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Article History

Accepted: 2 December 2021

First Online: 21 December 2021

Declarations

:

: All the expenses were covered from the Poznan Supercomputing and Networking Center’s ‘computational grant’ no. 437, titled <i>‘Molekularny mechanizm interakcji pomiędzy szlakami naprawy DNA w oporności na chemioterapię’</i>. Open access reimbursement will be granted based on Springer’s Read and Publish agreement.

: Alicja Woźna, Pawel Sztromwasser, Maciej Piernik, and Paweł Zawadzki are share owners in the company MNM Bioscience Inc. Marzena D. Wojtaszewska, Rafal Stępien, Maciej Dąbrowski, and Michał Gniot were employees of MNM Bioscience Inc. Marzena D. Wojtaszewska and Michal Gniot received conference reimbursements/speaker honoraria from Novartis in the past. Other authors declare no conflicts of interest.

: The collection of all primary data used in this study was performed by international Genomic Consortia, which provided de-identified samples. Data collection and transmission was approved by local medical ethics committees during design of the original studies. No additional approvals are needed, and our study was reviewed and deemed exempt by the Adam Mickiewicz University Review Board. The protocols are in accordance with the ethical standards of our institution and with the 1964 Helsinki Declaration and its later amendments.

: The written consent of each participant is in possession of Genomic Consortia. The primary data were collected in accordance with the standards set by the Declaration of Helsinki and the highest data security standards of ISO 27001. All necessary patient/participant consent has been obtained and the appropriate institutional forms have been archived during the design of the original studies.

: The investigators have adhered to controlled-access agreement conditions and obtained consent to publish the study results.

: The data that support the findings of this study are openly available in the following repositories: Hartwig Medical Foundation at , which was acquired under data request number DR-169 and International Cancer Genome Consortium at , which was acquired under data request number DACO-6030. The Cancer Genome Atlas data were acquired via dbGaP platform (project phs000178.v11.p8) at: , under data request number #86794-3. The processed genomic data from 551 samples used for external validation were extracted from the publication by Nik-Zainal et al., 2016 () [file 1 and 4 of the ESM]. Secondary data that support the findings of this study generated by the authors are available in the ESM.

: The code for HER2/<i>ERBB2</i> amplification classification is available at: .

: MW was responsible for the study design, manuscript preparation, and data analysis. AW is the main genomic data administrator and was responsible for the primary data acquisition. MP designed the computational framework for the machine learning approach. PS developed the pipeline and was responsible for bioinformatics support. MD refined the secondary data and helped to write the manuscript. MG conducted statistical analyses and verified the clinical actionability of genomic variants. SS curated medical data and made manuscript corrections. MS coordinated the statistical analysis. PK evaluated the concordance of the molecular and clinical data. RM provided expertise on molecular HER2 status assessment and evaluated the clinical data. PZ was the supervisor of the project, reviewed the methodology, and corrected and revised the manuscript.