Department of Pathology and Molecular Diagnostics, Aichi Cancer Center Hospital, Aichi, Japan.
Division of Molecular Therapeutics, Aichi Cancer Center Research Institute, Aichi, Japan.
Am J Clin Pathol. 2023 Sep 1;160(3):261-267. doi: 10.1093/ajcp/aqad046.
DNA integrity number (DIN) is a metric for assessing DNA degradation, calculated based on electrophoresis using the Agilent TapeStation System. The utility of DIN as a diagnostic indicator of sufficient DNA quality in clinical next-generation sequencing (NGS) has not been well described.
We evaluated the DINs of 166 tumor formalin-fixed, paraffin-embedded (FFPE) tissue samples submitted for 124-gene panel sequencing. We also investigated a new metric on the electropherogram that could improve the predictive accuracy of the DIN.
A DIN cutoff of 2.5 discriminated samples with successful analysis (n = 143) from samples with failed analysis (n = 23), with a sensitivity of 0.84 and a specificity of 0.78 (area under the curve [AUC] = 0.88). The DIN was positively correlated with the mean coverage (r = 0.72, P < .0001) but could not discriminate success from failure when the DIN was below 2.5 (negative predictive value, 0.44). We introduced a new metric, the peak/base ratio, that distinguished success from failure with higher accuracy than the DIN (cutoff = 1.6; sensitivity = 0.98, specificity = 0.83, and AUC =0.96).
To predict successful NGS, the DNA quality of FFPE tissue can be easily and reliably assessed using the DIN and peak/base ratio.
DNA 完整性数量（DIN）是一种评估 DNA 降解的指标，通过使用安捷伦 TapeStation 系统进行电泳计算得出。DIN 作为临床下一代测序（NGS）中足够 DNA 质量的诊断指标的实用性尚未得到很好的描述。
我们评估了 166 个福尔马林固定、石蜡包埋（FFPE）组织样本的 DIN，这些样本提交用于 124 基因面板测序。我们还研究了电泳图谱上的一个新指标，该指标可以提高 DIN 的预测准确性。
DIN 截断值为 2.5 可区分成功分析（n=143）和失败分析（n=23）的样本，敏感性为 0.84，特异性为 0.78（曲线下面积 [AUC] = 0.88）。DIN 与平均覆盖率呈正相关（r=0.72，P<.0001），但当 DIN 低于 2.5 时，无法区分成功与失败（阴性预测值，0.44）。我们引入了一个新的指标，峰/基底比，其比 DIN 具有更高的准确性来区分成功与失败（截断值=1.6；敏感性=0.98，特异性=0.83，AUC=0.96）。
为了预测成功的 NGS，可以使用 DIN 和峰/基底比轻松可靠地评估 FFPE 组织的 DNA 质量。
