Liver Surgery Department, Liver Cancer Institute, Zhongshan Hospital, Fudan University, Key Laboratory of Carcinogenesis and Cancer Invasion (Fudan University), Ministry of Education, Shanghai 200032, China.
BGI-Shenzhen, Shenzhen 518083, China; China National Genebank-Shenzhen, BGI-Shenzhen, Shenzhen 518083, China.
J Hepatol. 2017 Aug;67(2):293-301. doi: 10.1016/j.jhep.2017.03.005. Epub 2017 Mar 18.
BACKGROUND & AIMS: Identifying target genetic mutations in hepatocellular carcinoma (HCC) for therapy is made challenging by intratumoral heterogeneity. Circulating cell-free DNAs (cfDNA) may contain a more complete mutational spectrum compared to a single tumor sample. This study aimed to identify the most efficient strategy to identify all the mutations within heterogeneous HCCs.
Whole exome sequencing (WES) and targeted deep sequencing (TDS) were carried out in 32 multi-regional tumor samples from five patients. Matched preoperative cfDNAs were sequenced accordingly. Intratumoral heterogeneity was measured using the average percentage of non-ubiquitous mutations (present in parts of tumor regions). Profiling efficiencies of single tumor specimen and cfDNA were compared. The strategy with the highest performance was used to screen for actionable mutations.
Variable levels of heterogeneity with branched and parallel evolution patterns were observed. The heterogeneity decreased at higher sequencing depth of TDS compared to measurements by WES (28.1% vs. 34.9%, p<0.01) but remained unchanged when additional samples were analyzed. TDS of single tumor specimen identified an average of 70% of the total mutations from multi-regional tissues. Although genome profiling efficiency of cfDNA increased with sequencing depth, an average of 47.2% total mutations were identified using TDS, suggesting that tissue samples outperformed it. TDS of single tumor specimen in 66 patients and cfDNAs in four unresectable HCCs showed that 38.6% (26/66 and 1/4) of patients carried mutations that were potential therapeutic targets.
TDS of single tumor specimen could identify actionable mutations targets for therapy in HCC. cfDNA may serve as secondary alternative in profiling HCC genome.
Targeted deep sequencing of single tumor specimen is a more efficient method to identify mutations in hepatocellular carcinoma made from mixed subtypes compared to circulating cell-free DNA in blood. cfDNA may serve as secondary alternative in profiling HCC genome. Identifying mutations may help clinicians choose targeted therapy for better individual treatments.
由于肿瘤内异质性，鉴定肝细胞癌（HCC）的靶向基因突变用于治疗具有挑战性。与单个肿瘤样本相比，循环无细胞 DNA（cfDNA）可能包含更完整的突变谱。本研究旨在确定鉴定异质性 HCC 中所有突变的最有效策略。
对来自 5 名患者的 32 个多区域肿瘤样本进行了全外显子组测序（WES）和靶向深度测序（TDS）。相应地对术前 cfDNA 进行测序。使用非普遍突变（存在于肿瘤区域的某些部分）的平均百分比来测量肿瘤内异质性。比较了单个肿瘤标本和 cfDNA 的分析效率。使用性能最高的策略筛选可操作突变。
观察到具有分支和并行进化模式的可变水平异质性。与 WES 相比，TDS 的测序深度越高，异质性越低（28.1%比 34.9%，p<0.01），但当分析更多样本时，异质性保持不变。单个肿瘤标本的 TDS 平均可鉴定出多区域组织中总突变的 70%。尽管 cfDNA 的基因组分析效率随测序深度增加，但 TDS 平均可鉴定出 47.2%的总突变，表明组织样本优于它。对 66 例患者的单个肿瘤标本 TDS 和 4 例不可切除 HCC 的 cfDNA 分析表明，38.6%（26/66 和 1/4）的患者携带潜在治疗靶点的突变。
单个肿瘤标本的 TDS 可鉴定 HCC 中治疗的可操作突变靶标。cfDNA 可作为 HCC 基因组分析的次要替代方法。
与血液中的循环无细胞 DNA 相比，对单个肿瘤标本进行靶向深度测序是鉴定混合亚型肝细胞癌突变的更有效方法。cfDNA 可作为 HCC 基因组分析的次要替代方法。鉴定突变可能有助于临床医生选择靶向治疗，以获得更好的个体化治疗。
