment.
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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.