Table 4.

Main QC measures for nucleic acids from FFPE samples ⁴ , ³¹ , ³²

QC measure	Target	Explanation
C t value (ΔC t , ΔΔC t )	DNA/RNA	It is a simple method requiring no special instrument to assess the quality of nucleic acids using C t (also called Cq) values obtained by real‐time PCR (DNA) or real‐time RT‐PCR (RNA). In the quality assessment method for DNA, the difference between C t values (ΔC t value) obtained from two amplicons of different lengths (e.g., a short‐chain amplicon of 50–100 bp and a long‐chain amplicon of 100–300 bp) is usually used. In the SCRUM‐Japan/GI‐SCREEN study, 30 ΔC t value calculation was performed for over 2000 FFPE samples, demonstrating its usefulness
DIN	DNA	DIN is a value on a 1–10 scale that is assigned based on the degradation of gDNA as measured by the Genomic DNA ScreenTape assay using the Agilent 2200/4200 TapeStation system to assess the quality of DNA from FFPE samples
Q‐value	DNA	The Q‐value is a measure of the quality of DNA developed by the National Cancer Center, 31 which is calculated by dividing the value measured using the real‐time PCR method (PCR‐active DNA quantity) by the value measured using the fluorescence method (dsDNA quantity). The success rate of sequencing (when an NCC Oncopanel v2 is used) is ~85% when the Q‐value is 0.2 or higher
DV200	RNA	DV200 is a measure of RNA quality that was developed by Illumina, and it calculates the proportion of RNA fragments equal to and longer than 200 nucleotides using Fragment Analyzer using AATI or an Agilent 2100 Bioanalyzer. The quality classification by DV200 is assigned as follows: >70% as high, 50%–70% as medium, 30%–50% as low, and <30% as too degraded. 32 FFPE samples that are too degraded at <30% are not recommended for use in library preparation for RNA sequencing

Abbreviations: Cq, quantification cycle; C _t , threshold cycle; DIN, DNA integrity number; FFPE, formalin‐fixed paraffin‐embedded; QC, quality control.