dPCR application in liquid biopsies: divide and conquer

Moreno‐Manuel, Andrea; Calabuig, Silvia; Obrador‐Hevia, Antònia; Blasco, Ana; Fernandez-Diaz, Amaya B; Sirera, Rafael; Camps, Carlos; Jantus‐Lewintre, Eloísa

doi:10.1080/14737159.2021.1860759

Cited by 19 publications

(11 citation statements)

References 113 publications

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“…In fact, in the current context, simple, automatable, and serial technologies are preferred. Moreover, with new applications, such as microchimerism ( 28 ), with new clinical practices, such as microtransplantation ( 29 ), and with new types of low concentration samples, such as cfDNA ( 30 ), a very good sensitivity is increasingly needed.…”

Section: Discussionmentioning

confidence: 99%

New methods for the quantification of mixed chimerism in transplantation

Picard

Frassati²,

Cherouat³

et al. 2023

Front. Immunol.

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BackgroundQuantification of chimerism showing the proportion of the donor in a recipient is essential for the follow-up of hematopoietic stem cell transplantation but can also be useful to document an immune tolerance situation after solid organ transplantation. Historically, chimerism has been quantified from genomic DNA, but with technological advances, chimerism from donor-derived cell-free DNA seems particularly relevant in solid organ transplantation.MethodsThe reference method was until recently the short tandem repeat technique, but new innovative techniques as digital PCR (dPCR) and NGS, have revolutionized the quantification of chimerism, such as the so-called microchimerism analysis. After a short review of chimerism methods, a comparison of chimerism quantification data for two new digital PCR systems (QIAcuity™ dPCR (Qiagen®) and QuantStudio Absolute Q (ThermoFisher®) and two NGS-based chimerism quantification methods (AlloSeq HCT™ (CareDx®) and NGStrack™ (GenDX®)) was performed.ResultsThese new methods were correlated and concordant to routinely methods (r²=0.9978 and r²=0.9974 for dPCR methods, r²=0.9978 and r²=0.9988 for NGS methods), and had similar high performance (sensitivity, reproductibility, linearity).ConclusionFinally, the choice of the innovative method of chimerism within the laboratory does not depend on the analytical performances because they are similar but mainly on the amount of activity and the access to instruments and computer services.

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Section: Discussionmentioning

confidence: 99%

New methods for the quantification of mixed chimerism in transplantation

Picard

Frassati²,

Cherouat³

et al. 2023

Front. Immunol.

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“…Compared with conventional real-time PCR, dPCR is superior in its extreme sensitivity, unprecedented quantification capability and tolerance to PCR inhibitors. Today, the applications surrounding dPCR are mounting, and in oncology, dPCR is widely used for quantification and tracking of tumor-specific mutations during the course of cancer treatments [ 10 , 11 ]. Here, we conducted a comparison study of two dPCR platforms, QS3D dPCR and droplet dPCR, to determine their clinical ability to monitor variants in cfDNA at disease progression status using EGFR T790M mutation as an example.…”

Section: Discussionmentioning

confidence: 99%

Comparative analysis of QS3D versus droplet digital PCR for quantitative measures of EGFR T790M mutation from identical plasma

Guo¹,

Wang²,

Liang³

et al. 2022

Heliyon

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“…Both technologies employ digital PCR principles, which involve sample division or partitioning, where each partition occurs via independent reactions. Subsequently, a digital system allows fluorescence quantification in each partition, and combining the value of each partition affords a final quantification of molecules of interest[ 22 ]. In ddPCR, sample reactions occur within water-in-oil droplets, which act as a system of encapsulated molecules, where millions of PCR reactions can be simultaneously quantified[ 22 , 23 ].…”

Section: Advances In Liquid Biopsy Detection Technologymentioning

confidence: 99%

“…Subsequently, a digital system allows fluorescence quantification in each partition, and combining the value of each partition affords a final quantification of molecules of interest[ 22 ]. In ddPCR, sample reactions occur within water-in-oil droplets, which act as a system of encapsulated molecules, where millions of PCR reactions can be simultaneously quantified[ 22 , 23 ]. The BEAMing technique involves digital PCR in emulsions combined with flow cytometry to quantify DNA molecules.…”

Section: Advances In Liquid Biopsy Detection Technologymentioning

confidence: 99%

“…NGS techniques are based on massively parallel sequencing of selected or unselected genes; thus, millions of DNA sequences can be read simultaneously[ 25 ]. One main advantage of NGS is its ability to detect new mutations or mutations that rarely appear[ 22 ]. In addition, NGS offers high sensitivity and specificity for mutation detection; however, it exhibits considerable variability, ranging from 0.1% to 1%, depending on the technique or platform used[ 26 ].…”

Section: Advances In Liquid Biopsy Detection Technologymentioning

confidence: 99%

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Liquid biopsy to detect resistance mutations against anti-epidermal growth factor receptor therapy in metastatic colorectal cancer

Valenzuela¹,

Burotto²,

Marcelain³

et al. 2022

WJGO

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Colorectal cancer (CRC) is a major cause of mortality worldwide, associated with a steadily growing prevalence. Notably, the identification of KRAS , NRAS , and BRAF mutations has markedly improved targeted CRC therapy by affording treatments directed against the epidermal growth factor receptor (EGFR) and other anti-angiogenic therapies. However, the survival benefit conferred by these therapies remains variable and difficult to predict, owing to the high level of molecular heterogeneity among patients with CRC. Although classification into consensus molecular subtypes could optimize response prediction to targeted therapies, the acquisition of resistance mutations to targeted therapy is, in part, responsible for the lack of response in some patients. However, the acquisition of such mutations can induce challenges in clinical practice. The utility of liquid biopsy to detect resistance mutations against anti-EGFR therapy has recently been described. This approach may constitute a new standard in the decision algorithm for targeted CRC therapy.

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dPCR application in liquid biopsies: divide and conquer

Cited by 19 publications

References 113 publications

New methods for the quantification of mixed chimerism in transplantation

New methods for the quantification of mixed chimerism in transplantation

Comparative analysis of QS3D versus droplet digital PCR for quantitative measures of EGFR T790M mutation from identical plasma

Liquid biopsy to detect resistance mutations against anti-epidermal growth factor receptor therapy in metastatic colorectal cancer

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