Illumina, Inc., San Diego, The University of Texas MD Anderson Cancer Center, Houston, USA.
Illumina, Inc., San Diego, The University of Texas MD Anderson Cancer Center, Houston, USA.
Ann Oncol. 2018 Jun 1;29(6):1445-1453. doi: 10.1093/annonc/mdy119.
Targeted methylation sequencing of plasma cell-free DNA (cfDNA) has a potential to expand liquid biopsies to patients with tumors without detectable oncogenic alterations, which can be potentially useful in early diagnosis.
We developed a comprehensive methylation sequencing assay targeting 9223 CpG sites consistently hypermethylated according to The Cancer Genome Atlas. Next, we carried out a clinical validation of our method using plasma cfDNA samples from 78 patients with advanced colorectal cancer, non-small-cell lung cancer (NSCLC), breast cancer or melanoma and compared results with patients' outcomes.
Median methylation scores in plasma cfDNA samples from patients on therapy were lower than from patients off therapy (4.74 versus 85.29; P = 0.001). Of 68 plasma samples from patients off therapy, methylation scores detected the presence of cancer in 57 (83.8%), and methylation-based signatures accurately classified the underlying cancer type in 45 (78.9%) of these. Methylation scores were most accurate in detecting colorectal cancer (96.3%), followed by breast cancer (91.7%), melanoma (81.8%) and NSCLC (61.1%), and most accurate in classifying the underlying cancer type in colorectal cancer (88.5%), followed by NSCLC (81.8%), breast cancer (72.7%) and melanoma (55.6%). Low methylation scores versus high were associated with longer survival (10.4 versus 4.4 months, P < 0.001) and longer time-to-treatment failure (2.8 versus 1.6 months, P = 0.016).
Comprehensive targeted methylation sequencing of 9223 CpG sites in plasma cfDNA from patients with common advanced cancers detects the presence of cancer and underlying cancer type with high accuracy. Methylation scores in plasma cfDNA correspond with treatment outcomes.
靶向检测血浆游离 DNA（cfDNA）的甲基化具有扩大液体活检范围的潜力，可应用于检测无明显致癌突变的肿瘤患者，有助于早期诊断。
我们开发了一种全面的甲基化测序分析方法，靶向 9223 个 CpG 位点，这些位点根据癌症基因组图谱（The Cancer Genome Atlas）数据在所有肿瘤中持续呈高甲基化状态。然后，我们使用 78 例晚期结直肠癌、非小细胞肺癌（NSCLC）、乳腺癌或黑色素瘤患者的血浆 cfDNA 样本对该方法进行了临床验证，并将结果与患者的治疗效果进行了比较。
接受治疗的患者血浆 cfDNA 样本的中位甲基化评分低于未接受治疗的患者（4.74 比 85.29；P=0.001）。在 68 例未接受治疗的患者的血浆样本中，甲基化评分在 57 例（83.8%）中检测到癌症的存在，在这 57 例患者中，基于甲基化的特征准确地对潜在的癌症类型进行了分类（45 例，78.9%）。甲基化评分在检测结直肠癌方面最准确（96.3%），其次是乳腺癌（91.7%）、黑色素瘤（81.8%）和 NSCLC（61.1%），在结直肠癌中对潜在癌症类型的分类最准确（88.5%），其次是 NSCLC（81.8%）、乳腺癌（72.7%）和黑色素瘤（55.6%）。低甲基化评分与高甲基化评分相比，患者的总生存期更长（10.4 个月比 4.4 个月，P<0.001），治疗失败时间更长（2.8 个月比 1.6 个月，P=0.016）。
对常见晚期癌症患者的血浆游离 DNA 进行 9223 个 CpG 位点的综合靶向甲基化测序，可以准确检测癌症的存在和潜在的癌症类型。血浆游离 DNA 的甲基化评分与治疗结果相关。
