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 107 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 mutations in TP53 and KMT2C . 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 . More copy number variations (CNVs) was detected in distant metastases than in local recurrence ( P =0.030).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 mutations and CNV in metastatic breast cancers.