Application of next-generation sequencing (NGS) enables to reveal genetic diversity of malignant tumors. Here we report our experience with targeted NGS in Asian patients with primary breast cancer.
We identified 150 Asian patients who had genotyping by targeted NGS between April 2017 and Mar 2018 in a single institution. The genetic mutation patterns of the patients were analyzed retrospectively. Targeted NGS with the Oncomine™ comprehensive panel including 143 genes was conducted on Ion Torrent S5 XL (Thermo Fisher Scientific, Waltham, MA, USA). All patients had stage I-III by AJCC 7th edition.
Targeted NGS was conducted in a total of 150 primary breast cancer including 98 (65.3%) patients of the luminal/HER2-negative subtype, 28 (18.7%) patients of the HER2 subtype, and 24 patients of the (16.0%) TNBC subtype. Of the 150 patients, 138 patients had 432 genomic alterations including 306 mutations and 126 aberrant copy number variations (CNV). The most common genetic mutation was PIK3CA mutation (64 patients, 42.7%), followed by TP53 mutation (48 patients, 32.0%), TET2 mutation (26 patients, 17.3%) and ERBB2 mutation (6 patients, 4.0%). Of the 6 patients with ERBB2 mutations, 5 patients were in the luminal/HER2-negative subtype and 1 in the HER2 subtype. When ERBB2 amplification excluded, most common CNV was found in FGFR1 (12 patients, 8.0 %) followed by CCND1 (10 patients, 6.7 %). In 35 ER-positive/HER2-negative patients who agreed to receive Oncotype DX assay, 18 patients (48.6%) had PIK3CA mutation. In patients with PIK3CA mutation, 13 (72.2%) had a low RS, and 5 patients (27.8%) had an intermediate RS. A patient with RS of 27, which is recognized as high score by the criteria of TAILORx trial, had co-mutations as PIK3CAH1047R and P53K132N.
Our data with targeted NGS panel suggested that genomic landscape of Asian breast cancer is in accordance with previous NGS studies with Western women. In addition, our subgroup study with Oncotype DX supports early notion that ER-positive breast cancer patients with PIK3CA mutation show a better prognosis compared with those without PIK3CA mutation.
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