ArticleGenome biology2023
Quartet DNA reference materials and datasets for comprehensively evaluating germline variant calling performance.
Article in Genome biology, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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Who cites it
19 citing papers in PubMed.
- Benchmarking Q40 sequencing for sensitive and efficient detection of rare genomic variants.Genome biology · 2026Article
- A Telomere-to-telomere Diploid Reference Genome and Centromere Structure of the Chinese Quartet.Genomics, proteomics & bioinformatics · 2025Article
- Genomic and transcriptomic dynamics in the stepwise progression of lung adenocarcinoma.Cell research · 2025Article
- Protein-level batch-effect correction enhances robustness in MS-based proteomics.Nature communications · 2025Article
- Short tandem repeats in populations of the Qinghai-Tibet Plateau and adjacent regions provide insights into high-altitude adaptation.Science advances · 2025Article
- Methylation reference datasets from quartet DNA materials for benchmarking epigenome sequencing.Nature communications · 2025Article
- Construction of RNA reference materials for improving the quantification of transcriptomic data.Nature protocols · 2025Review
- Long-read sequencing of 945 Han individuals identifies structural variants associated with phenotypic diversity and disease susceptibility.Nature communications · 2025Article
- Assessing and mitigating batch effects in large-scale omics studies.Genome biology · 2024Review
- 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
- Multi-omics data integration using ratio-based quantitative profiling with Quartet reference materials.Nature biotechnology · 2024Article
- Quartet RNA reference materials improve the quality of transcriptomic data through ratio-based profiling.Nature biotechnology · 2024Article
- Quartet metabolite reference materials for inter-laboratory proficiency test and data integration of metabolomics profiling.Genome biology · 2024Article
- Haplotype-resolved assemblies and variant benchmark of a Chinese Quartet.Genome biology · 2023Article
- The Quartet Data Portal: integration of community-wide resources for multiomics quality control.Genome biology · 2023Article
- Genomic, transcriptomic and epigenomic sequencing data of the B-cell leukemia cell line REH.BMC research notes · 2023Article
- Correcting batch effects in large-scale multiomics studies using a reference-material-based ratio method.Genome biology · 2023Article
- Comprehensive SMN1 and SMN2 profiling for spinal muscular atrophy analysis using long-read PacBio HiFi sequencing.American journal of human genetics · 2023Article
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Authors and funding
35 authors.
Funding
Abstract
backgroundGenomic DNA reference materials are widely recognized as essential for ensuring data quality in omics research. However, relying solely on reference datasets to evaluate the accuracy of variant calling results is incomplete, as they are limited to benchmark regions. Therefore, it is important to develop DNA reference materials that enable the assessment of variant detection performance across the entire genome.
resultsWe established a DNA reference material suite from four immortalized cell lines derived from a family of parents and monozygotic twins. Comprehensive reference datasets of 4.2 million small variants and 15,000 structural variants were integrated and certified for evaluating the reliability of germline variant calls inside the benchmark regions. Importantly, the genetic built-in-truth of the Quartet family design enables estimation of the precision of variant calls outside the benchmark regions. Using the Quartet reference materials along with study samples, batch effects are objectively monitored and alleviated by training a machine learning model with the Quartet reference datasets to remove potential artifact calls. Moreover, the matched RNA and protein reference materials and datasets from the Quartet project enables cross-omics validation of variant calls from multiomics data.
conclusionsThe Quartet DNA reference materials and reference datasets provide a unique resource for objectively assessing the quality of germline variant calls throughout the whole-genome regions and improving the reliability of large-scale genomic profiling.
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