ArticleNucleic acids research2018
Novel diagnostic tool for prediction of variant spliceogenicity derived from a set of 395 combined in silico/in vitro studies: an international collaborative effort.
Article in Nucleic acids research, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 47 papers.
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47 citing papers in PubMed, 109 citations in OpenAlex.
- HydraRNA: a hybrid architecture based full-length RNA language model.Genome biology · 2025Article
- A cardiovascular, craniofacial, and neurodevelopmental disorder caused by loss-of-function variants in the eIF3 complex component genes EIF3A and EIF3B.American journal of human genetics · 2025Article
- The SeqSplice multiplexed minigene splicing assay for characterization and quantitation of variant-inducedGenome research · 2025Article
- New genetic diagnoses for inherited retinal dystrophies by integrating splicing tools into NGS pipelines.NPJ genomic medicine · 2025Article
- Identification of a newMolecular genetics and metabolism reports · 2025Article
- Nanopore Deep Sequencing as a Tool to Characterize and Quantify Aberrant Splicing Caused by Variants in Inherited Retinal Dystrophy Genes.International journal of molecular sciences · 2024Article
- Variant Impact Predictor database (VIPdb), version 2: trends from three decades of genetic variant impact predictors.Human genomics · 2024Article
- Variant Impact Predictor database (VIPdb), version 2: Trends from 25 years of genetic variant impact predictors.bioRxiv : the preprint server for biology · 2024Article
- All exons are not created equal-exon vulnerability determines the effect of exonic mutations on splicing.Nucleic acids research · 2024Article
- Combining full-length gene assay and SpliceAI to interpret the splicing impact of all possible SPINK1 coding variants.Human genomics · 2024Article
- Benchmarking splice variant prediction algorithms using massively parallel splicing assays.Genome biology · 2023Article
- Long noncoding RNA study: Genome-wide approaches.Genes & diseases · 2023Review
- Targeted sequencing and in vitro splice assays shed light on ABCA4-associated retinopathies missing heritability.HGG advances · 2023Article
- Frameshift coding sequence variants in the LPL gene: identification of two novel events and exploration of the genotype-phenotype relationship for variants reported to date.Lipids in health and disease · 2023Article
- In silico methods for predicting functional synonymous variants.Genome biology · 2023Review
- Introme accurately predicts the impact of coding and noncoding variants on gene splicing, with clinical applications.Genome biology · 2023Article
- Benchmarking splice variant prediction algorithms using massively parallel splicing assays.bioRxiv : the preprint server for biology · 2023Article
- Identification and in-silico characterization of splice-site variants from a large cardiogenetic national registry.European journal of human genetics : EJHG · 2023Article
- Test development, optimization and validation of a WGS pipeline for genetic disorders.BMC medical genomics · 2023Article
- VariBench, new variation benchmark categories and data sets.Frontiers in bioinformatics · 2023Article
Corrections and comments
- Erratum issued
- Erratum issued
Authors and funding
34 authors at 20 institutions in 5 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Variant interpretation is the key issue in molecular diagnosis. Spliceogenic variants exemplify this issue as each nucleotide variant can be deleterious via disruption or creation of splice site consensus sequences. Consequently, reliable in silico prediction of variant spliceogenicity would be a major improvement. Thanks to an international effort, a set of 395 variants studied at the mRNA level and occurring in 5' and 3' consensus regions (defined as the 11 and 14 bases surrounding the exon/intron junction, respectively) was collected for 11 different genes, including BRCA1, BRCA2, CFTR and RHD, and used to train and validate a new prediction protocol named Splicing Prediction in Consensus Elements (SPiCE). SPiCE combines in silico predictions from SpliceSiteFinder-like and MaxEntScan and uses logistic regression to define optimal decision thresholds. It revealed an unprecedented sensitivity and specificity of 99.5 and 95.2%, respectively, and the impact on splicing was correctly predicted for 98.8% of variants. We therefore propose SPiCE as the new tool for predicting variant spliceogenicity. It could be easily implemented in any diagnostic laboratory as a routine decision making tool to help geneticists to face the deluge of variants in the next-generation sequencing era. SPiCE is accessible at (https://sourceforge.net/projects/spicev2-1/).
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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.