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| Status |
Public on Aug 07, 2019 |
| Title |
Genome-wide Mapping of 5-Hydroxymethylcytosines in Circulating Cell-free DNA as a Non-invasive Approach for Early Detection of Hepatocellular Carcinoma |
| Organism |
Homo sapiens |
| Experiment type |
Methylation profiling by high throughput sequencing
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| Summary |
Background: The lack of highly sensitive and specific diagnostic biomarkers is a major contributor to the poor outcomes of patients with hepatocellular carcinoma (HCC). We sought to develop a non-invasive diagnostic approach using circulating cell-free DNA (cfDNA) for the early detection of HCC.
Methods: Applying the 5hmC-Seal technique, we obtained genome-wide 5-hydroxymethylcytosines (5hmC) in cfDNA samples from 2,554 Chinese subjects: 1,204 HCC patients, 392 patients with chronic hepatitis B virus infection (CHB) or liver cirrhosis (LC), and 958 healthy individuals and patients with benign liver lesions. A diagnostic model for early HCC was developed through case-control analyses using the elastic net regularization for feature selection.
Results: The 5hmC-Seal data from HCC patients showed a genome-wide distribution enriched with liver-derived enhancer marks. We developed a 32-gene diagnostic model that accurately distinguished early HCC (stage 0/A) based on the Barcelona Clinic Liver Cancer (BCLC) staging system from non-HCC (validation set: AUC = 88.4%; 95% CI, 85.8-91.1%), showing superior performance over α-fetoprotein (AFP). Besides detecting patients with early stage or small tumors (e.g., ≤ 2.0 cm) from non-HCC, the 5hmC model showed high capacity for distinguishing early HCC from high risk subjects with CHB or LC history (validation set: AUC = 84.6%; 95% CI, 80.6-88.7%), also significantly outperforming AFP. Furthermore, the 5hmC diagnostic model appeared to be independent from potential confounders (e.g., smoking/alcohol intake history).
Conclusions: We have developed and validated a non-invasive approach with clinical application potential for the early detection of HCC that are still surgically resectable in high risk individuals.
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| Overall design |
Applying the 5hmC-Seal technique, we obtained genome-wide 5-hydroxymethylcytosines (5hmC) in cfDNA samples from 2,554 Chinese subjects: 1,204 HCC patients, 392 patients with chronic hepatitis B virus infection (CHB) or liver cirrhosis (LC), and 958 healthy individuals and patients with benign liver lesions. A diagnostic model for early HCC was developed through case-control analyses using the elastic net regularization for feature selection.
UPDATE: [06-05-2023] The submitter reports that there is a potential sample mixup leading to inaccuracies in the "diagnosis" and "BCLC stage" characteristics. Therefore, the "diagnosis" and "BCLC stage" characteritics have been removed from the Sample records. The submitter declares that they are currently in the process of rectifying and updating the clinical information.
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| Contributor(s) |
Cai J, Chen L, Zhang Z, Zhang X, Lu X, Liu W, Shi G, Yang G, Gao P, Yang Y, Ke A, Xiao L, Dong R, Zhu Y, Yang X, Wang J, Zhu T, Yang D, Huang X, Sui C, Qiu S, Shen F, Sun H, Zhou W, Zhou J, Nie J, Chang Z, Stroup EK, Zhang X, Brian CC, Wan Yee L, He C, Wang H, Zhang W, Fan J |
| Citation(s) |
31358576 |
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| Submission date |
Apr 04, 2018 |
| Last update date |
Jun 05, 2023 |
| Contact name |
Zhou Zhang |
| E-mail(s) |
zhou.zhang@northwestern.edu
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| Organization name |
Northwestern University
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| Department |
Preventive Medicine
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| Street address |
680 North Lake Shore Drive, Suite 1400
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| City |
Chicago |
| State/province |
IL |
| ZIP/Postal code |
60611 |
| Country |
USA |
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| Platforms (1) |
| GPL18573 |
Illumina NextSeq 500 (Homo sapiens) |
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| Samples (2606)
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| Relations |
| BioProject |
PRJNA448890 |
| SRA |
SRP137706 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE112679_RAW.tar |
264.9 Mb |
(http)(custom) |
TAR (of TXT) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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