ArticleScientific reports2015
Leveraging long read sequencing from a single individual to provide a comprehensive resource for benchmarking variant calling methods.
Article in Scientific reports, 2015. 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.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
9 citing papers in PubMed.
- Article
- Variant calling and benchmarking in an era of complete human genome sequences.Nature reviews. Genetics · 2023Review
- A robust benchmark for detection of germline large deletions and insertions.Nature biotechnology · 2020Article
- Best practices for variant calling in clinical sequencing.Genome medicine · 2020Review
- A random forest-based framework for genotyping and accuracy assessment of copy number variations.NAR genomics and bioinformatics · 2020Article
- Next Generation Sequencing in Newborn Screening in the United Kingdom National Health Service.International journal of neonatal screening · 2019Article
- Haplotypes spanning centromeric regions reveal persistence of large blocks of archaic DNA.eLife · 2019Article
- An open resource for accurately benchmarking small variant and reference calls.Nature biotechnology · 2019Article
- Extensive and deep sequencing of the Venter/HuRef genome for developing and benchmarking genome analysis tools.Scientific data · 2018Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
9 authors.
Funding
Abstract
A high-confidence, comprehensive human variant set is critical in assessing accuracy of sequencing algorithms, which are crucial in precision medicine based on high-throughput sequencing. Although recent works have attempted to provide such a resource, they still do not encompass all major types of variants including structural variants (SVs). Thus, we leveraged the massive high-quality Sanger sequences from the HuRef genome to construct by far the most comprehensive gold set of a single individual, which was cross validated with deep Illumina sequencing, population datasets, and well-established algorithms. It was a necessary effort to completely reanalyze the HuRef genome as its previously published variants were mostly reported five years ago, suffering from compatibility, organization, and accuracy issues that prevent their direct use in benchmarking. Our extensive analysis and validation resulted in a gold set with high specificity and sensitivity. In contrast to the current gold sets of the NA12878 or HS1011 genomes, our gold set is the first that includes small variants, deletion SVs and insertion SVs up to a hundred thousand base-pairs. We demonstrate the utility of our HuRef gold set to benchmark several published SV detection tools.
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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.