Deliverable

5Data description

In this section, we describe the INTEGRATE data that will be used for cancer modelling. Data from the TOP clinical trial will be the first data to be shared on the INTEGRATE platform and use for modelling and thus we will start this section by describing them. After this, we will present other data types that are likely to be shared on the INTEGRATE platform and will be useful for cancer modelling.

5.1Available data from TOP clinical trial

5.1.1Clinical Data

These data are available for all patients from the TOP clinical trial. The clinical data, presented in Table , comprise information on tumour size, axillary lymph node status, tumor grade, biomarker expression status (estrogen receptor, progesterone receptor, HER2, TOP2A), and several clinical endpoints such as pathological complete response, distant metastasis-free survival and overall survival.

Variable	Supplementary Information
geo_accn	GEO accession numbers.
age.bin	years old, years old.
T	, , tumor of any size with direct extension to the chest wall or skin.
N	Axillary lymph node status: N0: no axillary lymph node metastasis, N1: metastasis in movable ipsilateral axillary lymph node(s), N2: metastasis in fixed ipsilateral axillary lymph node(s) or in clinically apparent ipsilateral internal mammary lymph node(s) in the absence of clinically evident axillary lymph node metastasis, N3=metastasis in ipsilateral infraclavicular lymph node(s) with or without axillary lymph node involvement; or in clinically apparent* ipsilateral internal mammary lymph node(s) in the presence of clinically evident axillary lymph node metastasis; or metastasis in ipsilateral supraclavicular lymph node(s) with or without axillary or internal mammary lymph node involvement.
Grade	Tumor grade (1, 2, 3)
HER2.bin	HER2 status by fluorescent in situ hybridization (FISH): 0: not amplified (), 1: amplified ().
TOP2A.tri	TOP2A status by FISH: -1: deleted (), 0: not amplified (), 1: amplified ().
topo.IHC	Topo by immunohistochemistry (%).
ESR1.bimod	ER status identified by bimodality of ESR1 gene expression.
ERBB2.bimod	HER2 status identified by bimodality of ERBB2 gene expression.
FINAL_ANALYSIS	Eligible patients included in the prediction analyses [15].
pCR	Pathological complete response. 0: no pCR, 1: pCR
DMFS_event	Distant metastasis free survival event.
DMFS_time	Distant metastasis free survival (days).
OS_event	Overall survival (event)

Table Clinical TOP Trial dataset