ArticleHuman mutation2022
An expanded phenotype centric benchmark of variant prioritisation tools.
Article in Human mutation, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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Who cites it
14 citing papers in PubMed.
- Whole exome sequencing uncovers genetic syndromes and putative candidate genes underlying orofacial clefts presenting with limb abnormalities in a Sub-Saharan African cohort.BMC medical genomics · 2026Article
- Toward universal screening for disease-causing alleles: Mendelian susceptibility to mycobacterial disease as a model.Journal of human immunity · 2025Review
- Pharmacogenomics in Orofacial Clefts Care: Insights from Whole-Genome Sequencing of Case-Parents Trios.Journal of personalized medicine · 2025Article
- Evaluating variant pathogenicity prediction tools to establish African inclusive guidelines for germline genetic testing.Communications medicine · 2025Article
- A graph neural network approach for accurate prediction of pathogenicity in multi-type variants.Briefings in bioinformatics · 2025Article
- Breaking barriers: fostering equitable access to pediatric genomics through innovative care models and technologies.Pediatric research · 2025Review
- PSAP-Genomic-Regions: A Method Leveraging Population Data to Prioritize Coding and Non-Coding Variants in Whole Genome Sequencing for Rare Disease Diagnosis.Genetic epidemiology · 2025Article
- Detection of germline variants with pathogenic potential in 48 patients with familial colorectal cancer by using whole exome sequencing.BMC medical genomics · 2023Article
- SRSF1 haploinsufficiency is responsible for a syndromic developmental disorder associated with intellectual disability.American journal of human genetics · 2023Article
- Phenotypic Diversity in GNAO1 Patients: A Comprehensive Overview of Variants and Phenotypes.Human mutation · 2023Review
- VariBench, new variation benchmark categories and data sets.Frontiers in bioinformatics · 2023Article
- Editorial: Identification of phenotypically important genomic variants.Frontiers in bioinformatics · 2023Article
- An expanded phenotype centric benchmark of variant prioritisation tools.Human mutation · 2022Article
- Computational approaches for predicting variant impact: An overview from resources, principles to applications.Frontiers in genetics · 2022Review
Corrections and comments
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Authors and funding
2 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Identifying the causal variant for diagnosis of genetic diseases is challenging when using next-generation sequencing approaches and variant prioritization tools can assist in this task. These tools provide in silico predictions of variant pathogenicity, however they are agnostic to the disease under study. We previously performed a disease-specific benchmark of 24 such tools to assess how they perform in different disease contexts. We found that the tools themselves show large differences in performance, but more importantly that the best tools for variant prioritization are dependent on the disease phenotypes being considered. Here we expand the assessment to 37 tools and refine our assessment by separating performance for nonsynonymous single nucleotide variants (nsSNVs) and missense variants (i.e., excluding nonsense variants). We found differences in performance for missense variants compared to nsSNVs and recommend three tools that stand out in terms of their performance (BayesDel, CADD, and ClinPred).
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