Kousuke Watanabe, Shinji Kohsaka, Kenji Tatsuno, Aya Shinozaki-Ushiku, Hideaki Isago, Hidenori Kage, Tetsuo Ushiku, Hiroyuki Aburatani, Hiroyuki Mano, Katsutoshi Oda
BACKGROUND: The nucleic acid quality from formalin-fixed paraffin-embedded (FFPE) tumor vary among samples, resulting in substantial variability in the quality of comprehensive cancer genomic profiling tests. The objective of the study is to investigate how nucleic acid quality affects sequencing quality. We also examined the variations in nucleic acid quality among different hospitals or cancer types. METHODS: Three nucleic acid quality metrics (ddCq, Q-value, and DV200) and five sequencing quality metrics (on-target rate, mean depth, coverage uniformity, target exon coverage, and coverage of the housekeeping gene) were examined using 585 samples from the Todai OncoPanel, a dual DNA-RNA panel...
March 2024: Practical Laboratory Medicine