Discoveries made using Bio-Rad’s Droplet Digital PCR (ddPCR) technology were presented by researchers at the American Association for Cancer Research (AACR) Annual Meeting in Philadelphia.
Since its introduction in 2012, the QX100TM Droplet Digital PCR system has been used in oncology research with an objective of tailoring cancer treatments on a tumour-by-tumour basis – by reading the genetic mutations, amplifications, and rearrangements that make each tumour unique.
Researchers are leveraging the ability of the ddPCR technology to detect a very small amount of variant DNA – specifically, oncogenic mutant DNA – quickly, inexpensively, and reliably.
From developing a ddPCR-based test that could help physicians guide personalised therapy to tracking tumour mutations that cause drug resistance, researchers from more than a dozen academic institutions and biotech companies highlighted the latest advancements using ddPCR technology in cancer research.
To date, more than 200 peer-reviewed studies have employed ddPCR systems, of which more than 20 involve their use in research using a cancer liquid biopsy.
Droplet Digital PCR is more sensitive at detetcing gene amplifications in tumors than next-generation sequencing clinical methods.
Gene amplifications of oncogenes are hallmarks of certain cancer types that are directly linked to FDA-approved treatments, but tests that can adequately detect these copy number alterations have been limited by DNA quantity and tumour purity and heterogeneity.
Furthermore, biopsies stored as formalin-fixed paraffin-embedded (FFPE) samples are notoriously difficult to work with and yield limited amounts of DNA as the samples can become easily degraded.
In a joint research venture, TOMA Biosciences in Foster City, CA, and the Intermountain Precision Genomics in Saint George, UT, found that a new ddPCR-based test using FFPE samples called the Amplinome Test is more than ten times more sensitive than next-generation sequencing (NGS) clinical methods in detecting gene amplifications of 12 genes commonly amplified in cancer.
The Amplinome Test detected gene amplifications that that the NGS method missed.
Patients can develop additional mutations within the tumour as a result of cancer treatment, leading to drug resistance.
Researchers from The Royal Marsden NHS Foundation Trust and The Institute of Cancer Research, London presented findings that used patient blood plasma with ddPCR methods to track the evolution of tumour resistance to treatment with anti-EGFR monoclonal antibodies.
For high sensitivity measurements of circulating cell-free DNA (cfDNA), scientists are given samples of plasma with extremely small amounts of tumour-derived DNA that they use to determine a patient’s cancer mutations.
Multiplexing allows the detection of multiple mutations in a single reaction. The University of Texas MD Anderson Cancer Center in Houston, TX presented research that demonstrated multiplex testing for KRAS mutations does not sacrifice accuracy, even with volumes of DNA as low as 16 ng.
It is also claimed that multiplexing saves time, money and is feasible in samples with small proportions of cancer-derived mutant DNA.
Dawne Shelton, Bio-Rad, spoke about the use of ddPCR technology in the tracking of cell-free tumour DNA for early detection of tumour DNA in blood as well as the monitoring of patient treatment and disease progression.
Shelton also highlighted how ddPCR technology has been used to detect copy number amplifications of genes commonly associated with cancer, such as MYC, HER2, and EGFR, and for the detection of KRAS mutations using a multiplex screening strategy.