Tissue recommendations for precision cancer therapy using next generation sequencing: a comprehensive single cancer center’s experiences

Abstract

// Minho Cho 1, 8, * , Soomin Ahn 2, * , Mineui Hong 1, 2 , Heejin Bang 1, 2 , Michael Van Vrancken 3 , Seungtae Kim 4 , Jeeyun Lee 4 , Se Hoon Park 4 , Joon Oh Park 4 , Young Suk Park 4 , Ho Yeong Lim 4 , Won Ki Kang 4 , Jong-Mu Sun 4 , Se Hoon Lee 4 , Myung-Ju Ahn 4 , Keunchil Park 4 , Duk Hwan Kim 5 , Seunggwan Lee 6 , Woongyang Park 7 and Kyoung-Mee Kim 2 1 Center for Cancer Companion Diagnostics, The Innovative Cancer Medicine Institute, Samsung Medical Center, Seoul, Korea 2 Department of Pathology and Translational Genomics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea 3 Department of Pathology and Laboratory Medicine, Tulane University School of Medicine, New Orleans, Louisiana, USA 4 Department of Medicine, Division of Hematology-Oncology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea 5 Medical Translational Research Center, Samsung Biological Research Institute, Seoul, Korea 6 Department of Integrated Health and Environmental Science, College of Health Science, Korea University, Seoul, Korea 7 Samsung Genome Institute, Seoul, Korea 8 Present address: Department of Integrated Health and Environmental Science, College of Health Science, Korea University, Seoul, Korea * These authors contributed equally to this work Correspondence to: Kyoung-Mee Kim, email: kkmkys@skku.edu Keywords: cancer, DNA, next generation sequencing, therapy, target Received: February 24, 2017      Accepted: April 05, 2017      Published: April 18, 2017 ABSTRACT To generate accurate next-generation sequencing (NGS) data, the amount and quality of DNA extracted is critical. We analyzed 1564 tissue samples from patients with metastatic or recurrent solid tumor submitted for NGS according to their sample size, acquisition method, organ, and fixation to propose appropriate tissue requirements. Of the 1564 tissue samples, 481 (30.8%) consisted of fresh-frozen (FF) tissue, and 1,083 (69.2%) consisted of formalin-fixed paraffin-embedded (FFPE) tissue. We obtained successful NGS results in 95.9% of cases. Out of 481 FF biopsies, 262 tissue samples were from lung, and the mean fragment size was 2.4 mm. Compared to lung, GI tract tumor fragments showed a significantly lower DNA extraction failure rate (2.1 % versus 6.1%, p = 0.04). For FFPE biopsy samples, the size of biopsy tissue was similar regardless of tumor type with a mean of 0.8 × 0.3 cm, and the mean DNA yield per one unstained slide was 114 ng. We obtained highest amount of DNA from the colorectum (2353 ng) and the lowest amount from the hepatobiliary tract (760.3 ng) likely due to a relatively smaller biopsy size, extensive hemorrhage and necrosis, and lower tumor volume. On one unstained slide from FFPE operation specimens, the mean size of the specimen was 2.0 × 1.0 cm, and the mean DNA yield per one unstained slide was 1800 ng. In conclusions, we present our experiences on tissue requirements for appropriate NGS workflow: > 1 mm 2 for FF biopsy, > 5 unstained slides for FFPE biopsy, and > 1 unstained slide for FFPE operation specimens for successful test results in 95.9% of cases.