Detailed Information

Cited 0 time in webofscience Cited 0 time in scopus
Metadata Downloads

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

Authors
Cho, MinhoAhn, SoominHong, MineuiBang, HeejinVan Vrancken, MichaelKim, SeungtaeLee, JeeyunPark, Se HoonPark, Joon OhPark, Young SukLim, Ho YeongKang, Won KiSun, Jong-MuLee, Se HoonAhn, Myung-JuPark, KeunchilKim, Duk HwanLee, SeunggwanPark, WoongyangKim, Kyoung-Mee
Issue Date
27-6월-2017
Publisher
IMPACT JOURNALS LLC
Keywords
cancer; DNA; next generation sequencing; therapy; target
Citation
ONCOTARGET, v.8, no.26, pp.42478 - 42486
Indexed
SCIE
SCOPUS
Journal Title
ONCOTARGET
Volume
8
Number
26
Start Page
42478
End Page
42486
URI
https://scholar.korea.ac.kr/handle/2021.sw.korea/83088
DOI
10.18632/oncotarget.17199
ISSN
1949-2553
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 x 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 x 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.
Files in This Item
There are no files associated with this item.
Appears in
Collections
College of Health Sciences > School of Health and Environmental Science > 1. Journal Articles

qrcode

Items in ScholarWorks are protected by copyright, with all rights reserved, unless otherwise indicated.

Altmetrics

Total Views & Downloads

BROWSE