Comparison of three lung cancer subtypes

Comprehensive comparison of three lung cancer subtypes

Weak overlap of three lung cancer subtypes

This website is the companion to the paper "Weak sharing of genetic association signals in three lung cancer subtypes: evidence at the SNP, gene, regulation, and pathway levels". On this website, we have included the code that was used to generate the results in the paper in addition to other useful files from the paper.

For this study, we performed an interrogation into the features and overlap of single nucleotide polymorphisms (SNPs) identified from a genome-wide association study (GWAS) of lung adenocarcinoma (LUAD), lung squamous cell carcinoma (LUSC), and small cell lung cancer (SCLC). We first expanded these sets of SNPs using linkage disequilibrium (LD) information from the 1000 Genomes Project. We used these expanded sets of SNPs to identify variants that may be acting in regulatory roles (eQTLs or within enhancers) and their target genes in each subtype. We also identifed overlapping and unique biological pathways for each subtype.

Below is the code used to generate our results

Pipeline to obtain the germline-regulated genes for LUAD SNPs from the GWAS summary results: analysis_pipeline_for_LUAD_SNPs.txt
Pipeline to obtain the germline-regulated genes for LUSC SNPs from the GWAS summary results: analysis_pipeline_for_LUSC_SNPs.txt
Pipeline to obtain the germline-regulated genes for SCLC SNPs from the GWAS summary results: analysis_pipeline_for_SCLC_SNPs.txt
Java plink_glist code needed for the three pipelines above: plink_glist.class
Pipeline to obtain the germline-regulated genes for GWAS Catalog SNPs from the GWAS Catalog: analysis_pipeline_for_GWAS_Catalog_SNPs.txt
Code used for the randomization analysis with the GWAS summary results: code_for_randomization_analysis.txt
Code used for the principal components analysis: code_for_pca_with_TCGA_data.txt
Code used for the locus level analysis for germline-regulated genes unique to LUAD: code_for_locus_level_analysis_luad_unique.txt
Code used for the locus level analysis for germline-regulated genes unique to LUSC: code_for_locus_level_analysis_luscunique.txt
Code used for the locus level analysis for germline-regulated genes unique to SCLC: code_for_locus_level_analysis_sclc_unique.txt
Code used for the locus level analysis for germline-regulated genes shared by LUAD and LUSC: code_for_locus_level_analysis_luad_overlap_lusc.txt
Code used for the locus level analysis for germline-regulated genes shared by LUSC and SCLC: code_for_locus_level_analysis_lusc_overlap_sclc.txt

Below are additional files

Citation

O'Brien TD, Jia P, Caporaso NE, Landi MT, Zhao Z. Weak sharing of genetic association signals in three lung cancer subtypes: evidence at the SNP, gene, regulation, and pathway levels. Genome Medicine. In revision.

Contact

Peilin Jia: peilin.jia@uth.tmc.edu

Zhongming Zhao: zhongming.zhao@uth.tmc.edu