Researchers develop ’more cost-effective method’ to detect early-stage cancers
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A collaboration of researchers has developed a testing method for methylome sequencing of cell-free DNA that accurately detects and locates certain types of early-stage cancer, study results published in Nature Communications showed.
The newly developed screening procedure involves a novel methylome assay to sequence cell-free DNA in patients’ blood plus a computational model to gather information from DNA sequencing to assist researchers in early detection and diagnosis of tumors.
The process offers an approximate 12-fold cost savings over currently available DNA sequencing, the investigators noted.
Background
Current hurdles to using cell-free DNA for detection of early-stage tumors include typically low concentrations of tumor fragments in patients' blood and the molecular diversity of solid tumors, according to Xianghong “Jasmine” Zhou, PhD, professor of pathology and laboratory medicine at University of California, Los Angeles.
“Our aim was to develop a more cost-effective method that can capture more tumor fragments,” she told Healio. “So, we decided that we must cast a wider net to detect these tumor fragments. The panel we use to diagnose cancer is getting larger because to detect early-stage cancer requires detection of a large number of heterogeneous cancer biomarkers that may vary from patient to patient.”
Methodology
Zhou and colleagues developed an experimental assay, referred to as cell-free DNA methylome sequencing. They tested the assay on 408 samples, including 217 patients with colon (n = 49), liver (n = 30), lung (n = 106) or stomach cancer (n = 32) and 191 control patients.
They then evaluated the samples using a computational method to extract four types of cell-free DNA methylation features and perform ensemble machine learning for detecting and locating cancer.
Key findings
At a specificity of 97.9% (one false-positive), results showed the model had:
74.5% (95% CI, 54.1-87.7) sensitivity for detecting stage I and stage II disease (area under the receiver operating characteristic curve = 0.964; 95% CI, 0.897-0.999);
80.7% sensitivity for detection of all-stage cancer;
89.1% accuracy for locating tissue-of-origin for all-stage cancer; and
85% accuracy for locating tissue-of-origin for early-stage cancer.
Clinical implications
“We have developed a cost-effective method for methylome sequencing of cell-free DNA with high accuracy for early detection of cancer,” Zhou told Healio. “We are storing all the information we gather on our patients, so as our sample size increases, it may help us detect new biomarkers that can help detect and diagnose disease in the future.”
The researchers are working to secure funding and confirm these findings by conducting a large national clinical trial they hope will lead to filing for regulatory approval of their diagnostic method, Zhou said.
For more information :
Xianghong “Jasmine” Zhou, PhD, can be reached at xjzhou@mednet.ucla.edu.
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