Research Papers:
Tissue recommendations for precision cancer therapy using next generation sequencing: a comprehensive single cancer center’s experiences
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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: [email protected]
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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