Initial validation of liquid biopsy mass sequencing assay for detection of the oncogenic marker PIK3CA in breast cancer patients

Authors

DOI:

https://doi.org/10.52611/confluencia.2024.1061

Keywords:

Validation study, High-Throughput nucleotide sequencing, Real-Time polymerase chain reaction, Breast cancer

Abstract

In Chile, the techniques approved for mutation detection in liquid biopsies are variants of the polymerase chain reaction. However, massive sequencing has certain advantages, serving for the monitoring and treatment selection for pathologies such as breast cancer. According to international clinical laboratory standards, a comparison between the evaluated technique and the reference one was carried out, necessary for the validation and implementation of this technique in patients with breast cancer. Objective: To carry out the initial validation of a massive sequencing protocol capable of detecting PIK3CA mutations in the circulating tumor DNA of these patients. Methodology: 11 blood samples were obtained from patients with advanced breast cancer, where the extracted DNA was sequenced and the detection of 3 mutations in PIK3CA was evaluated by a real time polymerase chain reaction, and the results were compared using a table of contingency and the McNemar test. Result: McNemar's exact test gave a p value > 0,05 and the evaluated technique had a sensitivity and specificity of 100%, with an agreement of 1 according to Cohen's kappa coefficient. Discussion: The cost-effectiveness of massive sequencing is greater than single genetic assays, but the limitations of both techniques must be taken into account. Conclusion: A high level of agreement was found between the techniques, but the results were not statistically significant. Even so, the validation of this assay should continue in the future with a larger number of samples.

Downloads

Download data is not yet available.

References

Sung H, Ferlay J, Siegel RL, Laversanne M, Soerjomataram I, Jemal A, et al. Global Cancer Statistics 2020: GLOBOCAN Estimates of Incidence and Mortality Worldwide for 36 Cancers in 185 Countries. CA Cancer J Clin. 2021 [citado 5 de abril de 2022];71(3):209–49. Disponible en: https://doi.org/10.3322/caac.21660.

Gote V, Nookala AR, Bolla PK, Pal D. Drug Resistance in Metastatic Breast Cancer: Tumor Targeted Nanomedicine to the Rescue. Int J Mol Sci. 2021 [citado 5 de abril de 2022];22(9):4673. Disponible en: https://doi.org/10.3390%2Fijms22094673.

Panagopoulou M, Esteller M, Chatzaki E. Circulating cell-free dna in breast cancer: Searching for hidden information towards precision medicine. Cancers (Basel). 2021 [citado 5 de abril de 2022];13(4):728. Disponible en: https://doi.org/10.3390/cancers13040728.

Cheung AHK, Chow C, To KF. Latest development of liquid biopsy. J Thorac Dis. 2018 [citado 5 de abril de 2022];10(Suppl 14):S1645. Disponible en: https://doi.org/10.21037%2Fjtd.2018.04.68.

Pecorino L. Molecular Biology of Cancer: Mechanisms, Targets, and Therapeutics. 5a ed. Oxford University Press; 2021.

Departamento de Epidemiología Ministerio de Salud. Informe de vigilancia de cáncer. Análisis de mortalidad prematura y años de vida potencialmente perdidos (AVPP) por cáncer década 2009-2018 [Internet]. Minsal.cl. 2021 [citado 15 de mayo de 2022]. Disponible en: https://www.minsal.cl/wpcontent/uploads/2022/01/Informe-MortalidadPrematura-y-AVPP-por-C%C3%A1ncer-2009- 2018.pdf

Orrantia-Borunda E, Anchondo-Nuñez P, AcuñaAguilar L, Gómez-Valles F, Ramírez-Valdespino C. Subtypes of Breast Cancer. Exon Publications [Internet]. 2022 [citado 6 de junio de 2022];31–42. Disponible en: https://doi.org/10.36255/exonpublications-breast-cancer-subtypes

Martínez BEH, Fernández HG. Caracterización del cáncer de mama triple negativo. Revista Finlay. 2020; [citado 5 de abril de 2022] 10(3):259–68. Disponible en: https://revfinlay.sld.cu/index.php/finlay/article/view/850

Benozzi S, Coniglio RI. Aterosclerosis: biomarcadores plasmáticos emergentes. Acta bioquím. clín. latinoam. 2010; [citado 20 de junio de 2022] 44(3):317–28. Disponible en: http://www.scielo.org.ar/scielo.php?script=sci_arttext&pid=S0325-29572010000300003&lng=es&nrm=iso

Califf RM. Biomarker definitions and their applications. Sage journals. 2018; [citado 5 de abril de 2022] 243(3):213–21. Disponible en: https://doi.org/10.1177/1535370217750088

Najjar S, Allison KH. Updates on breast biomarkers. Virchows Archiv. 2022; [citado 29 de marzo de 2023] 480(1):163–76. Disponible en: https://doi.org/10.1007/s00428-022-03267-x

Dong C, Wu J, Chen Y, Nie J, Chen C. Activation of PI3K/AKT/mTOR Pathway Causes Drug Resistance in Breast Cancer. Front Pharmacol. 2021; [citado 29 de marzo de 2023] 12:628690. Disponible en: https://doi.org/10.3389%2Ffphar.2021.628690

Verret B, Cortes J, Bachelot T, Andre F, Arnedos M. Efficacy of PI3K inhibitors in advanced breast cancer. Annals of Oncology. 2019; [citado 29 de marzo de 2023] 30(10):x12–20. Disponible en: https://doi.org/10.1093/annonc/mdz381

Alvarez-Garcia V, Bartos C, Keraite I, Trivedi U, Brennan PM, Kersaudy-Kerhoas M, et al. A simple and robust real-time qPCR method for the detection of PIK3CA mutations. Sci Rep. 2018; [citado 6 de junio de 2022] 8(1):1–10. Disponible en: https://doi.org/10.1038/s41598-018-22473-9

André F, Ciruelos E, Rubovszky G, Campone M, Loibl S, Rugo HS, et al. Alpelisib for PIK3CA-mutated, hormone receptor-positive advanced breast cancer. 2019;380(20):1929–40. Disponible en: https://doi.org/10.1056/nejmoa1813904

Taylor SC, Nadeau K, Abbasi M, Lachance C, Nguyen M, Fenrich J. The ultimate qPCR experiment: producing publication quality, reproducible data the first time. Trends Biotechnol. 2019 [citado 5 de abril de 2022];37(7):761–74. Disponible en: http://dx.doi.org/10.1016/j.tibtech.2018.12.002

Raby BA. Polymerase chain reaction (PCR) [Internet]. UpToDate. 2021 [citado 5 de abril de 2022]. Disponible en: https://www.uptodate.com/contents/polymerasechain-reaction-pcr

Hulick PJ. Next-generation DNA sequencing (NGS): Principles and clinical applications [Internet]. UpToDate. 2021 [citado 5 de abril de 2022]. Disponible en: https://www.uptodate.com/contents/next-generation-dna-sequencing-ngs-principles-andclinical-applications

Illumina Inc. Advantages of next-generation sequencing vs. qPCR [Internet]. Illumina.com. 2018 [citado 5 de abril de 2021]. Disponible en: https://www.illumina.com/science/technology/nextgeneration-sequencing/ngs-vs-qpcr.html

Pérez-Barrios C. Estudio de biomarcadores a partir de ADN tumoral circulante en pacientes con cáncer de pulmón no microcítico avanzado [Tesis doctoral]. [Madrid]; 2019 [citado 5 de abril de 2021]. Disponible en: http://hdl.handle.net/20.500.14352/17352

Asensio-Del-Barrio C, Garcia-Carpintero EE, Carmona M. Validez, utilidad clínica y seguridad de la nueva plataforma genómica de secuenciación de próxima generación (NGS) FoundationOne® en el cáncer de pulmón no microcítico y otros tipos de tumores sólidos [Internet]. Ministerio de Sanidad, Consumo y Bienestar Social (MSCBS); 2019 [citado 5 de abril de 2022]. Disponible en: http://hdl.handle.net/20.500.12105/9064

Ivanov M, Laktionov K, Breder V, Chernenko P, Novikova E, Telysheva E, et al. Towards standardization of next-generation sequencing of FFPE samples for clinical oncology: Intrinsic obstacles and possible solutions. J Transl Med. 2017; [citado 4 de mayo de 2021] 15(1):1–13. Disponible en: https://doi.org/10.1186%2Fs12967-017-1125-8

Vanderpoel J, Stevens AL, Emond B, Lafeuille MH, Hilts A, Lefebvre P, et al. Total cost of testing for genomic alterations associated with next-generation sequencing versus polymerase chain reaction testing strategies among patients with metastatic non-small cell lung cancer. J Med Econ. 2022; [citado 12 de octubre de 2022] 25(1):457–68. Disponible en: https://doi.org/10.1080/13696998.2022.2053403

Arriola E, Bernabé R, Campelo RG, Biscuola M, Enguita AB, López-Ríos F, et al. Cost-Effectiveness of Next-Generation Sequencing Versus Single-Gene Testing for the Molecular Diagnosis of Patients With Metastatic Non-Small-Cell Lung Cancer From the Perspective of Spanish Reference Centers. JCO Precis Oncol. 2023; [citado 12 de octubre de 2023] 7(7). Disponible en: https://doi.org/10.1200/po.22.00546

Tébar Martínez R. Impacto de la tecnología de secuenciación masiva en el cáncer de pulmón no microcítico. [València]; 2016 [citado 12 de octubre de 2023]. Disponible en: http://hdl.handle.net/10251/68731

Sepúlveda-Hermosilla G, Freire M, Blanco A, Cáceres J, Lizana R, Ramos L, et al. Concordance Analysis of ALK Gene Fusion Detection Methods in Patients with Non–Small-Cell Lung Cancer from Chile, Brazil, and Peru. The Journal of Molecular Diagnostics. 2021; [citado 29 de marzo de 2023] 23(9):1127–37. Disponible en: https://doi.org/10.1016/j.jmoldx.2021.05.018

Published

2024-05-31

How to Cite

1.
Maldonado Brito ID, Vera Leonelli VB, D'Achiardi Meza IS. Initial validation of liquid biopsy mass sequencing assay for detection of the oncogenic marker PIK3CA in breast cancer patients. Rev. Conflu [Internet]. 2024 May 31 [cited 2024 Nov. 23];7. Available from: https://revistas.udd.cl/index.php/confluencia/article/view/1061

Issue

Section

Investigación Cuantitativa

Similar Articles

<< < 9 10 11 12 13 14 15 16 17 > >> 

You may also start an advanced similarity search for this article.