Abstract 2971: Whole exome sequencing reveals heterogeneity within lobular carcinoma in situ (LCIS) and clonal selection in the progression to malignant lesions

INTRODUCTION: Lobular carcinoma in situ (LCIS) is considered both a risk factor and non-obligate precursor of low-grade estrogen receptor-positive breast cancer. We sought to define the mutational repertoire, subclone complexity and heterogeneity of LCIS, and whether invasive lobular carcinomas (ILCs) would stem from specific subclones within a LCIS. METHODS: Patients with a history of LCIS undergoing therapeutic or prophylactic mastectomy were prospectively enrolled in an IRB approved protocol. Frozen tissue blocks were collected, screened for lesions of interest (LCIS, ductal carcinoma in situ (DCIS), ILC, invasive ductal carcinoma (IDC)) and subject to microdissection and DNA extraction. Matched germline DNA was available for all cases. Whole exome sequencing was performed on a HiSeq2000 (Illumina) and data were aligned to the reference human genome hg19 and processed using GATK. SNVs were called using MuTect, and indels were called using a combination of Varscan and Strelka. Purity and ploidy estimates were calculated by ABSOLUTE. Clonal frequencies were estimated using Pyclone. RESULTS: 30 LCIS, 10 ILCs, 6 IDCs and 7 DCIS from 15 patients qualified for data analysis, resulting in 18 LCIS-ILC pairs, 22 LCIS-LCIS pairs, 12 LCIS-DCIS pairs, and 14 LCIS-IDC pairs for comparison. 9/18 (50%) LCIS-ILC pairs and 8/22 (36%) LCIS-LCIS pairs were clonally related, supported by several shared mutations (median 18, range 7-81 for LCIS-ILC; median 14, range 5-22 for LCIS-LCIS). All related LCIS-ILC pairs and 6/8 related LCIS-LCIS pairs shared a pathogenic CDH1 mutation; 75% of related LCIS-ILC pairs also shared a PIK3CA hotspot mutation. 7/12 (58%) LCIS-DCIS pairs were found to be clonally related but the number of shared mutations was generally lower than that found in LCIS-ILC pairs (median 9, range 2-11). No evidence of a clonal relationship was found in any of the LCIS-IDC pairs tested. Clonal composition analysis revealed that samples of LCIS display intra-lesion genetic heterogeneity in the form of the presence of a minor clone in 70% of cases. In one case, the LCIS minor subclone (∼15%) constituted the major clone in the ILC and in another case the LCIS minor subclone constituted the major clone in the associated DCIS. The majority of the clonally related lesions were located in the same quadrant of the breast, however evidence of clonality was found in 5 LCIS-LCIS and 3 LCIS-DCIS pairs located in separate quadrants of the breast. CONCLUSIONS: Intra-lesion genetic heterogeneity is a common phenomenon in LCIS. The dominant clone of a LCIS may not always be the clone directly involved in the progression to malignancy. The spatial relationships of clonally related lesions in this study suggest that anatomy does not always infer clonality, as lesions located in separate quadrants of the breast may be clonally related. Citation Format: Michail Schizas, Rita A. Sakr, Britta Weigelt, Charlotte KY Ng, Jose Victor S. Carniello, Dilip Giri, Salvatore Piscuoglio, Luciano G. Martelotto, Russell Towers, Victor P. Andrade, Raymond Lim, David B. Solit, Jorge S. Reis-Filho, Tari A. King. Whole exome sequencing reveals heterogeneity within lobular carcinoma in situ (LCIS) and clonal selection in the progression to malignant lesions. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 2971. doi:10.1158/1538-7445.AM2015-2971