Proteogenomic characterization of invasive breast tumors in young women

NPJ Breast Cancer. Volume 11, Issue 1: p. 94, 18 August 2025
10.1038/s41523-025-00793-0

APOLLO-BRCA-1 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 68 invasive breast tumors collected from women less than 40 years of age (n = 34) and from women 60 years or older (n = 34), matched by immunohistochemistry subtype and patient race. Tumor tissues were enriched by laser microdissection and profiled by whole genome sequencing, transcriptome sequencing, MS-based proteomics and phosphoproteomics, and reverse phase protein arrays. Clinical and sample data include overall survival, progression-free survival times, patient features, and tumor characteristics.

Data in the GDC

• GDC Manifests
  • Open-Access Data - Download Manifest (9 Files)
  • Controlled-Access Data - Download Manifest (4 Files)

Supplemental Data

• Associated Data Files
  • apollo-brca1.somatic.snv.vcf.protected.tar.gz - Somatic Variant Calls (VCF) (Controlled)
  • apollo-brca1.somatic.maf.protected.txt - Somatic Mutation Annotation File (MAF) (Controlled)
  • apollo-brca1.cnv.seg.protected.txt - Copy Number Segments (Controlled)
  • apollo-brca1.cnv.expressed_genes_Canvas.protected.txt - Gene-level Copy Number (Controlled)
  • apollo-brca1.rnaseq.expressed_genes.level3.UQnorm_log2.txt - RNA Expression Quantification (Level 3)
  • apollo-brca1.globalproteomics_level3_Imputed.txt - MS Proteomics Expression Quantification
  • apollo-brca1.globalproteomics_level3_unimputed.txt - MS Proteomics Expression Quantification (Unimputed)
  • apollo-brca1.phosphoproteomics_level3_raw_Imputed.txt - Phosphoproteomics Quantification
  • apollo-brca1.phosphoproteomics_level3_raw_unimputed.txt - Phosphoproteomics Quantification (Unimputed)
  • apollo-brca1.phosphoproteomics_level3_adjusted_by_global_Imputed.txt - Phosphoproteomics Quantification (Global-adjusted)
  • apollo-brca1.phosphoproteomics_level3_adjusted_by_global_unimputed.txt - Phosphoproteomics Quantification (Global-adjusted, Unimputed)
  • apollo-brca1.proteomics_phopho_Datadictionary.xlsx - Proteomics/Phosphoproteomics Data Dictionary
  • apollo-brca1.RPPA_level3_imputed.xlsx - RPPA Expression Quantification