TY - JOUR
T1 - Best practices for the extraction of genomic DNA from formalin-fixed paraffin-embedded tumor tissue for cancer genomic profiling tests
AU - Inoue, Hirofumi
AU - Tomida, Shuta
AU - Horiguchi, Shigeru
AU - Kato, Hironari
AU - Matsuoka, Hiromi
AU - Sanehira, Etsuko
AU - Matsuoka, Masashi
AU - Yanai, Hiroyuki
AU - Hirasawa, Akira
AU - Toyooka, Shinichi
N1 - Funding Information:
This work was partially supported by JSPS KAKENHI (Grant‐in‐Aid for Scientific Research (B) for ST) grant number JP20H03771.
Publisher Copyright:
© 2021 Japanese Society of Pathology and John Wiley & Sons Australia, Ltd
PY - 2021/5
Y1 - 2021/5
N2 - Recently, two cancer genomic profiling tests have been approved in Japan and implemented in routine clinical practice: the FDA-approved FoundationOne CDx test, and the OncoGuide NCC Oncopanel test. The quality and quantity of DNA significantly affects the sequencing results; therefore, preparing a sufficient amount of high-quality DNA for clinical cancer genomic profiling tests is important. We examined the best practices for the extraction of cancer genomic DNA from formalin-fixed paraffin-embedded (FFPE) tumor tissues of pancreatic, lung and colon cancer specimens. We found that the quality of cancer genomic DNA extracted from 10-μm-thick FFPE samples improved significantly, compared with that from 4-μm-thick FFPE samples, suggesting that 10-μm-thick FFPE samples are preferable for clinical cancer genomic profiling tests. For convenience, we created a quick reference table for calculating the required number of FFPE slides.
AB - Recently, two cancer genomic profiling tests have been approved in Japan and implemented in routine clinical practice: the FDA-approved FoundationOne CDx test, and the OncoGuide NCC Oncopanel test. The quality and quantity of DNA significantly affects the sequencing results; therefore, preparing a sufficient amount of high-quality DNA for clinical cancer genomic profiling tests is important. We examined the best practices for the extraction of cancer genomic DNA from formalin-fixed paraffin-embedded (FFPE) tumor tissues of pancreatic, lung and colon cancer specimens. We found that the quality of cancer genomic DNA extracted from 10-μm-thick FFPE samples improved significantly, compared with that from 4-μm-thick FFPE samples, suggesting that 10-μm-thick FFPE samples are preferable for clinical cancer genomic profiling tests. For convenience, we created a quick reference table for calculating the required number of FFPE slides.
KW - cancer genomic profiling tests
KW - formalin-fixed paraffin-embedded (FFPE) tumor tissue
KW - genomic DNA extraction
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U2 - 10.1111/pin.13086
DO - 10.1111/pin.13086
M3 - Article
C2 - 33657250
AN - SCOPUS:85101900498
SN - 1320-5463
VL - 71
SP - 360
EP - 364
JO - Acta Pathologica Japonica
JF - Acta Pathologica Japonica
IS - 5
ER -
