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nicolynnvila/splicing_epistasis_okgp_tcga_silent_control

Splicing epistasis — TCGA-silent control panel (Panel C) 143,408 cis-double SNV pairs (71,704 observed + 71,704 unobserved-matched) in 1000 Genomes across 719 randomly sampled protein-coding genes that have zero TCGA double-mutation pairs in tcga_de_novo_pairs_clean_relaxed.csv (the broad TCGA pair pool). Built as the null arm of a three-panel strict test. These genes show no evidence of recurrent doublet events in TCGA — the prediction is that they should show no 1KG depletion… See the full description on the dataset page: https://huggingface.co/datasets/nicolynnvila/splicing_epistasis_okgp_tcga_silent_control.

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Splicing epistasis — TCGA-silent control panel (Panel C)

143,408 cis-double SNV pairs (71,704 observed + 71,704 unobserved-matched) in 1000 Genomes across 719 randomly sampled protein-coding genes that have zero TCGA double-mutation pairs in tcga_de_novo_pairs_clean_relaxed.csv (the broad TCGA pair pool).

Built as the null arm of a three-panel strict test. These genes show no evidence of recurrent doublet events in TCGA — the prediction is that they should show no 1KG depletion either.

Methodology

Same as paper §2 ¶1-5:

  • —Sample 719 protein-coding MANE-select genes uniformly at random from the TCGA-silent universe
  • —≤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

Panel size (719) matches the combined size of Panel A (56 drivers) + Panel B (663 non-drivers).

Files

  • —inputs.parquet — 143,408 matched-arm pairs
  • —gene_panel.txt — the 719-gene list
  • —stats.json — enumeration / matching counts