The DNA integrity number and concentration are useful parameters for successful comprehensive genomic profiling test for cancer using formalin-fixed paraffin embedded tissue

Emmy Yanagita, Hiroshi Yamada, Tetsuro Kobayashi, Eriko Aimono, Kohei Nakamura, Akira Hirasawa, Hiroshi Nishihara

Research output: Contribution to journalArticlepeer-review

Abstract

The acquisition of high-quality biospecimens and the appropriate handling of these materials are indispensable for successful clinical sequencing. We developed a cancer clinical sequencing system targeting 160 cancer genes: PleSSision-Rapid. Through the PleSSision-Rapid system, we have analyzed DNA quality evaluated by DIN (DNA integrity number) with 1329 formalin-fixed paraffin embedded (FFPE) samples including 477 prospectively collected tissues for genomic test (P) and 852 archival samples after routine pathological diagnosis (A1/A2). As a result, the samples with more than DIN 2.1 was 92.0% (439/477) in prospectively collected sample (P), while it was 85.6% (332/388) and 76.7% (356/464) in two types of archival samples (A1/A2). We performed the PleSSision-Rapid sequence using the samples with over DIN 2.1 and DNA concentration >10 ng/μL with which we were able to construct a DNA library, and the probability of sequence success was almost equivalent during all types of specimen processing, at 90.7% (398/439) in (P), 92.5% (307/332) in (A1) and 90.2% (321/356) in (A2), respectively. Our result indicated the clinical benefit to prepare the prospective collection of FFPE materials for indisputable clinical sequence, and that DIN ≥ 2.1 would be a solid parameter for sample preparation of comprehensive genomic profiling tests.

Original languageEnglish
Pages (from-to)198-206
Number of pages9
JournalPathology international
Volume73
Issue number5
DOIs
Publication statusPublished - 2023 May

Keywords

  • DNA concentration
  • DNA integrity number
  • DNA quality
  • clinical sequence
  • formalin-fixed paraffin embedded tissue
  • next generation sequencer

ASJC Scopus subject areas

  • Pathology and Forensic Medicine

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