ArticleBMC bioinformatics2018
The VAAST Variant Prioritizer (VVP): ultrafast, easy to use whole genome variant prioritization tool.
Article in BMC bioinformatics, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
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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
21 citing papers in PubMed.
- A Randomized, Controlled Trial of the Analytic and Diagnostic Performance of Singleton and Trio, Rapid Genome and Exome Sequencing in Ill Infants.American journal of human genetics · 2019Trial
- Leveraging protein language models and a scoring function for indel characterization and transfer learning.Patterns (New York, N.Y.) · 2026Article
- Digenic variant interpretation with hypothesis-driven explainable AI.NAR genomics and bioinformatics · 2025Article
- Breast Cancer Is Increased in Women With Primary Ovarian Insufficiency.The Journal of clinical endocrinology and metabolism · 2025Article
- Article
- Genetic and clinical variables act synergistically to impact neurodevelopmental outcomes in children with single ventricle heart disease.Communications medicine · 2023Article
- Phenotypic screening models for rapid diagnosis of genetic variants and discovery of personalized therapeutics.Molecular aspects of medicine · 2023Review
- Evaluation of in silico pathogenicity prediction tools for the classification of small in-frame indels.BMC medical genomics · 2023Article
- Genomic study ofFrontiers in genetics · 2023Article
- Computational and experimental methods for classifying variants of unknown clinical significance.Cold Spring Harbor molecular case studies · 2022Article
- Causal and Candidate Gene Variants in a Large Cohort of Women With Primary Ovarian Insufficiency.The Journal of clinical endocrinology and metabolism · 2022Observational
- Artificial intelligence enables comprehensive genome interpretation and nomination of candidate diagnoses for rare genetic diseases.Genome medicine · 2021Article
- Predicting pathogenic non-coding SVs disrupting the 3D genome in 1646 whole cancer genomes using multiple instance learning.Scientific reports · 2021Article
- Rapid whole genome sequencing impacts care and resource utilization in infants with congenital heart disease.NPJ genomic medicine · 2021Article
- Whole Genome Interpretation for a Family of Five.Frontiers in genetics · 2021Article
- Deep whole-genome sequencing of multiple proband tissues and parental blood reveals the complex genetic etiology of congenital diaphragmatic hernias.HGG advances · 2020Article
- Disruption ofHGG advances · 2020Article
- De novo and recessive forms of congenital heart disease have distinct genetic and phenotypic landscapes.Nature communications · 2019Article
- ClinPred: Prediction Tool to Identify Disease-Relevant Nonsynonymous Single-Nucleotide Variants.American journal of human genetics · 2018Article
- OligoPVP: Phenotype-driven analysis of individual genomic information to prioritize oligogenic disease variants.Scientific reports · 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
12 authors.
Funding
Abstract
backgroundPrioritization of sequence variants for diagnosis and discovery of Mendelian diseases is challenging, especially in large collections of whole genome sequences (WGS). Fast, scalable solutions are needed for discovery research, for clinical applications, and for curation of massive public variant repositories such as dbSNP and gnomAD. In response, we have developed VVP, the VAAST Variant Prioritizer. VVP is ultrafast, scales to even the largest variant repositories and genome collections, and its outputs are designed to simplify clinical interpretation of variants of uncertain significance.
resultsWe show that scoring the entire contents of dbSNP (> 155 million variants) requires only 95 min using a machine with 4 cpus and 16 GB of RAM, and that a 60X WGS can be processed in less than 5 min. We also demonstrate that VVP can score variants anywhere in the genome, regardless of type, effect, or location. It does so by integrating sequence conservation, the type of sequence change, allele frequencies, variant burden, and zygosity. Finally, we also show that VVP scores are consistently accurate, and easily interpreted, traits not shared by many commonly used tools such as SIFT and CADD.
conclusionsVVP provides rapid and scalable means to prioritize any sequence variant, anywhere in the genome, and its scores are designed to facilitate variant interpretation using ACMG and NHS guidelines. These traits make it well suited for operation on very large collections of WGS sequences.
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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.