Data Description

Data Availability

The AURORA manuscript dataset comprises data from 617 samples from 371 patients, with the molecular data distributed as follows:

Data Type	Patients with data from primary tumor	Patients with data from metastatic tumor	Patients with data from both primary and metastatic tumor
Ion Torrent TGS (441 genes)	19	113	239
Illumina RNA-Seq	51	103	156
Affymetrix Oncoscan CNV	81	51	60

Data Description

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

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)

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

Variant at the amino acid level

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 Predicto

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

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

End 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

TGS_CNA.csv

Gene-level copy number estimates from TGS with FACETS

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 if requested in the research proposal application form.