Open Access
Cancers, volume 12, issue 12, pages 1-18
Development of sensitive droplet digital PCR assays for detecting urinary TERT promoter mutations as non-invasive biomarkers for detection of urothelial cancer
Hosen Ismail
1, 2
,
Forey Nathalie
2
,
Durand Geoffroy
2
,
Voegele Catherine
2
,
Bilici Selin
2
,
Avogbe Patrice Hodonou
2
,
Foll Matthieu
2
,
MANEL ARNAUD
3
,
Vian Emmanuel
4
,
Meziani Sonia
2
,
De Tilly Berengere
4
,
Polo Gilles
4
,
Lole Olesia
2
,
Pauline Francois
2
,
Boureille Antoine
2
,
Pisarev Eduard
5
,
Salas Andrei R O S E
2, 6
,
Henrique Rui
7, 8, 9
,
Byrnes Graham
2
,
Jeronimo Carmen
7, 8, 9
,
Scelo Ghislaine
2, 10
,
McKay James D.
2
,
Zvereva Maria
2, 11
1
Department of Biochemistry and Molecular Biology, Faculty of Biological Sciences, University of Dhaka, Dhaka 1000, Bangladesh
|
2
International Agency for Research on Cancer (IARC), 69372 Lyon, France
|
3
Le Creusot Hospital, 71200 Le Creusot, France
|
4
Department of Urology, Protestant Clinic of Lyon, 69300 Caluire-et-Cuire, France
|
6
Santa Casa de Sao Paulo School of Medical Sciences, Sao Paulo 01221-020, Brazil
|
7
Portuguese Oncology Institute of Porto, Research Center (CI-IPOP), 4200-072 Porto, Portugal
|
8
Department of Pathology, Portuguese Oncology Institute of Porto (IPOP), 4200-072 Porto, Portugal
|
9
Institute of Biomedical Sciences Abel Salazar, University of Porto (ICBAS-UP), 4099-002 Porto, Portugal
|
Publication type: Journal Article
Publication date: 2020-11-27
PubMed ID:
33260905
Cancer Research
Oncology
Abstract
Somatic mutations in the telomerase reverse transcriptase (TERT) promoter regions are frequent events in urothelial cancer (UC) and their detection in urine (supernatant cell-free DNA or DNA from exfoliated cells) could serve as putative non-invasive biomarkers for UC detection and monitoring. However, detecting these tumor-borne mutations in urine requires highly sensitive methods, capable of measuring low-level mutations. In this study, we developed sensitive droplet digital PCR (ddPCR) assays for detecting TERT promoter mutations (C228T, C228A, CC242-243TT, and C250T). We tested the C228T and C250T ddPCR assays on all samples with sufficient quantity of urinary DNA (urine supernatant cell-free DNA (US cfDNA) or urine pellet cellular DNA (UP cellDNA)) from the DIAGURO (n = 89/93 cases and n = 92/94 controls) and from the IPO-PORTO (n = 49/50 cases and n = 50/50 controls) series that were previously screened with the UroMuTERT assay and compared the performance of the two approaches. In the DIAGURO series, the sensitivity and specificity of the ddPCR assays for detecting UC using either US cfDNA or UP cellDNA were 86.8% and 92.4%. The sensitivity was slightly higher than that of the UroMuTERT assay in the IPO-PORTO series (67.4% vs. 65.3%, respectively), but not in the DIAGURO series (86.8% vs. 90.7%). The specificity was 100% in the IPO-PORTO controls for both the UroMuTERT and ddPCR assays, whereas in the DIAGURO series, the specificity dropped for ddPCR (92.4% versus 95.6%). Overall, an almost perfect agreement between the two methods was observed for both US cfDNA (n = 164; kappa coefficient of 0.91) and UP cellDNA (n = 280; kappa coefficient of 0.94). In a large independent series of serial urine samples from DIAGURO follow-up BC cases (n = 394), the agreement between ddPCR and UroMuTERT was (i) strong (kappa coefficient of 0.87), regardless of urine DNA types (kappa coefficient 0.89 for US cfDNA and 0.85 for UP cellDNA), (ii) the highest for samples with mutant allelic fractions (MAFs) > 2% (kappa coefficient of 0.99) and (iii) only minimal for the samples with the lowest MAFs (< 0.5%; kappa coefficient 0.32). Altogether, our results indicate that the two methods (ddPCR and UroMuTERT) for detecting urinary TERT promoter mutations are comparable and that the discrepancies relate to the detection of low-allelic fraction mutations. The simplicity of the ddPCR assays makes them suitable for implementation in clinical settings.
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- We do not take into account publications that without a DOI.
- Statistics recalculated only for publications connected to researchers, organizations and labs registered on the platform.
- Statistics recalculated weekly.
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Hosen I. et al. Development of sensitive droplet digital PCR assays for detecting urinary TERT promoter mutations as non-invasive biomarkers for detection of urothelial cancer // Cancers. 2020. Vol. 12. No. 12. pp. 1-18.
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Hosen I., Forey N., Durand G., Voegele C., Bilici S., Avogbe P. H., Delhomme T. M., Foll M., MANEL A., Vian E., Meziani S., De Tilly B., Polo G., Lole O., Pauline F., Boureille A., Pisarev E., Salas A. R. O. S. E., Monteiro-Reis S., Henrique R., Byrnes G., Jeronimo C., Scelo G., McKay J. D., Le Calvez-Kelm F., Zvereva M. Development of sensitive droplet digital PCR assays for detecting urinary TERT promoter mutations as non-invasive biomarkers for detection of urothelial cancer // Cancers. 2020. Vol. 12. No. 12. pp. 1-18.
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TY - JOUR
DO - 10.3390/cancers12123541
UR - https://doi.org/10.3390%2Fcancers12123541
TI - Development of sensitive droplet digital PCR assays for detecting urinary TERT promoter mutations as non-invasive biomarkers for detection of urothelial cancer
T2 - Cancers
AU - Forey, Nathalie
AU - Durand, Geoffroy
AU - Voegele, Catherine
AU - Bilici, Selin
AU - Avogbe, Patrice Hodonou
AU - MANEL, ARNAUD
AU - Meziani, Sonia
AU - De Tilly, Berengere
AU - Polo, Gilles
AU - Lole, Olesia
AU - Pauline, Francois
AU - Boureille, Antoine
AU - Byrnes, Graham
AU - Scelo, Ghislaine
AU - McKay, James D.
AU - Hosen, Ismail
AU - Delhomme, Tiffany M.
AU - Foll, Matthieu
AU - Vian, Emmanuel
AU - Pisarev, Eduard
AU - Salas, Andrei R O S E
AU - Monteiro-Reis, Sara
AU - Henrique, Rui
AU - Jeronimo, Carmen
AU - Le Calvez-Kelm, Florence
AU - Zvereva, Maria
PY - 2020
DA - 2020/11/27 00:00:00
PB - Multidisciplinary Digital Publishing Institute (MDPI)
SP - 1-18
IS - 12
VL - 12
PMID - 33260905
SN - 2072-6694
ER -
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@article{2020_Hosen,
author = {Nathalie Forey and Geoffroy Durand and Catherine Voegele and Selin Bilici and Patrice Hodonou Avogbe and ARNAUD MANEL and Sonia Meziani and Berengere De Tilly and Gilles Polo and Olesia Lole and Francois Pauline and Antoine Boureille and Graham Byrnes and Ghislaine Scelo and James D. McKay and Ismail Hosen and Tiffany M. Delhomme and Matthieu Foll and Emmanuel Vian and Eduard Pisarev and Andrei R O S E Salas and Sara Monteiro-Reis and Rui Henrique and Carmen Jeronimo and Florence Le Calvez-Kelm and Maria Zvereva},
title = {Development of sensitive droplet digital PCR assays for detecting urinary TERT promoter mutations as non-invasive biomarkers for detection of urothelial cancer},
journal = {Cancers},
year = {2020},
volume = {12},
publisher = {Multidisciplinary Digital Publishing Institute (MDPI)},
month = {nov},
url = {https://doi.org/10.3390%2Fcancers12123541},
number = {12},
pages = {1--18},
doi = {10.3390/cancers12123541}
}
Cite this
MLA
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Hosen, Ismail, et al. “Development of sensitive droplet digital PCR assays for detecting urinary TERT promoter mutations as non-invasive biomarkers for detection of urothelial cancer.” Cancers, vol. 12, no. 12, Nov. 2020, pp. 1-18. https://doi.org/10.3390%2Fcancers12123541.