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 language | English |
|---|---|
| Pages (from-to) | 42478-42486 |
| Number of pages | 9 |
| Journal | Oncotarget |
| Volume | 8 |
| Issue number | 26 |
| DOIs | |
| Publication status | Published - 2017 Jan 1 |
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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 journal › Article
}
TY - JOUR
T1 - Tissue recommendations for precision cancer therapy using next generation sequencing
T2 - A comprehensive single cancer center's experiences
AU - Cho, Minho
AU - Ahn, Soomin
AU - Hong, Mineui
AU - Bang, Heejin
AU - Van Vrancken, Michael
AU - Kim, Seungtae
AU - Lee, Jeeyun
AU - Park, Se Hoon
AU - Park, Joon Oh
AU - Park, Young Suk
AU - Lim, Ho Yeong
AU - Kang, Won Ki
AU - Sun, Jong Mu
AU - Lee, Se Hoon
AU - Ahn, Myung Ju
AU - Park, Keunchil
AU - Kim, Duk Hwan
AU - Lee, Seung Kwan
AU - Park, Woongyang
AU - Kim, Kyoung Mee
PY - 2017/1/1
Y1 - 2017/1/1
N2 - 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.
AB - 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.
KW - Cancer
KW - DNA
KW - Next generation sequencing
KW - Target
KW - Therapy
UR - http://www.scopus.com/inward/record.url?scp=85021305692&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=85021305692&partnerID=8YFLogxK
U2 - 10.18632/oncotarget.17199
DO - 10.18632/oncotarget.17199
M3 - Article
AN - SCOPUS:85021305692
VL - 8
SP - 42478
EP - 42486
JO - Oncotarget
JF - Oncotarget
SN - 1949-2553
IS - 26
ER -