AURORA Manuscript data sharing

Data availability

The AURORA manuscript data allows the replication of the main analyses in the Aftimos et al article. It comprises data from 617 samples from 375 patients, with the molecular data distributed like this:

Data type	Patients with primary data	Patients with meta data	Patients with both data
Ion Torrent TGS (441 genes)	19	114	242
Illumina RNA-Seq	53	109	152
Affymetrix Oncoscan CNV	110	67	67

Data description

The processed data is distributed in 5 files. Please refer to the article methods section for additional details on the computed variables.

File 1 Aurora_clinical_data.csv: Clinical data

PAM50_primary: PAM50 subtype of the primary tumor
PAM50_meta: PAM50 subtype of the biopsied metastatic lesion
IHC_primary: Biological subtype (HR+/HER2-, HER2+, TNBC) of the primary tumor
IHC_meta: Biological subtype (HR+/HER2-, HER2+, TNBC) of the biopsied metastatic lesion
metastatic_biopsy_site: Site of the metastatic biopsy
is_de_novo: Is it de novo metastatic breast cancer?
adjuvant: Did the patient receive an adjuvant treatment?
neodajuvant: Did the patient receive a neoadjuvant treatment?
block_before_or_after_neo_treatement: If patient received a neoadjuvant treatment, was the sample collected before or after it?
metastatic_tx_lines_before_aurora: Number of metastatic treatment lines (0 or 1) before enrolment
num_metastatic_sites_at_inclusion: Number of metastatic sites at inclusion in the study
primary_grade: Grade of the primary tumor
primary_patho_node_status: Lymph node involvement for primary lesion
primary_size_t1_or_t2: Size (T1 or T2) of the primary tumor
overall_survival_days: Overall survival in days
death_events: Did the patient die (1) during the study, or not (0)
time_to_metatstatic_relapse_days: Time from primary diagnosis to metastaic relapse in days
patient_in_oncoplot: Is patient is included in the Oncoplot (1), or not (0)

File 2 AURORA_table_mutations.csv: Sequence variants detected with Targeted Gene Sequencing

sample_type: Type of sample (primary or meta)
chrom: Chromosome
pos: Genomic coordinates (hg19 genome reference)
ref: Reference allele
alt: Alternative allele detected in the tumor
type: Type of variant (INS, DEL, SNV)
symbol: Gene symbol
VAF: Variant allele frequence
coverage: Sequencing coverage
effect: Consequence of the mutation
AA: Variant at the amino acid level
CN: Copy number estimate
purity_affy: Purity estimate based on the Affymetrix OncoScan data
purity_facets: Putity estimate based on TGS with FACETS
CCF: Estimate of the cancer cell fraction
cellular_prevalence: Estimate of the cellular prevalence
cDNA: Variant at the cDNA level
census_role_in_cancer: Role of the gene in the COSMIC Cancer census
cosmic_mutation_significance_tier: Significance tier in COSMIC for the variant
Protein_position: Amino acid position in the protein
vep_consequence: Predicted consequence by the Variant Effect Predictor
SIFT: Predicted pathogenicity by SIFT
PolyPhen: Predicted pathogenicity by Polyphen
FATHMM_pred: Predicted pathogencity by FATHMM
aurora_driver_call: Aggregated pathogenicity call
aurora_driver_call_source: Source of the aggregated pathogenicity call

File 3 OncoScan_CNA.csv: Affymetric OncoScan CNA regions

sample: Type of sample (primary or meta)
chrom: Chromosome
start: Start coordinate of the CNA region (hg19 reference genome)
end: Start coordinate of the CNA region (hg19 reference genome)
nMajor: Copy number of major haplotype in sample
nMinor: Copy number of minor haplotype in sample
nAraw: Unajusted copy number of major haplotype in sample
nBraw: Unajusted copy number of minor haplotype in sample

File 4 TGS_CNA.csv: Gene-level copy number estimates from TGS with FACETS

File 5 RNA.zip: Raw gene counts from RNA-Seq

In addition to the processed data, the corresponding raw data (BAM files and FASTQ files for the sequencing data, OSCHP files for the CNV data) are available in the context of a research proposal if requested.