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. 2025 Nov 20;43(1):9.
doi: 10.1007/s12032-025-03122-4.

Translating genomic insights into therapy: an NGS-based mutation profiling study in breast cancer

Hunayna M Bhavnagari  1 , Apexa P Raval  1 , Bhoomi V Tarapara  1 , Jigna S Joshi  1 , Franky D Shah  2
Affiliations

Translating genomic insights into therapy: an NGS-based mutation profiling study in breast cancer

Hunayna M Bhavnagari et al. Med Oncol. .

Abstract

The high prevalence of breast cancer is fairly frequent among women worldwide. In the current era of personalized medicine, understanding the molecular etiology of Breast Cancer is essential for better treatment options. Our investigation of the molecular alterations in tumors using next-generation sequencing targeted panels, specifically the Oncomine Precision Assay, has revealed clinically substantial somatic mutations. A total of 32 pretherapeutic invasive ductal carcinoma patients were enrolled in this study. The DNA extraction and quantification were carried out from tumor tissues and proceeded for the run and analyzed with genexus software. The analysis revealed a highly prevalent PIK3CA mutation which plays a significant role in tumorigenesis. PIK3CA mutation incorporated different single nucleotide variations including H1047R (COSMIC ID -775), E545K (COSMIC ID-763), E542K (COSMIC ID-760), H1047L (COSMIC ID-776) and N345K (COSMIC ID-754). While the most frequent copy number variations (CNV) were found for the ERBB2 gene. Apart from these frequent mutations, TP53 SNVs, FGFR, EGFR, CDKN2A, CD274, and PTEN Copy Number Variations were also present in the study cohort. The noteworthy observation is out of 7 Triple Negative Breast Cancer patients three patients were negative for any mutation. Hence, the association of genetic variation with clinicopathological parameters will be helpful in the selection of targeted treatment.

Keywords: Breast cancer; Copy number variations; Genexus™; Next-Generation sequencing; Oncomine precision assay; Single nucleotide variations.

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Conflict of interest statement

Declarations. Competing interests: The authors declare no competing interests. Consent to participate: An informed consent was obtained from all the subjects prior to their enrolment in the study. Consent to publish: Not applicable. Ethical approval: This study was approved by the GCRI/GCS Ethics Committee-BHR, The Gujarat Cancer and Research Institute, Asarwa, Ahmedabad 380016. GCRI/GCS Ethics Committee-BHR Reference number-EC/BHR/11/2022.

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