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Researchers Demonstrate Utility of Droplet Digital PCR for Informing Treatment Decisions at AMP 2019 Annual Meeting and Expo

Many of the studies used liquid biopsy based on ddPCR technology to predict treatment response or track disease progression

by Bio-Rad Laboratories
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Researchers Demonstrate Utility of Droplet Digital PCR for Informing Treatment Decisions at AMP 2019 Annual Meeting and ExpoJonathan Tsai, MD, PhD, of Brigham and Women's Hospital, and Michelle Freed, Zaina Iemeir, Nathan Sepulveda, and Prasanthi Bhagavatula of Bio-Rad Laboratories, presented research using Droplet Digital PCR (ddPCR) at the AMP 2019 Annual Meeting and Expo in Baltimore.Credit: Bio-Rad LaboratoriesHERCULES, CA — Scientists presented more than 25 abstracts demonstrating how Droplet Digital PCR (ddPCR) guides treatment decisions at the Association of Molecular Pathology (AMP) 2019 Annual Meeting and Expo in Baltimore on November 7–9. The studies presented at the conference spanned the research to clinical sectors.

Many of the studies used liquid biopsy based on ddPCR technology to predict treatment response or track disease progression. Other ddPCR presentations showed the technology’s ability to inform clinicians of a patient’s eligibility for a specific treatment. Some of these ddPCR assays are already being used in the clinical setting, such as the BCR-ABL %IS Kit, which received FDA clearance in February 2019 to monitor treatment response. Research presented at AMP evaluated the clinical utility of these tests compared to other existing tests.

Study 1: Researchers validate use of ddPCR technology when performing liquid biopsy to predict treatment response in patients with progressive metastatic melanoma

Jonathan Tsai, MD, PhD, and his colleagues at the Center for Advanced Molecular Diagnostics at the Brigham and Women's Hospital in Boston wanted to see whether ddPCR technology could detect BRAF V600 mutations, a mutation that can cause melanomas, in plasma ctDNA. In their validation study, ddPCR technology was able to detect these mutations in more than half of patients with metastatic melanoma and in 100 percent of patients with advanced metastasis. It was sensitive down to a fractional abundance of about 0.2–0.5 percent and did not identify any false positives.

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The researchers at the Center for Advanced Molecular Diagnostics at the Brigham and Women's Hospital as well as the Dana Farber Cancer Institute are currently determining the ddPCR Assay’s limit of detection. The data can be useful to laboratories seeking to identify patient cohorts for ctDNA assay validation, and clinicians are interested in the data for understanding when ctDNA testing is most useful.

Study 2: Novel microsatellite instability ddPCR Assay demonstrates high sensitivity and exemplary analytical performance

Michelle Freed and Zaina Iemeir of Bio-Rad presented research-use-only data that support a novel ddPCR Assay to test for tumor microsatellite instability (MSI), a key factor in understanding a patient’s prognosis and the therapeutic options for patients with colorectal cancer. Current clinical methods to assess MSI status tend to have low analytical sensitivity and are invasive, requiring both tumor and normal tissue samples. But Freed and Iemeir’s work suggests their new test has high sensitivity and does not require a matched normal tissue sample for analysis.

Using contrived samples, Freed, Iemeir, and colleagues found that the Bio-Rad ddPCR MSI Assay has an analytical sensitivity of at least 0.125 percent. For each of the five microsatellite markers used, the assay detected as few as one mutant copy per test. While current methods require tissue samples in order to produce results, obtaining such samples is not always practical in a clinical setting. But the Bio-Rad ddPCR MSI Test can be used with a wide range of samples, including those with an extremely low tumor cell count. This provides much-needed flexibility and allows researchers to work with either tissue or plasma cell–free DNA (liquid biopsy) samples.

“The Bio-Rad Droplet Digital PCR MSI Assay demonstrated 100 percent concordance in tissue MSI status with the gold standard PCR-CE MSI test method and 97 percent concordance across all other common MSI testing modalities,” Freed said, adding “and the assay is fast and easy to use.”

Study 3: QXDx BCR-ABL %IS Kit exhibits excellent clinical performance and reproducibility for monitoring CML treatment response

Nathan Sepulveda and Prasanthi Bhagavatula of Bio-Rad and their team compared a new test, the QXDx BCR-ABL %IS Kit, against an existing FDA-cleared test. This test monitors the concentration of the BCR-ABL1 gene, which helps clinicians assess how the standard tyrosine kinase inhibitor (TKI) treatment is working against chronic myelogenous leukemia (CML), a condition accounting for 15 to 20 percent of all leukemia cases. 

In February 2019, Bio-Rad received FDA clearance for its QXDx BCR-ABL %IS Kit, which tracks the effectiveness of TKI therapy through quantifying the BCR-ABL1 transcript. Researchers compared the test kit against other tests in the College of American Pathologists challenge, a neutral third-party assessment of the accuracy and reliability of clinical testing. The challenge compares results of the test on unknown samples to those of other users applying similar methods to determine whether results align across methods. In addition, reproducibility was measured across multiple sites, instruments, users, and kit lots.

The QXDx BCR-ABL %IS Kit performed well in the challenge, tracking the mean results closely for 10 different testing instances. The test also demonstrated excellent correlation (0.99) with the predicate FDA-cleared test. In terms of reproducibility, results showed the kit’s contributions to variance were negligible across site, instrument, day, user, and kit lot.

“These results prove the kit’s real-world reproducibility and reliability compared to other tests on the market,” said Sepulveda. 

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