Oncotarget

Research Papers:

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

Minho Cho, Soomin Ahn, Mineui Hong, Heejin Bang, Michael Van Vrancken, Seungtae Kim, Jeeyun Lee, Se Hoon Park, Joon Oh Park, Young Suk Park, Ho Yeong Lim, Won Ki Kang, Jong-Mu Sun, Se Hoon Lee, Myung-Ju Ahn, Keunchil Park, Duk Hwan Kim, Seunggwan Lee, Woongyang Park and Kyoung-Mee Kim _

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Oncotarget. 2017; 8:42478-42486. https://doi.org/10.18632/oncotarget.17199

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Abstract

Minho Cho1,8,*, Soomin Ahn2,*, Mineui Hong1,2, Heejin Bang1,2, Michael Van Vrancken3, Seungtae Kim4, Jeeyun Lee4, Se Hoon Park4, Joon Oh Park4, Young Suk Park4, Ho Yeong Lim4, Won Ki Kang4, Jong-Mu Sun4, Se Hoon Lee4, Myung-Ju Ahn4, Keunchil Park4, Duk Hwan Kim5, Seunggwan Lee6, Woongyang Park7 and Kyoung-Mee Kim2

1Center for Cancer Companion Diagnostics, The Innovative Cancer Medicine Institute, Samsung Medical Center, Seoul, Korea

2Department of Pathology and Translational Genomics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea

3Department of Pathology and Laboratory Medicine, Tulane University School of Medicine, New Orleans, Louisiana, USA

4Department of Medicine, Division of Hematology-Oncology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea

5Medical Translational Research Center, Samsung Biological Research Institute, Seoul, Korea

6Department of Integrated Health and Environmental Science, College of Health Science, Korea University, Seoul, Korea

7Samsung Genome Institute, Seoul, Korea

8Present 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 mm2 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.


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