Targeted next generation sequencing assays using triplet samples of normal breast tissue, primary breast cancer, and recurrent/metastatic lesions
Abstract Background: Next generation sequencing (NGS) has shown that recurrent/metastatic breast cancer lesions may have additional genetic changes compared with the primary tumour. These additional changes may be related to tumour progression and/or drug resistance. The breast cancer-targeted NGS, however, is not still widely used for comparing genomic profile of primary breast cancer and recurrent/metastatic lesions in clinical practice.Methods: Genomic DNA was extracted from normal breast tissue, primary breast cancer, and recurrent/metastatic lesion(s) from the same patient. A DNA library was constructed using the QIAseq Human Breast Cancer Panel (93 genes, Qiagen) and then sequenced by a MiSeq (Illumina). The Qiagen web portal was utilized for data analysis.Results: Of 35 breast cancer cases with recurrence/metastases, successful results for three or four samples (normal breast tissue, primary tumour, and at least one metastatic/recurrent lesion) were obtained for 11 patients (36 samples). We detected shared somatic mutations in all but one patient, who had germline mutation in TP53. Additional mutations were detected in recurrent/metastatic lesions compared with primary tumour 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 82% (9/11) of recurrent/metastatic breast cancer cases.Conclusions: The QIAseq Human Breast Cancer Panel assay could identify driver mutations in both primary breast tumour tissue and recurrent/metastatic lesions in almost all patients. This method can assist in identifying drug-targetable mutation and CNV in metastatic breast cancers.