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, Seung Kwan Lee, Woongyang Park, Kyoung Mee Kim

Research output: Contribution to journalArticle

8 Citations (Scopus)

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.

Original languageEnglish
Pages (from-to)42478-42486
Number of pages9
JournalOncotarget
Volume8
Issue number26
DOIs
Publication statusPublished - 2017 Jan 1

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Paraffin
Formaldehyde
Biopsy
Neoplasms
DNA
Therapeutics
Sample Size
Lung
Workflow
Tumor Burden
Gastrointestinal Tract
Necrosis
Hemorrhage

Keywords

  • Cancer
  • DNA
  • Next generation sequencing
  • Target
  • Therapy

ASJC Scopus subject areas

  • Oncology

Cite this

Tissue recommendations for precision cancer therapy using next generation sequencing : A comprehensive single cancer center's experiences. / Cho, Minho; Ahn, Soomin; Hong, Mineui; Bang, Heejin; Van Vrancken, Michael; Kim, Seungtae; Lee, Jeeyun; Park, Se Hoon; Park, Joon Oh; Park, Young Suk; Lim, Ho Yeong; Kang, Won Ki; Sun, Jong Mu; Lee, Se Hoon; Ahn, Myung Ju; Park, Keunchil; Kim, Duk Hwan; Lee, Seung Kwan; Park, Woongyang; Kim, Kyoung Mee.

In: Oncotarget, Vol. 8, No. 26, 01.01.2017, p. 42478-42486.

Research output: Contribution to journalArticle

Cho, M, Ahn, S, Hong, M, Bang, H, Van Vrancken, M, Kim, S, Lee, J, Park, SH, Park, JO, Park, YS, Lim, HY, Kang, WK, Sun, JM, Lee, SH, Ahn, MJ, Park, K, Kim, DH, Lee, SK, Park, W & Kim, KM 2017, 'Tissue recommendations for precision cancer therapy using next generation sequencing: A comprehensive single cancer center's experiences', Oncotarget, vol. 8, no. 26, pp. 42478-42486. https://doi.org/10.18632/oncotarget.17199
Cho, Minho ; Ahn, Soomin ; Hong, Mineui ; Bang, Heejin ; Van Vrancken, Michael ; Kim, Seungtae ; Lee, Jeeyun ; Park, Se Hoon ; Park, Joon Oh ; Park, Young Suk ; Lim, Ho Yeong ; Kang, Won Ki ; Sun, Jong Mu ; Lee, Se Hoon ; Ahn, Myung Ju ; Park, Keunchil ; Kim, Duk Hwan ; Lee, Seung Kwan ; Park, Woongyang ; Kim, Kyoung Mee. / Tissue recommendations for precision cancer therapy using next generation sequencing : A comprehensive single cancer center's experiences. In: Oncotarget. 2017 ; Vol. 8, No. 26. pp. 42478-42486.
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