Robustness of a cancer profiling test using formalin-fixed paraffin embedded tumor specimens

Shin Ito; Ikuro Sato; Mai Mochizuki; Kazunori Yamaguchi; Keiichi Tamai; Takamichi Minato; Nobuhiro Tanuma; Hiroshi Shima; Jun Yasuda

doi:10.21873/anticanres.14891

Robustness of a cancer profiling test using formalin-fixed paraffin embedded tumor specimens

Shin Ito, Ikuro Sato, Mai Mochizuki, Kazunori Yamaguchi, Keiichi Tamai, Takamichi Minato, Nobuhiro Tanuma, Hiroshi Shima, Jun Yasuda

Research output: Contribution to journal › Article › peer-review

2 Citations (Scopus)

Abstract

Background/Aim: Cancer profiling tests using formalin-fixed paraffin-embedded (FFPE) specimens with various conditions have become an essential tool for cancer treatment. The robustness of these tests needs to be addressed. Materials and Methods: A cancer profiling test, NCC oncopanel, was tested with FFPE specimens from various tissues with different storage conditions and fixation lengths. Next generation sequencing was performed with Miseq and the data were assembled using the human reference genome hg19. Results: Duration of storage and fixation affected the mapping statistics. Prolonged storage increased outward read paring and longer fixation rates caused increased singletons and unmapped reads. Conclusion: Our results indicate that a cancer profiling test with target capturing method, NCC oncopanel, shows robustness for FFPE cancer specimens with various storage conditions.

Original language	English
Pages (from-to)	1341-1348
Number of pages	8
Journal	Anticancer research
Volume	41
Issue number	3
DOIs	https://doi.org/10.21873/anticanres.14891
Publication status	Published - 2021 Mar
Externally published	Yes

Keywords

Cancer profiling test
Formalin-fixed paraffin-embedded samples
Next generation sequencing

ASJC Scopus subject areas

Oncology
Cancer Research

UN SDGs

This output contributes to the following UN Sustainable Development Goals (SDGs)

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10.21873/anticanres.14891

Cite this

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title = "Robustness of a cancer profiling test using formalin-fixed paraffin embedded tumor specimens",

abstract = "Background/Aim: Cancer profiling tests using formalin-fixed paraffin-embedded (FFPE) specimens with various conditions have become an essential tool for cancer treatment. The robustness of these tests needs to be addressed. Materials and Methods: A cancer profiling test, NCC oncopanel, was tested with FFPE specimens from various tissues with different storage conditions and fixation lengths. Next generation sequencing was performed with Miseq and the data were assembled using the human reference genome hg19. Results: Duration of storage and fixation affected the mapping statistics. Prolonged storage increased outward read paring and longer fixation rates caused increased singletons and unmapped reads. Conclusion: Our results indicate that a cancer profiling test with target capturing method, NCC oncopanel, shows robustness for FFPE cancer specimens with various storage conditions.",

keywords = "Cancer profiling test, Formalin-fixed paraffin-embedded samples, Next generation sequencing",

author = "Shin Ito and Ikuro Sato and Mai Mochizuki and Kazunori Yamaguchi and Keiichi Tamai and Takamichi Minato and Nobuhiro Tanuma and Hiroshi Shima and Jun Yasuda",

note = "Funding Information: The Authors thank Ms. Mika Takeuchi and Ms. Miyuki Ueki for their assistance with the sample preparation. They also thank H. Nikki March, Ph.D., from Edanz Group (https://en-author-services. edanzgroup.com/ac) for editing a draft of this manuscript. This work was supported by JSPS KAKENHI with the following grant numbers: JP19H01036 (to N. Tanuma), JP17K07187 (to H. Shima), JP19K08430 (Tamai), JP18K09363 (Mochizuki), and JP17K07193 (to J. Yasuda). This work was also supported by Foundation for Promotion of Cancer Research in Japan (Tamai) and Takeda Medical Foundation (Tamai). Publisher Copyright: {\textcopyright} 2021 International Institute of Anticancer Research. All rights reserved.",

year = "2021",

month = mar,

doi = "10.21873/anticanres.14891",

language = "English",

volume = "41",

pages = "1341--1348",

journal = "Anticancer Research",

issn = "0250-7005",

publisher = "International Institute of Anticancer Research",

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T1 - Robustness of a cancer profiling test using formalin-fixed paraffin embedded tumor specimens

AU - Ito, Shin

AU - Sato, Ikuro

AU - Mochizuki, Mai

AU - Yamaguchi, Kazunori

AU - Tamai, Keiichi

AU - Minato, Takamichi

AU - Tanuma, Nobuhiro

AU - Shima, Hiroshi

AU - Yasuda, Jun

N1 - Funding Information: The Authors thank Ms. Mika Takeuchi and Ms. Miyuki Ueki for their assistance with the sample preparation. They also thank H. Nikki March, Ph.D., from Edanz Group (https://en-author-services. edanzgroup.com/ac) for editing a draft of this manuscript. This work was supported by JSPS KAKENHI with the following grant numbers: JP19H01036 (to N. Tanuma), JP17K07187 (to H. Shima), JP19K08430 (Tamai), JP18K09363 (Mochizuki), and JP17K07193 (to J. Yasuda). This work was also supported by Foundation for Promotion of Cancer Research in Japan (Tamai) and Takeda Medical Foundation (Tamai). Publisher Copyright: © 2021 International Institute of Anticancer Research. All rights reserved.

PY - 2021/3

Y1 - 2021/3

N2 - Background/Aim: Cancer profiling tests using formalin-fixed paraffin-embedded (FFPE) specimens with various conditions have become an essential tool for cancer treatment. The robustness of these tests needs to be addressed. Materials and Methods: A cancer profiling test, NCC oncopanel, was tested with FFPE specimens from various tissues with different storage conditions and fixation lengths. Next generation sequencing was performed with Miseq and the data were assembled using the human reference genome hg19. Results: Duration of storage and fixation affected the mapping statistics. Prolonged storage increased outward read paring and longer fixation rates caused increased singletons and unmapped reads. Conclusion: Our results indicate that a cancer profiling test with target capturing method, NCC oncopanel, shows robustness for FFPE cancer specimens with various storage conditions.

AB - Background/Aim: Cancer profiling tests using formalin-fixed paraffin-embedded (FFPE) specimens with various conditions have become an essential tool for cancer treatment. The robustness of these tests needs to be addressed. Materials and Methods: A cancer profiling test, NCC oncopanel, was tested with FFPE specimens from various tissues with different storage conditions and fixation lengths. Next generation sequencing was performed with Miseq and the data were assembled using the human reference genome hg19. Results: Duration of storage and fixation affected the mapping statistics. Prolonged storage increased outward read paring and longer fixation rates caused increased singletons and unmapped reads. Conclusion: Our results indicate that a cancer profiling test with target capturing method, NCC oncopanel, shows robustness for FFPE cancer specimens with various storage conditions.

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KW - Formalin-fixed paraffin-embedded samples

KW - Next generation sequencing

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Robustness of a cancer profiling test using formalin-fixed paraffin embedded tumor specimens

Abstract

Keywords

ASJC Scopus subject areas

UN SDGs

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