Abstract P2-05-07: Feasibility and sensitivity of fine-needle aspiration biopsies for the detection of somatic mutations using next-generation sequencing in breast cancer
Authors: Lee Han-Byoel , Kim Jisun , Lee Kyung-Min , Joung Je-Gun , Lee Hae-ock , Kim Min Kyoon , Lee Eunshin , Kim Jongjin , Yoo Tae-Kyung , Kim Yun-Gyoung , Kang Young Joon , Ryu Han Suk , Park In-Ae , Moon Hyeong-Gon , Noh Dong-Young , Park Woong-Yang , Han Wonshik 
Published: May 2015

Abstract
Background/Purpose: Next-generation sequencing (NGS) is being incorporated rapidly into clinical practice. Fine-needle aspiration biopsy (FNAB) specimens have been used feasibly in molecular analysis including direct sequencing and microarrays. They are readily available and enriched in malignant cells, thus providing opportunities for genomic analysis for more clinical samples. In this study, we assessed the feasibility and sensitivity of FNAB for the detection of somatic mutations by NGS compared to bulk tissue.
Methods: Bulk tissue and FNAB was sampled via skin superficial to the palpable tumor from surgically resected breast cancer specimen. DNA was extracted from the bulk tissues and FNAB samples obtained from twelve patients. Somatic mutations detected from whole exome sequencing (WES) by next-generation sequencing (NGS) (HiSeq 2500, Illumina) were analyzed for corresponding pairs of bulk tissue and FNAB. Verification of somatic mutations detected exclusively from FNAB and known to be clinically relevant to breast cancer was carried out by Sanger sequencing. Invasive tumor percentages of bulk tissues were evaluated using hematoxylin and eosin (H&E)-stained sections.
Results: Average depth of coverage were 158.8x and 158.3x for bulk tissue and FNAB, respectively. Number of detected somatic mutations ranged from 2 to 153 (median 18.5) and 19 to 210 (median 39.5) for bulk tissue and FNAB, respectively. Ten specimens had more mutations detected exclusively from FNAB than from bulk tissue. Allele fractions plotting of corresponding pairs of bulk tissue and FNAB showed good, intermediate, and poor correlation in five, two, and five specimens, respectively. H&E-stained sections of bulk tissue from the five specimens with good correlation contained an invasive tumor percentage of 45 to 98%, whereas those from five specimens with poor correlation contained 0 to 25%. Three of the poorly correlated bulk tissues were judged to have 0% of invasive tumor. Among mutations detected exclusively from FNAB, eighteen different genes of interest in 22 foci were evaluated for both FNAB and corresponding bulk tissue by Sanger sequencing. In the results, three mutations (PIK3CA, TP53 x2) were verified in FNAB samples but not in the bulk tissue.
Conclusion: WES was successfully carried out in all pairs of bulk tissue and FNAB from twelve breast cancer patients. In samples with high tumor content somatic mutation profiles showed high correlation between the two samples whereas samples with low tumor content failed to show correlation. The failure was mostly due to the scarcity of tumor portions in the bulk tissues, indicating that FNAB more reliably retained malignant tumor portion. This study suggests that FNAB is an easy and feasible method, and furthermore, provides a more reliable specimen for NGS analysis where somatic mutations could be identified for potential prognostic or therapeutic benefits.
Citation Format: Han-Byoel Lee, Jisun Kim, Kyung-Min Lee, Je-Gun Joung, Hae-ock Lee, Min Kyoon Kim, Eunshin Lee, Jongjin Kim, Tae-Kyung Yoo, Yun-Gyoung Kim, Young Joon Kang, Han Suk Ryu, In-Ae Park, Hyeong-Gon Moon, Dong-Young Noh, Woong-Yang Park, Wonshik Han. Feasibility and sensitivity of fine-needle aspiration biopsies for the detection of somatic mutations using next-generation sequencing in breast cancer [abstract]. In: Proceedings of the Thirty-Seventh Annual CTRC-AACR San Antonio Breast Cancer Symposium: 2014 Dec 9-13; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2015;75(9 Suppl):Abstract nr P2-05-07.