ArticleNature methods2025
The Platinum Pedigree: a long-read benchmark for genetic variants.
Article in Nature methods, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 26 papers.
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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
26 citing papers in PubMed.
- Hunting for microsatellite instability in long-read data with Owl.PLoS computational biology · 2026Article
- Article
- Long-read based detection of large copy number variants with potential functional significance using the ContextSV structural variant caller.NAR genomics and bioinformatics · 2026Article
- Article
- Computational strategies for copy number variation detection, disease association, and beyond.Genome biology · 2026Review
- Near-perfect genome sequencing in medical genetics.Nature genetics · 2026Review
- Fiber-TEnCATS reveals haplotype-specific chromatin accessibility and DNA methylation at human L1HS loci.bioRxiv : the preprint server for biology · 2026Article
- Genomic Variability of the HCT116 Cell Line Identified Using Oxford Nanopore Sequencing.International journal of molecular sciences · 2026Article
- Aardvark: sifting through differences in a mound of variants.Genome biology · 2026Article
- Benchmarking Q40 sequencing for sensitive and efficient detection of rare genomic variants.Genome biology · 2026Article
- Whole-genome sequencing with AVITI and NovaSeq X Plus reveals comparable performance with contextual biases.NAR genomics and bioinformatics · 2026Article
- A family portrait of the genomic factors shaping tandem repeat mutagenesis.bioRxiv : the preprint server for biology · 2026Article
- Sex-aware genome-wide assessment of de novo variants in autism across coding and noncoding regions.Human genomics · 2026Article
- Linked origins but distinct roles for extreme length and sequence variation at a tandem repeat inbioRxiv : the preprint server for biology · 2026Article
- cuteHap: Haplotype-Aware Structural Variant Detection in Phased Long-Read Sequencing Data.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- ANOMALY: a Snakemake pipeline for identifying NuMTs from long-read sequencing data.NAR genomics and bioinformatics · 2026Article
- Complete genomes of a multi-generational pedigree to expand studies of genetic and epigenetic inheritance.bioRxiv : the preprint server for biology · 2025Article
- CiFi: accurate long-read chromosome conformation capture with low-input requirements.Nature communications · 2025Article
- Complex structural variant visualization with SVTopo.BMC genomics · 2025Article
- A complete diploid human genome benchmark for personalized genomics.bioRxiv : the preprint server for biology · 2025Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
34 authors.
Funding
Abstract
Recent advances in genome sequencing have improved variant calling in complex regions of the human genome. However, it is difficult to quantify variant calling performance because existing standards often focus on specificity, neglecting completeness in difficult-to-analyze regions. To create a more comprehensive truth set, we used Mendelian inheritance in a large pedigree (CEPH-1463) to filter variants across PacBio high-fidelity (HiFi), Illumina and Oxford Nanopore Technologies platforms. This generated a variant map with over 4.7 million single-nucleotide variants, 767,795 insertions and deletions (indels), 537,486 tandem repeats and 24,315 structural variants, covering 2.77 Gb of the GRCh38 genome. This work adds ~200 Mb of high-confidence regions, including 8% more small variants, and introduces the first tandem repeat and structural variant truth sets for NA12878 and her family. As an example of the value of this improved benchmark, we retrained DeepVariant using these data to reduce genotyping errors by ~34%.
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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.