Simultaneous detection of eight cancer types using a multiplex droplet digital PCR assay
DNA methylation biomarkers have emerged as promising tools for cancer detection. Common methylation patterns across tumor types allow multi‐cancer detection. Droplet digital PCR (ddPCR) has gained considerable attention for methylation detection. However, multi‐cancer detection using multiple target...
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| Main Authors: | , , , , , , , |
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| Format: | Article |
| Language: | English |
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Wiley
2025-01-01
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| Series: | Molecular Oncology |
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| Online Access: | https://doi.org/10.1002/1878-0261.13708 |
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| author | Isabelle Neefs Nele De Meulenaere Thomas Vanpoucke Janah Vandenhoeck Dieter Peeters Marc Peeters Guy Van Camp Ken Op de Beeck |
| author_facet | Isabelle Neefs Nele De Meulenaere Thomas Vanpoucke Janah Vandenhoeck Dieter Peeters Marc Peeters Guy Van Camp Ken Op de Beeck |
| author_sort | Isabelle Neefs |
| collection | DOAJ |
| description | DNA methylation biomarkers have emerged as promising tools for cancer detection. Common methylation patterns across tumor types allow multi‐cancer detection. Droplet digital PCR (ddPCR) has gained considerable attention for methylation detection. However, multi‐cancer detection using multiple targets in ddPCR has never been performed before. Therefore, we developed a multiplex ddPCR assay for multi‐cancer detection. Based on previous data analyses using The Cancer Genome Atlas (TCGA), we selected differentially methylated targets for eight frequent tumor types (lung, breast, colorectal, prostate, pancreatic, head and neck, liver, and esophageal cancer). Three targets were validated using ddPCR in 103 tumor and 109 normal adjacent fresh frozen samples. Two distinct ddPCR assays were successfully developed. Output data from both assays is combined to obtain a read‐out from the three targets together. Our overall ddPCR assay has a cross‐validated area under the curve (cvAUC) of 0.948. Performance between distinct cancer types varies, with sensitivities ranging from 53.8% to 100% and specificities ranging from 80% to 100%. Compared to previously published single‐target parameters, we show that combining targets can drastically increase sensitivity and specificity, while lowering DNA input. In conclusion, we are the first to report a multi‐cancer methylation ddPCR assay, which allows for highly accurate tumor predictions. |
| format | Article |
| id | doaj-art-f79bf26df1f64f20ae9d210da2e502e4 |
| institution | Kabale University |
| issn | 1574-7891 1878-0261 |
| language | English |
| publishDate | 2025-01-01 |
| publisher | Wiley |
| record_format | Article |
| series | Molecular Oncology |
| spelling | doaj-art-f79bf26df1f64f20ae9d210da2e502e42025-01-07T14:42:32ZengWileyMolecular Oncology1574-78911878-02612025-01-0119118820310.1002/1878-0261.13708Simultaneous detection of eight cancer types using a multiplex droplet digital PCR assayIsabelle Neefs0Nele De Meulenaere1Thomas Vanpoucke2Janah Vandenhoeck3Dieter Peeters4Marc Peeters5Guy Van Camp6Ken Op de Beeck7Center of Medical Genetics University of Antwerp and Antwerp University Hospital Edegem BelgiumCenter of Medical Genetics University of Antwerp and Antwerp University Hospital Edegem BelgiumCenter of Medical Genetics University of Antwerp and Antwerp University Hospital Edegem BelgiumCenter of Medical Genetics University of Antwerp and Antwerp University Hospital Edegem BelgiumDepartment of Pathology Antwerp University Hospital Edegem BelgiumCenter for Oncological Research University of Antwerp and Antwerp University Hospital Wilrijk BelgiumCenter of Medical Genetics University of Antwerp and Antwerp University Hospital Edegem BelgiumCenter of Medical Genetics University of Antwerp and Antwerp University Hospital Edegem BelgiumDNA methylation biomarkers have emerged as promising tools for cancer detection. Common methylation patterns across tumor types allow multi‐cancer detection. Droplet digital PCR (ddPCR) has gained considerable attention for methylation detection. However, multi‐cancer detection using multiple targets in ddPCR has never been performed before. Therefore, we developed a multiplex ddPCR assay for multi‐cancer detection. Based on previous data analyses using The Cancer Genome Atlas (TCGA), we selected differentially methylated targets for eight frequent tumor types (lung, breast, colorectal, prostate, pancreatic, head and neck, liver, and esophageal cancer). Three targets were validated using ddPCR in 103 tumor and 109 normal adjacent fresh frozen samples. Two distinct ddPCR assays were successfully developed. Output data from both assays is combined to obtain a read‐out from the three targets together. Our overall ddPCR assay has a cross‐validated area under the curve (cvAUC) of 0.948. Performance between distinct cancer types varies, with sensitivities ranging from 53.8% to 100% and specificities ranging from 80% to 100%. Compared to previously published single‐target parameters, we show that combining targets can drastically increase sensitivity and specificity, while lowering DNA input. In conclusion, we are the first to report a multi‐cancer methylation ddPCR assay, which allows for highly accurate tumor predictions.https://doi.org/10.1002/1878-0261.13708biomarkersddPCRDNA methylationmulti‐cancer detectionmultiplexing |
| spellingShingle | Isabelle Neefs Nele De Meulenaere Thomas Vanpoucke Janah Vandenhoeck Dieter Peeters Marc Peeters Guy Van Camp Ken Op de Beeck Simultaneous detection of eight cancer types using a multiplex droplet digital PCR assay Molecular Oncology biomarkers ddPCR DNA methylation multi‐cancer detection multiplexing |
| title | Simultaneous detection of eight cancer types using a multiplex droplet digital PCR assay |
| title_full | Simultaneous detection of eight cancer types using a multiplex droplet digital PCR assay |
| title_fullStr | Simultaneous detection of eight cancer types using a multiplex droplet digital PCR assay |
| title_full_unstemmed | Simultaneous detection of eight cancer types using a multiplex droplet digital PCR assay |
| title_short | Simultaneous detection of eight cancer types using a multiplex droplet digital PCR assay |
| title_sort | simultaneous detection of eight cancer types using a multiplex droplet digital pcr assay |
| topic | biomarkers ddPCR DNA methylation multi‐cancer detection multiplexing |
| url | https://doi.org/10.1002/1878-0261.13708 |
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