Abstract A2-03: Hotspot mutation in breast benign biopsy associated with subsequent progression to malignant breast cancer
Authors: Wang Jun , Feng Gang , Jafari Nadereh , Shidfar Ali , Ivanicic David , Sullivan Megan E. , Khan Seema A. 
Published: November 2015

Abstract
Background: Breast cancer prevention is currently in a challenge due to the inability to identify high-risk women accurately only based on family history and pathologic evaluation of benign biopsy. Somatic molecular changes in clinically normal breasts have potential value for to improve the assessment of truly high-risk women. The identification of risk biomarkers in benign biopsy material will directly benefit the millions of women who undergo benign breast biopsy annually, adding precision to the risk implied by the histologic features of the benign biopsy. Therefore, we are pursuing robust biomarkers for breast cancer risk by sequencing pre-cancer benign biopsies, which may lead to discovery of genomic variation responsible for initiation and early progression of breast cancer.
Methods: We are assembling a case-control set of benign breast biopsy matched by age, race, and duration of follow-up. The cases were the benign biopsies from women who subsequently developed breast cancer after at least one year, and the controls were the benign biopsy samples obtained from women who remain cancer free. 10-micron sections from formalin-fixed, paraffin-embedded tissue blocks are used for laser capture microdissection of selected epithelial areas and extraction of DNA. As a pilot experiment, we examined hotspot mutation in 4 cases and 4 control samples, using Ion AmpliSeq cancer hotspot panel consisting of 50 oncogenes/tumor suppressor and detecting 2855 hotspot mutation from COSMIC (Catalogue Of Somatic Mutations In Cancer). The average amplicon length was 154 (111-187) with average depth coverage of 1400x. SNP detection sensitivity was 98% for 5% variant frequency.
Results: Among the 2855 hotspot mutation in 50 oncogenes/tumor suppressor detected, 153 mutation in 27 genes were identified in cases, and 62 mutations in 18 genes were found in controls. The most frequent mutanted gene was TP53 (71 mutation in cases, 24 mutation in controls). In 6 genes (CTNNB1, CDKN2A, ATM, KRAS, STK11 and SMARCB1), hotspot mutation was identified in at least two cases, but no hotspot mutation was identified in controls. Among the 4 cases, one cases had 95 hotspot mutation, much higher than the other 3 cases (5, 16, 37 mutation, respectively) and 4 controls (8, 11, 14, 29 mutation, respectively). This case progressed to triple negative (ER-, PR-, HER2-) breast cancer, a very aggressive subtype of cancer with poor prognosis.
Conclusion: The pilot study of deep sequencing of breast benign biopsy suggested that the overall hotspot mutation frequency was higher in cases which progressed to malignant cancer compared to controls which did not progress to malignant cancer. Several genes were identified to be specifically associated with the progression.
Citation Format: Jun Wang, Gang Feng, Nadereh Jafari, Ali Shidfar, David Ivanicic, Megan E. Sullivan, Seema A. Khan. Hotspot mutation in breast benign biopsy associated with subsequent progression to malignant breast cancer. [abstract]. In: Proceedings of the AACR Special Conference on Translation of the Cancer Genome; Feb 7-9, 2015; San Francisco, CA. Philadelphia (PA): AACR; Cancer Res 2015;75(22 Suppl 1):Abstract nr A2-03.