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A novel, error-corrected technique for the detection of cancer through blood samples has shown to be significantly more sensitive and accurate than previously existing methods. This advancement may prove valuable for monitoring the condition of patients post-treatment, as outlined in research conducted by investigators from Weill Cornell Medicine and the New York Genome Center. This method, which utilizes whole-genome sequencing of DNA, marks a significant move towards the feasibility of routine blood tests for early cancer screening.
The research, published on April 11 in Nature Methods, focuses on assessing the cancer detection capabilities of a new commercial sequencing platform developed by Ultima Genomics. The study highlights that this cost-effective platform allows for a deep level of coverage, a critical factor that enhances the quality of sequencing data, thereby enabling the detection of minuscule amounts of circulating tumor DNA. The integration of an error-correcting technique has further refined the precision of this method.
“We are transitioning into a new era where low-cost DNA sequencing is becoming a reality. This study leverages that potential by employing whole-genome sequencing techniques that were once deemed impractical,” stated Dr. Dan Landau, the senior author and a prominent figure in the Bibliowicz Family Professor of Medicine at Weill Cornell Medicine, with affiliations to the Englander Institute for Precision Medicine and the Sandra and Edward Meyer Cancer Center, along with being a core faculty member at the New York Genome Center.
The introduction of “liquid biopsy” technology—blood tests designed to detect and monitor cancer at an early stage—holds promise for transforming the landscape of cancer treatment. However, the task of accurately identifying the mutational signatures related to cancer from trace amounts of tumor DNA in blood has posed significant challenges. For nearly ten years, the Landau lab has focused on overcoming these hurdles using an approach based on whole-genome sequencing, as opposed to traditional targeted sequencing methods. In an earlier study, the team successfully detected advanced cases of melanoma and lung cancer in patient blood samples without requiring prior access to tumor sequencing data.
In this latest investigation, the researchers advanced their methodology by demonstrating how the affordability of a new sequencing platform facilitates extensive whole-genome sequencing that was once prohibitively expensive with older technologies. Using this platform, they identified tumor DNA in patient blood samples at concentrations as low as parts per million. All blood samples were collected from patients with obtained informed consent.
The team further enhanced the reliability of their detection method through an innovative error-correction technique, which capitalizes on the naturally occurring redundancies in two-stranded DNA. Their findings indicated that this combined approach yields remarkably low error rates, suggesting it could be applied to blood samples without requiring tumor access.
In collaboration with other research teams, the researchers showcased the high sensitivity and low error rates of their method by successfully detecting and evaluating minimal levels of cancer markers in blood samples from patients diagnosed with bladder cancer and melanoma.
“Our partnership enabled the evaluation of circulating tumor DNA from bladder cancer patients, allowing us to pinpoint unique mutational signatures that my lab has researched extensively,” commented Dr. Bishoy M. Faltas, Chief Research Officer at the Englander Institute for Precision Medicine and Associate Professor at Weill Cornell Medicine and an oncologist at NewYork-Presbyterian/Weill Cornell Medical Center. “Integrating these signatures into our analysis significantly bolstered the sensitivity of our detection of circulating tumor DNA.”
“For instance, we observed increases in circulating tumor DNA levels after treatment in patients whose cancers advanced or recurred, whereas we saw decreases in those whose cancers responded fully or partially,” explained Dr. Alexandre Cheng, the first author and a postdoctoral researcher in the Landau lab during the study.
“These findings pave the way for a future where cancer tracking and detection could be conducted solely through blood tests,” remarked Dr. Landau, who also practices as an oncologist at NewYork-Presbyterian/Weill Cornell Medical Center.
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