在一项用于检测结直肠癌和胰腺腺癌的商业游离DNA下一代测序检测中，确定用于检测激活型、、和突变的最佳突变等位基因频率。
Identification of an optimal mutant allele frequency to detect activating , , and mutations in a commercial cell-free DNA next-generation sequencing assay in colorectal and pancreatic adenocarcinomas.
作者信息
Caughey Bennett A, Umemoto Kumiko, Green Michelle F, Ikeda Masafumi, Lowe Melissa E, Ueno Makoto, Niedzwiecki Donna, Taniguchi Hiroya, Walden Daniel J, Komatsu Yoshito, D'Anna Rachel, Esaki Taito, Denda Tadamichi, Datto Michael B, Bando Hideaki, Bekaii-Saab Tanios, Yoshino Takayuki, Strickler John H, Nakamura Yoshiaki
机构信息
Division of Medical Oncology, Department of Medicine, Duke University Medical Center, Durham, NC, USA.
Department of Clinical Oncology, St. Marianna University School of Medicine, Kawasaki, Japan.
出版信息
J Gastrointest Oncol. 2023 Oct 31;14(5):2083-2096. doi: 10.21037/jgo-23-114. Epub 2023 Sep 19.
BACKGROUND
Evaluation for activating mutations in , , and in colorectal cancer (CRC) and in in pancreatic ductal adenocarcinoma (PDAC) is essential for clinical care. Plasma cell-free DNA (cfDNA) next-generation sequencing (NGS) allows convenient assessment of a tumor's molecular profile, however low tumor DNA shedding limits sensitivity. We investigated mutant allele frequency (MAF) of other oncogenic dominant genes to identify a threshold for accurate detection of and mutations in cfDNA.
METHODS
Molecular and clinical data were obtained from the Duke Molecular Registry of Tumors and the SCRUM-Japan GOZILA study. Patients with CRC or PDAC and a , , or activating single nucleotide variant (SNV) present on tissue NGS and with available cfDNA assays were included. Recursive partitioning and Wilcoxon-rank statistics methods identified potential cut-points for discriminative MAF values.
RESULTS
One hundred and thirty-five CRC and 30 PDAC cases with 198 total cfDNA assays met criteria. Greatest non- dominant gene MAF of 0.34% provided maximum discrimination for predicting SNV detection. Sensitivity for SNVs increased with dominant gene MAF, with MAF ≥1% predicting sensitivity >98%, MAF between 0.34 and 1% predicting sensitivity of 84.0%, and MAF £0.34% predicting sensitivity of 50%. For 43 cfDNA assays that did not detect SNVs, 18 assays detected 34 other oncogenic variants, of which 80.6% were not also detected on tissue.
CONCLUSIONS
Non- dominant oncogenic mutation MAF ≥1% on cfDNA NGS predicts high sensitivity to detect oncogenic SNVs in CRC and PDAC. MAF £0.34% indicates an assay may not reliably detect SNVs, despite detection on tissue testing. Most variants from assays that did not detect had MAF <1% and were not detected on tissue, suggesting potential confounding. These data suggest a practical approach to determining cfDNA assay adequacy, with implications for guiding clinical decisions in CRC and PDAC.
背景
评估结直肠癌（CRC）中 、 和 的激活突变以及胰腺导管腺癌（PDAC）中 的激活突变对临床治疗至关重要。血浆游离DNA（cfDNA）下一代测序（NGS）可方便地评估肿瘤的分子特征，然而肿瘤DNA低脱落率限制了检测灵敏度。我们研究了其他致癌显性基因的突变等位基因频率（MAF），以确定准确检测cfDNA中 和 突变的阈值。
方法
从杜克肿瘤分子登记处和日本SCRUM - GOZILA研究中获取分子和临床数据。纳入在组织NGS上存在 、 或 激活单核苷酸变异（SNV）且有可用cfDNA检测的CRC或PDAC患者。递归划分和Wilcoxon秩统计方法确定了判别MAF值的潜在切点。
结果
135例CRC和30例PDAC病例共进行了198次cfDNA检测，符合标准。最大非 显性基因MAF为0.34%时，对预测 SNV检测具有最大判别力。 SNV的检测灵敏度随显性基因MAF增加，MAF≥1%时预测灵敏度>98%，MAF在0.34%至1%之间时预测灵敏度为84.0%，MAF≤0.34%时预测灵敏度为50%。在43次未检测到 SNV的cfDNA检测中，18次检测到34个其他致癌变异，其中80.6%在组织检测中也未检测到。
结论
cfDNA NGS上非 显性致癌突变MAF≥1%预测在CRC和PDAC中检测 致癌SNV具有高灵敏度。MAF≤0.34%表明检测可能无法可靠检测到 SNV，尽管在组织检测中检测到。未检测到 的检测中的大多数变异MAF<1%且在组织中未检测到，提示可能存在混淆。这些数据提出了一种确定cfDNA检测是否充分的实用方法，对指导CRC和PDAC的临床决策具有重要意义。
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