Excess panel-matched rare variants in Genomics England rare-disease probands at panel-match odds ratio 2 (SpliceAI2 paper)
Number of variants above a model threshold that fall in the proband's dominant disease-panel genes in excess of phenotype-shuffled expectation, at the threshold where the panel-match odds ratio is 2.
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Sources and history
Release 2026-10-22-1b7cf027e4f6 · Record review: source checked
1 source record and release history
- A unified framework for quantitative splicing and transcript prediction (Jaganathan et al., bioRxiv 2026) · Original source · bioRxiv preprint version 1, posted 2026-10-11; full-text PDF (57 pages)
Technical metadata and extraction receipts
Stable ID: rna-splicing-20261013-spliceai2-protocol-gel-panel-enrichment
- areas
- dna-genomes
- contexts
- clinical_research
- protocol
- Exclude essential splice, stop-gained, start-lost, frameshift and missense variants; compare prioritised variants in panel and non-panel genes between observed and ten phenotype-shuffled cohorts; OR = (A*D)/(B*C), excess = A - C*B/D; read at OR 2.
- version
- bioRxiv v1 Main text and Fig. 4b
- metric
- count
- metric direction
- higher
- unit
- count
- source locator
- Main 'Contribution to rare genetic disease' paragraphs 1 and 2; Methods 'Panel-matched disease gene enrichment'; Fig. 4b
- limitations
- Proxy endpoint: enrichment in phenotype-matched genes, not confirmed splicing or diagnosis.; Only the SpliceAI2 value is printed; the text gives 114 for 'the next best model' without naming it, and the Fig. 4b curves (SpliceAI, Pangolin, AlphaGenome, the AlphaGenome AVI score and SpliceAI2) carry no printed values.; Developer-reported: the SpliceAI2 authors (Illumina) built the benchmark, chose comparator settings and ran every model; AlphaGenome was scored by co-authors at the University of Oxford.; Training overlap: SpliceAI2 was trained on all human genes except those on chromosomes 21 and 22, and the benchmark is genome-wide, so most variants lie in genes seen in training. Supplementary Table 1 does not list Genomics England data among the training sources.; Essential splice variants are excluded, so results do not cover canonical GT/AG disruption.; No confidence intervals or resampling uncertainty are printed.; Preprint (bioRxiv v1), not peer reviewed.