PDF(Pubmed)
Abstract：
Malignant melanoma (MM) is known for its abundance of genetic alterations and a tendency for rapid metastasizing. Identification of novel plasma biomarkers may enhance non-invasive diagnostics and disease monitoring. Initially, we examined copy number variations (CNV) in CDK genes (CDKN2A, CDKN2B, CDK4) using MLPA (gDNA) and ddPCR (ctDNA) analysis. Subsequently, low-coverage whole genome sequencing (lcWGS) was used to identify the most common CNV in plasma samples, followed by ddPCR verification of chosen biomarkers. CNV alterations in CDK genes were identified in 33.3% of FFPE samples (Clark IV, V only). Detection of the same genes in MM plasma showed no significance, neither compared to healthy plasmas nor between pre- versus post-surgery plasma. Sequencing data showed the most common CNV occurring in 6q27, 4p16.1, 10p15.3, 10q22.3, 13q34, 18q23, 20q11.21-q13.12 and 22q13.33. CNV in four chosen genes (KIF25, E2F1, DIP2C and TFG) were verified by ddPCR using 2 models of interpretation. Model 1 was concordant with lcWGS results in 54% of samples, for model 2 it was 46%. Although CDK genes have not been proven to be suitable CNV liquid biopsy biomarkers, lcWGS defined the most frequently affected chromosomal regions by CNV. Among chosen genes, DIP2C demonstrated a potential for further analysis.
摘要：
恶性黑色素瘤（MM）以其丰富的遗传改变和快速转移的趋势而闻名。新型血浆生物标志物的鉴定可以增强非侵入性诊断和疾病监测。最初，我们检查了CDK基因中的拷贝数变异(CNV)(CDKN2A，CDKN2B,CDK4)使用MLPA(gDNA)和ddPCR(ctDNA)分析。随后，低覆盖率全基因组测序（lcWGS）用于鉴定血浆样品中最常见的CNV，然后对所选的生物标志物进行ddPCR验证。在33.3%的FFPE样品中发现CDK基因的CNV改变(ClarkIV，仅限V）。在MM血浆中检测到相同的基因没有显著性,既不与健康血浆相比，也不与手术前血浆相比。测序数据显示最常见的CNV发生在6q27、4p16.1、10p15.3、10q22.3、13q34、18q23、20q11.21-q13.12和22q13.33。使用2个解释模型通过ddPCR验证四个选择的基因(KIF25、E2F1、DIP2C和TFG)中的CNV。在54%的样本中，模型1与lcWGS结果一致，对于模型2，它是46%。尽管CDK基因尚未被证明是合适的CNV液体活检生物标志物，lcWGS定义了受CNV影响最频繁的染色体区域。在选择的基因中，DIP2C显示出进一步分析的潜力。
