DNA Methylation Analysis for Early Detection of Various Cancers

When a cancer cell dies, its DNA is released into the blood. Once released this DNA is referred to as cell-free DNA (cfDNA). The cfDNA retains a DNA methylation pattern that corresponds to the cell it originated from. When a “normal” cell transforms into a cancer cell significant gene expression changes occur, and these alterations correlate to methylation pattern changes. It is therefore possible to differentiate between normal and cancer cells by detecting which sites within the DNA are methylated.

We recently spoke to Richard Brand, CFO and Dhruvajyoti Roy, Director of Technology from the Laboratory for Advanced Medicine (LAM) to learn more about how LAM is developing methylation-based tests for the early detection and intervention of cancer. 

Q: For our readers who may be less familiar with the Laboratory for Advanced Medicine (LAM), could you tell us a little more about the company? 

A: Laboratory for Advanced Medicine is a commercial-stage medical technology company focused on developing and commercializing new technologies, specifically for the early detection and intervention of cancer. With our streamlined product development, we can rapidly produce highly accurate, life-saving technologies that will alter the paradigm of cancer detection today.

Q: Your platform is based on cell-free DNA (cfDNA) methylation detection. Could you touch on the underlying science in more detail?

A: Alterations in DNA methylation play a key role in tumor initiation, and methylation markers are well established for detecting various cancer types at early stages of tumor development. Furthermore, cancer-specific DNA methylation patterns of cell-free DNA (cfDNA) isolated from blood samples is a non-invasive method to obtain representative epigenetic information from solid tumors, thus constituting a source for promising cancer detection biomarkers. We developed highly sensitive and specific methylation-based tests for the early detection of various cancer types.

Methylation is the next big cultural shift in cancer detection because large-scale epigenetic alterations potentially have a greater ability than somatic mutations to detect and classify cancers at early stages.  By analyzing methylation, which is an epigenetic process and is predictable in cancer and healthy patients, we are able to shift the industry from analyzing mutations, which, by nature, are harder to accurately predict. LAM has been analyzing methylation for years, while other companies have only just identified methylation analysis as the key for early cancer detection and differentiation.

Q: What is “IvyGene”? 

A: IvyGene is the product name for our services.

The IvyGene technology is the core foundation for our early cancer confirmation tests. We have two commercially available products, IvyGene CORE and IvyGene Liver, that confirm the presence of multiple cancers, as early as stage I, and provide measurable information about cancer. These tests are highly accurate in confirming cancer; IvyGene CORE with a sensitivity of 84% and specificity of 90% and the IvyGene Liver Test with a sensitivity of 80% and specificity of 86%. These are just the first of many products coming down LAM’s product pipeline.

You recently presented new data on the diagnosis of nasopharyngeal carcinoma during the American Society of Clinical Oncology (ASCO) annual meeting.

Q: Could you tell us more about nasopharyngeal carcinoma? 

A: Nasopharyngeal carcinoma (NPC) is a non-lymphomatous squamous cell carcinoma which is a distinct form of head and neck cancer that occurs in the epithelial lining of the nasopharynx. NPC is the third most prevalent malignancy among men in Southern China and the fourth most common cancer in Hong Kong, constituting one of the most prevalent malignancies among populations native to Southeast Asia, the Mediterranean Basin and the Arctic.

The nasopharynx is hard to examine, and traditional examination of NPC requires an invasive nasal endoscopy, which is not practical for early detection, screening and post-therapy disease monitoring. Therefore, early diagnosis of NPC from non-invasive liquid biopsy sample will improve the overall survival. In this context, the identification of cancer-specific DNA methylation patterns of cell-free DNA isolated from blood samples has great potential for early diagnosis and can improve the survival rate.

Q: What were the key study findings? 

A: The key study findings show an overall sensitivity of 97% and a combined specificity of 100%, demonstrating the high analytical potential of the IvyGene Test. The study was conducted using samples obtained from 168 subjects, including 59 subjects diagnosed with NPC (Stage I to IV), 14 subjects diagnosed with benign nasopharyngeal disease and 43 healthy subjects. From the 59 subjects diagnosed with NPC, a total of 57 subjects were correctly identified (sensitivity of 97%), with little difference between the sensitivity of detecting Stage I to Stage IV NPC (range 92% to 100%). Additionally, for subjects diagnosed with other cancers, a total of 86% of subjects were correctly identified as negative for NPC. Finally, all 43 samples drawn from healthy donors and all 14 samples drawn from subjects diagnosed with benign nasopharyngeal disease were correctly identified as negative for NPC (combined specificity of 100%).

Q: Could you touch on the implications of the findings and next steps? 

A: Due to minimal or non-specific local symptoms and the relative inaccessibility of the nasopharynx for a routine examination, most NPC patients have developed advanced disease at diagnosis, resulting in poor prognosis and low survival rate of these patients. Therefore, implementation of a non-invasive assay for early detection of NPC will greatly increase the chances of effective treatment and appropriate monitoring of the disease. Our test provides the hope to detect nasopharyngeal cancer at an early stage when the treatment options available to the physician are greater. The patients’ health outcomes can be improved at a lower cost.

We plan additional validation of a large cohort NPC population with the objective of making an accurate test commercially available to the at-risk population.

Richard Brand and Dhruvajyoti Roy were speaking to Laura Elizabeth Lansdowne, Science Writer for Technology Networks.