Proteogenomic Analysis of Lung Adenocarcinoma Reveals Tumor Heterogeneity, Survival Determinants and Therapeutically-Relevant Pathways

Cell Reports Medicine . Volume 3, Issue 11 p.6100819, November 15, 2022 10.1016/j.xcrm.2022.100819

APOLLO is a proteogenomic study seeking to describe the major genome, transcriptome, proteome and phosphoproteome alterations, subtypes, and molecular predictors of patient outcomes. This study includes 87 lung adenocarcinomas and matched normal tissues from the Lung Cancer Biospecimen Resource Network (https://lungbio.sites.virginia.edu/). Tumor tissues were profiled by whole genome sequencing, transcriptome sequencing, MS-based proteomics and phosphoproteomics, and reverse phase protein arrays. Matched normal tissues were profiled by whole genome sequencing. Clinical and sample data include survival times, patient features, and tumor characteristics.

Data in the GDC

• GDC Manifests
  • Open-Access Data - Download Manifest (8 Files)
  • Controlled-Access Data - Download Manifest (7 Files)

Supplemental Data

• RNA_quant_files_20181226.tar.gz - RNA Expression Quantification
• APOLLO1_Level3_Gprot_v061418.n87.csv - MS Proteomic Expression Quantification
• APOLLO1_Level3_GProt_RAW.txt - MS Proteomics, non-imputed
• 011720_APOLLO1_APROT_TMT11_Level3_Phospho_FINAL_020220PHOSPHO_RELATIVE_n87.csv - MS Phosphoproteomics Expression Quantification
• APOLLO1_RPPA_Ammended022519.csv - RPPA Expression Quantification
• APOLLO1_RPPA_AbID_conversion_table_20210608_reduce.txt - RPPA Annotation
• Combined Phosphoproteomic Data (MS and RPPA)
• Combined Phosphoproteomic Data (MS and RPPA), Global Protein Normalized
• apollo1.tagc.all.maf.102320.v20.1.protected.txt - Somatic Mutation Annotation File (Controlled)
• apollo1.n87.somatic.SV.protected.tar.gz - Somatic Structural Variant VCF (Controlled)
• apollo1.n87.somatic.SV.bpi.protected.tar.gz - Somatic Structural Variant annotated VCF (Controlled)
• apollo1.n87.somatic.snv.vcf.protected.tar.gz - Somatic SNV Mutations VCF (Controlled)
• apollo1_n87_TN_paths.segfile.protected.txt - Somatic DNA Copy Number Segments (Controlled)
• apollo1_expressed_genes_CNA.protected.txt - Somatic DNA Copy Number of Genes (Controlled)
• apollo1.n87.rna.fusions.protected.tar.gz - Tumor RNA Fusion Transcripts (Controlled)

Additional Resources

• Proteomics data at ProteomeXchange (link is external)
• APOLLO data at dbGaP (link is external)
• Proteome (link is external)
• Phosphoproteome - Ti02 (link is external)
• Phosphoproteome - FeNTA (link is external)

Instructions for Data Download

Open Access Data

1. Download the appropriate manifest file from the publication page
2. Use the manifest file to download data using the GDC Data Transfer Tool (DTT) or the GDC API
   • GDC DTT (Download, User's Guide)
   • GDC API (User’s Guide)

Controlled Access Data

1. Download the appropriate manifest file from the publication page
2. Download a token from the GDC Data Portal
   • GDC Data Portal (Launch, User’s Guide)
3. Use the manifest file and token to download data using the GDC DTT or the GDC API
   • GDC DTT (Download, User’s Guide)
   • GDC API (User’s Guide)

For assistance, please contact the GDC Help Desk: support@nci-gdc.datacommons.io.