Pancreatic ductal adenocarcinoma (PDAC) is one of the most lethal malignancies, largely because it is rarely caught early and diagnosed too late for curative treatment. The five-year survival rate remains around 12%, and currently tools-such as imaging and CA19-9 blood test-often miss early-stage cases. There is currently no recommended population-wide screening method for PDAC.

The new test model from Geneseeq analyzes cfDNA fragmentomics-specific patterns of DNA fragments shed into the bloodstream by cancer cells. By applying advanced machine learning algorithm to shallow whole-genome sequencing data, the test can detect subtle genomic and epigenetic changes associated with early-stage PDAC.

Key clinical results:

• Achieved 93.4% sensitivity and 95.2% specificity in the training cohort
• Reached 90.91-97.3% sensitivity and 92.8-94.5% specificity in multiple validation cohorts
• Demonstrated strong performance even in early-state cancers
• Outperformed CA19-9, especially in individuals with normal bilirubin levels

“Our cfDNA fragmentomics model offers a practical, highly accurate, and non-invasive option for detecting pancreatic cancer early,” said Dr. Hua Bao, VP of R&D at Geneseeq. “It could support earlier identification of at-risk individuals, allowing timely clinical follow-up and potentially improving outcomes.”

What makes this approach especially promising is its clinical feasibility. The test uses low-coverage sequencing (as little as 0.5×), making it cost-effective and suitable for broader population screening. The test also showed high stability, even with lower DNA sequencing data, and could be used to monitor high-risk patients or suspicious pancreatic lesions. The researchers also estimated that applying this test at the population level could reduce pancreatic cancer mortality by up to 27%, by catching more cancers at a treatable stage.

Further research is underway to refine the model’s application in screening programs and to validate its effectiveness in more diverse populations. Clinicians may soon have a powerful new tool to help combat one of the hardest-to-detect cancers.

About Geneseeq

Geneseeq Technology Inc. (Geneseeq) is a research-driven leader in precision oncology, utilizing cutting-edge next-generation sequencing (NGS) technologies to advance cancer care. The company provides comprehensive genomic profiling solutions for all tumor types, including pan-cancer and cancer-specific panels, alongside cutting-edge tools for minimal residual disease (MRD) monitoring and multi-cancer early detection (MCED). Geneseeq has reached key regulatory milestones to date, including CE-IVD certification for its solid tumor and hematologic cancer panels, and FDA Breakthrough Device Designation for its MCED test, CanScan®. The company has also received approval from the National Medical Products Administration (NMPA) for GeneseeqPrime, designed for tumor mutational burden (TMB) detection in lung cancer.

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Here are the key highlights from these studies:

• Performance of cfDNA fragmentonics-based early detection models in gastric cancer and breast cancer populations. The findings shed light on the potential of this approach in improving early diagnosis and subsequent treatment outcomes.
• Novel drug resistance mechanism in ROS1-rearranged non-small cell lung cancer patients. This research provides valuable insights into the development of targeted therapies and the management of treatment resistance in this subset of patients.
• Comprehensive analysis of homologous recombination repair gene reversion mutations. By examining a large pan-cancer population, this study sheds light on the prevalence, clinical implications, and potential therapeutic implications of these mutations.

Abstracts of the studies to be presented:

• Multi-dimensional cell-free DNA-based liquid biopsy for sensitive early detection of gastric cancer.
• Detecting Early Stage Breast Cancer Using Low-Depth Cell-Free DNA Fragmentomics: A Multi-Center Cohort Study.
• Mechanisms of Resistance to Tyrosine Kinase Inhibitor Treatments in ROS1 Fusion-Positive Non-Small Cell Lung Cancer Patients.
• A four-tier classification system of studying homologous recombination repair gene reversion mutations as a mechanism of resistance to PARP inhibitors and platinum-chemotherapy.

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This study enrolled 87 NSCLC patients who underwent curative surgical resections (23 patients experienced relapses during follow-up). A total of 163 plasma samples were collected at 7 days and 6 months post-surgery and were used for both whole-genome sequencing (WGS). The WGS-based cell-free DNA (cfDNA) fragment profile was used to develop regularized Cox regression models, and the models’ performance was evaluated using leave-one-out cross-validation.

The ultra-sensitive and affordable fragmentomic assay has shown promising results in detecting patients who are at high risk of recurrence. The fragmentomic model was able to detect high-risk patients at 7 days and 6 months post-surgery with an increased risk of 4.6 times and 8.3 times, outperforming the targeted sequencing-based circulating mutations. The overall sensitivity for detecting patients with recurrence reached 78.3% while using both fragmentomics and circulating mutation results from 7 days and 6 months postsurgical, which increased from the 43.5% sensitivity by using only the circulating mutations.

“The non-invasive liquid biopsy assay can effectively detect landmark MRD, which could aid in making informed decisions for post-surgery treatment.”, says Dr. Hua Bao, author and director of Geneseeq Research Institute.

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