WangZishan/TCGASecondaryPredisposition

Non-cancer-related pathogenic germline variants and expression consequences in ten-thousand cancer genomes

[Citation of our manuscript if help you https://link.springer.com/article/10.1186/s13073-021-00964-1]

Code for the analysis in this project.

./AlleleSpecificExpression

ASE_basic.R

Identification of rare NC P/LPs associated with allele specific expression (ASE).

ASE_Gene_Enrichment.R

Gene enrichment analysis for NC P/LPs showing significant ASE

ASE_MultiVars.R

Plots/Files for distribution of NC P/LPs with distinct ASE enrichment status across predicted variant function classes.

GeneVariant_Distribution.R

Extract information of NC P/LPs for genes of interest to generate the format required by online lolliplots software ProteinPaint at https://proteinpaint.stjude.org/.

./GeneralFunctions

Functions used in this analysis.

./VariantDistributionAcrossAncestries

AR.R

Plots for the carrier frequency and NC P/LPs count of autosomal recessive (AR) and autosomal dominant (AD) genes across ancestries.

Distribution_for_ACMG_classification.R

Plots for the frequency of NC P/LP carriers and count of NC P/LPs across ancestries.

Distribution_for_genes.R

Plots for the frequency/count of NC P/LP carriers in each ancestry among the ACMG 59 genes and the top 10% genes (ranked by sums of all defined ancestry frequencies, excluding Mix and Other).

./VariantImpactOnExp

VariantImpactOnExp.R

Identification of genes whose expression is affected by related NC P/LPs.

VariantImpactOnExp_Plot.R

Volcano plots for genes whose expression is affected by related NC P/LPs.

PlotPercentileExp.R

Distribution of percentile expression in a specific cancer at NC P/LP carriers of genes whose expression is significantly/suggestively impacted by NC P/LPs or enriched with significant ASE variants. Color of node represents variant type. Color of node edge represent ASE enrichment status.

PlotPercentileExp_DiffExpSplitCount.R

Count/Proportion of sample-variants across expression splits vs predicted variant function/ASE status for genes whose expression is significantly/suggestively impacted by NC P/LPs or enriched with significant ASE variants.

PlotPercentileExp_DiffExpSplitCount_GeneInfo.R

Detailed information for sample-variants of for genes whose expression is significantly/suggestively impacted by NC P/LPs or enriched with significant ASE variants.

./gnomad/bcftools

Command of bcftools to extract information of variant of interests from gnomad dataset.

./gnomad/ancestry_variant_distribution

count.R

Variant count of predisposing variants in the matched gnomAD ancestry (European of gnomAD is the union of FIN and NFE populations). TCGA population-specific NC P/LPs, exclusively found in a specific TCGA ancestry, are shown as a triangle. Top NC P/LP or top TCGA ancestry-specific NC P/LP, ranked by allele counts in TCGA or gnomAD, was labelled.

statistic.R

(Significance of) Correlations of variant frequencies in the matched ancestries between TCGA and gnomAD.

./gnomad/bcftools_process

process.R

Preprocess the information of variant of interests from gnomad dataset.

plot_ancestry.R

Plot for the frequency/count of ACMG status/genes across different ancestries.