epistasis
splicing_epistasis_okgp_cons_silent_control
CONSTRAINED TCGA-silent control (Panel F)
84,848 cis-double SNV pairs across 261 randomly sampled genes: LOEUF<0.7, ZERO TCGA pairs in any tier. Null reference.
Built with the standard paper §2 ¶1-5 methodology:
≤100 nt intra-gene window
≥3 1KG carriers per constituent
TopLD r² ≥ 0.2 dropped
Greedy 1:1 matched arms keyed on gene + log-rarity bin + distance ±2 nt
seed=42
Companion panels:
splicing_epistasis_okgp_cons_driver_tcgarec — Panel D… See the full description on the dataset page: https://huggingface.co/datasets/nicolynnvila/splicing_epistasis_okgp_cons_silent_control.splicing_epistasis_okgp_tcga_driver_recurrent
Splicing epistasis — Driver+TCGA-recurrent panel (Panel A)
12,714 cis-double SNV pairs (6,357 observed + 6,357 unobserved-matched) in 1000 Genomes
across 56 genes that satisfy:
listed in OncoKB cancerGeneList.tsv (any inclusion criterion), AND
carry ≥2 TCGA-clean double-mutation pairs each with ≥5 carriers
(per tcga_de_novo_pairs_clean.csv from the original paper-2 code dump)
Built as the driver arm of a three-panel strict test that disentangles cancer-driver
status from… See the full description on the dataset page: https://huggingface.co/datasets/nicolynnvila/splicing_epistasis_okgp_tcga_driver_recurrent.splicing_epistasis_okgp_noncancer1000
Splicing epistasis — non-cancer 1000-gene control set
167,322 cis-double SNV pairs (83,661 observed + 83,661 unobserved-matched) in 1000 Genomes,
enumerated within a 1000-gene random sample of protein-coding genes excluding all OncoKB entries.
Built as a control comparator for the OncoKB-987-driver dataset to test whether the splicing-epistasis
depletion signal (Lynn et al., Section 2 ¶1-5) is panel-specific or generalizes to non-cancer genes.
Same methodology as paper §2: ≤100… See the full description on the dataset page: https://huggingface.co/datasets/nicolynnvila/splicing_epistasis_okgp_noncancer1000.splicing_epistasis_okgp_oncokb987
Splicing epistasis — OncoKB-driver-extended 1000 Genomes matched-arms set
262,040 cis-double SNV pairs in 1000 Genomes, enumerated within the 987 OncoKB-annotated cancer driver genes, split into matched observed / unobserved arms for the splicing-epistasis depletion test (Lynn et al., Genome Medicine, in preparation).
Why this dataset
The paper's headline depletion test (Section 2 ¶1-5) runs on a 138-gene cancer panel and 28,642 matched-arms pairs. This dataset… See the full description on the dataset page: https://huggingface.co/datasets/nicolynnvila/splicing_epistasis_okgp_oncokb987.splicing_epistasis_okgp_cons_driver_tcgarec
CONSTRAINED OncoKB drivers with TCGA-recurrent doublets (Panel D)
10,864 cis-double SNV pairs across 41 genes: OncoKB cancer drivers, LOEUF<0.7, with ≥2 TCGA-clean pairs × ≥5 carriers each. Tests the RESCUE-enrichment hypothesis.
Built with the standard paper §2 ¶1-5 methodology:
≤100 nt intra-gene window
≥3 1KG carriers per constituent
TopLD r² ≥ 0.2 dropped
Greedy 1:1 matched arms keyed on gene + log-rarity bin + distance ±2 nt
seed=42
Companion panels:… See the full description on the dataset page: https://huggingface.co/datasets/nicolynnvila/splicing_epistasis_okgp_cons_driver_tcgarec.splicing_epistasis_okgp_tcga_nondriver_recurrent
Splicing epistasis — Non-driver+TCGA-recurrent panel (Panel B)
94,984 cis-double SNV pairs (47,492 observed + 47,492 unobserved-matched) in 1000 Genomes
across 663 genes that satisfy:
NOT in OncoKB cancerGeneList.tsv, AND
carry ≥2 TCGA-clean double-mutation pairs each with ≥5 carriers
(per tcga_de_novo_pairs_clean.csv from the original paper-2 code dump)
Built as the non-driver arm of a three-panel strict test. These are genes that show
recurrent doublet events in TCGA cancers… See the full description on the dataset page: https://huggingface.co/datasets/nicolynnvila/splicing_epistasis_okgp_tcga_nondriver_recurrent.