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Best practices for the extraction of genomic DNA from formalin‐fixed paraffin‐embedded tumor tissue for cancer genomic profiling tests
Author(s) -
Inoue Hirofumi,
Tomida Shuta,
Horiguchi Shigeru,
Kato Hironari,
Matsuoka Hiromi,
Sanehira Etsuko,
Matsuoka Masashi,
Yanai Hiroyuki,
Hirasawa Akira,
Toyooka Shinichi
Publication year - 2021
Publication title -
pathology international
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.73
H-Index - 74
eISSN - 1440-1827
pISSN - 1320-5463
DOI - 10.1111/pin.13086
Subject(s) - genomic dna , pancreatic cancer , pathology , dna extraction , medicine , cancer , dna , dna profiling , lung cancer , computational biology , biology , cancer research , gene , polymerase chain reaction , genetics
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.