ArticleNature protocols2019
Use of synthetic DNA spike-in controls (sequins) for human genome sequencing.
Article in Nature protocols, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
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Who cites it
22 citing papers in PubMed.
- Quantitative metagenomics using a portable protocol.Applied and environmental microbiology · 2026Article
- A method to validate viral copy-number assay involving a hybrid amplicon and duplex droplet digital PCR.Molecular therapy. Methods & clinical development · 2025Article
- Improvement of the sensitivity of circulating tumor DNA-based liquid biopsy: current approaches and future perspectives.Exploration of targeted anti-tumor therapy · 2025Review
- Dental caries shallow-layer microbe harvest and data display method shows taxa pre-harvest spatial positions, absolute and relative abundance and diversity related to lesion pulpal depth.Journal of oral microbiology · 2025Article
- Reference Materials for Improving Reliability of Multiomics Profiling.Phenomics (Cham, Switzerland) · 2024Review
- Reliable biological and multi-omics research through biometrology.Analytical and bioanalytical chemistry · 2024Review
- Considerations and Opportunities for Probe Capture Enrichment Sequencing of Emerging Viruses from Wastewater.Environmental science & technology · 2024Review
- A universal molecular control for DNA, mRNA and protein expression.Nature communications · 2024Article
- Early assessment of fungal and oomycete pathogens in greenhouse irrigation water using Oxford nanopore amplicon sequencing.PloS one · 2024Article
- The Quartet Data Portal: integration of community-wide resources for multiomics quality control.Genome biology · 2023Article
- Vibrio-Sequins - dPCR-traceable DNA standards for quantitative genomics of Vibrio spp.BMC genomics · 2023Article
- Carryover Contamination-Controlled Amplicon Sequencing Workflow for Accurate Qualitative and Quantitative Detection of Pathogens: a Case Study on SARS-CoV-2.Microbiology spectrum · 2023Article
- Assessing and removing the effect of unwanted technical variations in microbiome data.Scientific reports · 2022Article
- Library adaptors with integrated reference controls improve the accuracy and reliability of nanopore sequencing.Nature communications · 2022Article
- Sensitive and reproducible cell-free methylome quantification with synthetic spike-in controls.Cell reports methods · 2022Article
- Using synthetic chromosome controls to evaluate the sequencing of difficult regions within the human genome.Genome biology · 2022Article
- Evaluating the analytical validity of circulating tumor DNA sequencing assays for precision oncology.Nature biotechnology · 2021Article
- Establishing community reference samples, data and call sets for benchmarking cancer mutation detection using whole-genome sequencing.Nature biotechnology · 2021Article
- Toward Accurate and Robust Environmental Surveillance Using Metagenomics.Frontiers in genetics · 2021Article
- Performance of Multiple Metagenomics Pipelines in Understanding Microbial Diversity of a Low-Biomass Spacecraft Assembly Facility.Frontiers in microbiology · 2021Article
Corrections and comments
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Authors and funding
8 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Next-generation sequencing (NGS) has been widely adopted to identify genetic variants and investigate their association with disease. However, the analysis of sequencing data remains challenging because of the complexity of human genetic variation and confounding errors introduced during library preparation, sequencing and analysis. We have developed a set of synthetic DNA spike-ins-termed 'sequins' (sequencing spike-ins)-that are directly added to DNA samples before library preparation. Sequins can be used to measure technical biases and to act as internal quantitative and qualitative controls throughout the sequencing workflow. This step-by-step protocol explains the use of sequins for both whole-genome and targeted sequencing of the human genome. This includes instructions regarding the dilution and addition of sequins to human DNA samples, followed by the bioinformatic steps required to separate sequin- and sample-derived sequencing reads and to evaluate the diagnostic performance of the assay. These practical guidelines are accompanied by a broader discussion of the conceptual and statistical principles that underpin the design of sequin standards. This protocol is suitable for users with standard laboratory and bioinformatic experience. The laboratory steps require ~1-4 d and the bioinformatic steps (which can be performed with the provided example data files) take an additional day.
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