ArticleGenome research2017
A reference data set of 5.4 million phased human variants validated by genetic inheritance from sequencing a three-generation 17-member pedigree.
Article in Genome research, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 210 papers.
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Who cites it
210 citing papers in PubMed, 421 citations in OpenAlex.
- Next Generation-Targeted Amplicon Sequencing (NG-TAS): an optimised protocol and computational pipeline for cost-effective profiling of circulating tumour DNA.Genome medicine · 2019Trial
- Leveraging ONT move table values for signal aware variant calling.Bioinformatics (Oxford, England) · 2026Article
- Motif grammar and transcriptional programs decouple CTCF binding from nucleosome phasing to control cell-type-specific chromatin insulation.Cell reports · 2026Article
- Mapping functional non-coding variation in individual human genomes through haplotyping, multiomics, and deep learning.Nature communications · 2026Article
- Sample-specific haplotype-resolved protein isoform characterization via long-read RNA-seq-based proteogenomics.bioRxiv : the preprint server for biology · 2026Article
- Haplotype-aware segmentation with HapASeg increases accuracy of detecting homolog-specific somatic copy number alterations.Genome biology · 2026Article
- Postoperative Lymph Is a Proximal Source of ctDNA for Detection of Recurrence in HPV-Independent Head and Neck Cancer.Clinical cancer research : an official journal of the American Association for Cancer Research · 2026Article
- QPL-enabled HTSlib library: accelerating sequence file compression using Intel IAA.Bioinformatics advances · 2026Article
- Comparative assessment of SNP genotyping assays for challenging forensic samples utilizing ancient DNA methods.Genome biology · 2025Article
- Graph-based deep reinforcement learning for haplotype assembly with Ralphi.Genome research · 2025Article
- MOV&RSim: computational modelling of cancer-specific variants and sequencing reads characteristics for realistic tumoral sample simulation.BMC bioinformatics · 2025Article
- Image-based DNA sequencing encoding for detecting low-mosaicism somatic mobile element insertions.Nature communications · 2025Article
- The Platinum Pedigree: a long-read benchmark for genetic variants.Nature methods · 2025Article
- Accurate human genome analysis with element avidity sequencing.BMC bioinformatics · 2025Article
- Variant-aware Cas-OFFinder: web-based in silico variant-aware potential off-target site identification for genome editing applications.Nucleic acids research · 2025Article
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- Clinical and analytical validation of a combined RNA and DNA exome assay across a large tumor cohort.Communications medicine · 2025Article
- Origin and Evolution of Genes in Eukaryotes: Mechanisms, Dynamics, and Functional Implications.Genes · 2025Review
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- Unraveling the hidden complexity of cancer through long-read sequencing.Genome research · 2025Review
150 more citing papers are in PubMed but not listed here.
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Authors and funding
14 authors at 3 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Improvement of variant calling in next-generation sequence data requires a comprehensive, genome-wide catalog of high-confidence variants called in a set of genomes for use as a benchmark. We generated deep, whole-genome sequence data of 17 individuals in a three-generation pedigree and called variants in each genome using a range of currently available algorithms. We used haplotype transmission information to create a phased "Platinum" variant catalog of 4.7 million single-nucleotide variants (SNVs) plus 0.7 million small (1-50 bp) insertions and deletions (indels) that are consistent with the pattern of inheritance in the parents and 11 children of this pedigree. Platinum genotypes are highly concordant with the current catalog of the National Institute of Standards and Technology for both SNVs (>99.99%) and indels (99.92%) and add a validated truth catalog that has 26% more SNVs and 45% more indels. Analysis of 334,652 SNVs that were consistent between informatics pipelines yet inconsistent with haplotype transmission ("nonplatinum") revealed that the majority of these variants are de novo and cell-line mutations or reside within previously unidentified duplications and deletions. The reference materials from this study are a resource for objective assessment of the accuracy of variant calls throughout genomes.
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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.