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Updated: Dec 7, 2025
Comparative Lesions Analysis Through a Targeted Sequencing Approach
Published on: November 5, 2019
Targeted next-generation sequencing assays using triplet samples of normal breast tissue, primary breast cancer, and
Toshiaki Akahane1,2, Naoki Kanomata3,4, Oi Harada2
1Department of Pathology, Kagoshima University Graduate School of Medical and Dental Sciences, Kagoshima, Japan.
Background:
Next-generation sequencing (NGS) has shown that recurrent/metastatic breast cancer lesions may have additional genetic changes compared with the primary tumor. These additional changes may be related to tumor progression and/or drug resistance. However, breast cancer-targeted NGS is not still widely used in clinical practice to compare the genomic profiles of primary breast cancer and recurrent/metastatic lesions.
Methods:
Triplet samples of genomic DNA were extracted from each patient's normal breast tissue, primary breast cancer, and recurrent/metastatic lesion(s). A DNA library was constructed using the QIAseq Human Breast Cancer Panel (93 genes, Qiagen) and then sequenced using MiSeq (Illumina). The Qiagen web portal was utilized for data analysis.
Results:
Successful results for three or four samples (normal breast tissue, primary tumor, and at least one metastatic/recurrent lesion) were obtained for 11 of 35 breast cancer patients with recurrence/metastases (36 samples). We detected shared somatic mutations in all but one patient, who had a germline mutation in TP53. Additional mutations that were detected in recurrent/metastatic lesions compared with primary tumor were in genes including TP53 (three patients) and one case each of ATR, BLM, CBFB, EP300, ERBB2, MUC16, PBRM1, and PIK3CA. Actionable mutations and/or copy number variations (CNVs) were detected in 73% (8/11) of recurrent/metastatic breast cancer lesions.
Conclusions:
The QIAseq Human Breast Cancer Panel assay showed that recurrent/metastatic breast cancers sometimes acquired additional mutations and CNV. Such additional genomic changes could provide therapeutic target.
Insights
Genomic analysis reveals that recurrent breast cancers often acquire new mutations compared to the primary tumor. These genetic alterations in metastatic lesions may offer new therapeutic targets for advanced breast cancer.
Area of Science:
- Genomics
- Oncology
- Molecular Biology
Background:
- Recurrent/metastatic breast cancer can exhibit distinct genetic alterations compared to primary tumors.
- These genetic changes may drive tumor progression and the development of drug resistance.
- Targeted next-generation sequencing (NGS) for breast cancer is underutilized for comparing primary and metastatic lesion genomics.
Purpose of the Study:
- To investigate the genomic differences between primary breast cancer and its recurrent/metastatic lesions using targeted NGS.
- To identify potential therapeutic targets within the acquired mutations in metastatic breast cancer.
Main Methods:
- DNA was extracted from normal breast tissue, primary tumors, and recurrent/metastatic lesions from breast cancer patients.
- A targeted gene panel (QIAseq Human Breast Cancer Panel, 93 genes) was used for library construction and sequencing.
- Data analysis was performed using the Qiagen web portal.
Main Results:
- Genomic profiling was successful for 36 samples from 11 out of 35 patients.
- Shared somatic mutations were common, with one patient having a TP53 germline mutation.
- Recurrent/metastatic lesions showed additional mutations in genes like TP53, ATR, and PIK3CA.
- Actionable mutations or copy number variations (CNVs) were identified in 73% of metastatic lesions.
Conclusions:
- Targeted sequencing revealed that recurrent/metastatic breast cancers can acquire additional mutations and CNVs.
- These acquired genomic alterations represent potential therapeutic targets for advanced breast cancer.
