Abstract A29: Detection of ultra-rare mutations during breast stem cell tumor progression by Duplex Sequencing

Abstract

Abstract Most studies have mainly investigated clonal mutations due to the high background error frequencies of conventional next generation sequencing (NGS) methods. We have established a new method termed Duplex Sequencing (DS) that detects mutations with unprecedented accuracy and enables us to detect sub-clonal and rare mutations as well as clonal mutations. Using DS, we present our first genome-wide analysis of mitochondrial (mt) DNA mutations during the transformation of human normal breast stem cells to tumorigenic cells. We used a model system to dissect sequential steps in the progression of normal stem cells to tumorigenic cells. Significant differences have been found among normal stem cells, immortal cells, and tumorigenic cells. These cells differ in putative breast cancer stem cell (CSC) populations, mtDNA copy numbers, and the frequencies and types of mutations. We found that putative CSCs and mtDNA copy numbers increase as normal stem cells become tumorigenic cells. The vast majority of mutations identified in our study are stochastic (rare mutations) and the frequency of rare mutations is lower in transformed cells than in normal stem cells. This lower rare mutation load in transformed cells induces lower scores of predicted pathogenicity in transformed cells than in normal stem cells. C>T/G>A and A>G/T>C transitions are the major mutation types in normal stem cells, while only C>T/G>A are the major mutation types in transformed cells. Using DS, we detected a total of 1220 rare mutations and 678 of these variants have not been reported previously. The mtDNA mutation spectra of breast tumorigenic cells correlate with published nuclear DNA mutation signatures, which are found in the majority of tumors. We have identified mutations that can serve as potential biomarkers that indicate the different stages of breast carcinogenesis. These significant differences in mutation profiles could aid in characterizing different phenotypes between normal stem cells and transformed cells. Citation Format: Eun Hyun Ahn, Kensen Hirohata, Seung Hyuk Lee, Joon Yup Kim, Brendan F. Kohrn, Edward J. Fox, Chia-Cheng Chang, Lawrence A. Loeb. Detection of ultra-rare mutations during breast stem cell tumor progression by Duplex Sequencing. [abstract]. In: Proceedings of the AACR Special Conference on Advances in Breast Cancer Research; Oct 17-20, 2015; Bellevue, WA. Philadelphia (PA): AACR; Mol Cancer Res 2016;14(2_Suppl):Abstract nr A29.