Optimization of Sources of Circulating Cell-Free DNA Variability for Downstream Molecular Analysis

Till, Jacob E.; Black, Taylor A.; Gentile, Caren; Abdalla, Aseel; Wang, Zhuoyang; Sangha, Hareena K.; Roth, Jeffrey; Sussman, Robyn T.; Yee, Stephanie S.; O’Hara, Mark H.; Thompson, Jeffrey C.; Aggarwal, Charu; Hwang, Wei–Ting; Elenitoba‐Johnson, Kojo S.J.

doi:10.1016/j.jmoldx.2021.08.007

Cited by 9 publications

(4 citation statements)

References 28 publications

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“…Finally, a lack of interest in cfDNA as a biomarker for TGCT could very well be due to the shift in clinical interest to microRNAs that have exhibited a very high sensitivity and specificity for TGCT. 17 , 73 Studies have shown that quantification of miR-371a-3p (the M371 test) alone is sufficient for the detection of TGCT, 4 , 16 , 73 – 75 its accuracy is impacted very little by inter-lab heterogeneity and therefore holds the greatest potential for real-world clinical application, 4 , 17 with prospective trials under way. 42 …”

Section: Discussionmentioning

confidence: 99%

“…23,61 Everything from the time of day when sampling, the satiety and exertion level of the patient, the type of needle in blood drawing, the selection of blood tubes, sample transportation, the temperature, and time that takes from the blood to be processed, choice between blood serum and plasma, centrifugation protocols, storage of plasma or serum before cfDNA isolation, freeze-thawing of plasma or serum, HIL (hemolysis, icterus and lipemia) presence, choice of cfDNA isolation and quantification methods as well as cfDNA storage methods and duration has been shown to create variability in the final analysis results, especially with regards to cfDNA concentration and fragmentation. 23,[62][63][64][65][66] This is both due to the effects of these variables on cfDNA degradation and isolation, but even more importantly, variations in sample processing can lead to genomic DNA contamination. 23,62,67 Even when certain procedures have become widely accepted or suggested, such as double-step centrifugation in blood plasma or serum preparation, minimizing the number of freeze-thawing events, usage of blood plasma and use of automated methods for cfDNA isolation the variations persist.…”

Section: Challenges In Cfdna Application In Tgct Patient Managementmentioning

confidence: 99%

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The utility of cfDNA in TGCT patient management: a systematic review

et al. 2022

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Background: Testicular germ cell tumors (TGCTs) are the most common young male malignancy with a steadily rising incidence. Standard clinical practice is radical orchidectomy of suspicious lumps followed by histopathological diagnosis and tumor subtyping. This practice can lead to complications and quality of life issues for the patients. Liquid biopsies, especially cell-free DNA (cfDNA), promised to be true surrogates for tissue biopsies, which are considered dangerous to perform in cases of testicular tumors. In this study, we have performed a systematic review on the potential of cfDNA in TGCT patient management, its potential challenges in translation to clinical application and possible approaches in further research. Materials & Methods: The review was performed according to the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines on EuropePMC and PUBMED electronic databases, with the last update being on October 21, 2021. Due to the high heterogeneity in identified research articles, we have performed an overview of their efficacy. Results: Eight original articles have been identified on cfDNA in TGCT patients published from 2004 to 2021, of which six had more than one TGCT patient enrolled and were included in the final analysis. Three studies investigated cfDNA methylation, one has investigated mutations in cfDNA, two have investigated cfDNA amount, and one has investigated cfDNA integrity in TGCT. The sensitivity of cfDNA for TGCT was found to be higher than in serum tumor markers and lower than miR-371a-3p, with comparable specificity. cfDNA methylation analysis has managed to accurately detect teratoma in TGCT patients. Conclusion: Potential challenges in cfDNA application to TGCT patient management were identified. The challenges relating to the biology of TGCT with its low mutational burden and low cfDNA amounts in blood plasma make next-generation sequencing (NGS) methods especially challenging. We have also proposed possible approaches to help find clinical application, including a focus on cfDNA methylation analysis, and potentially solving the challenge of teratoma detection.

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Section: Discussionmentioning

confidence: 99%

Section: Challenges In Cfdna Application In Tgct Patient Managementmentioning

confidence: 99%

The utility of cfDNA in TGCT patient management: a systematic review

et al. 2022

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“…The first is a low-speed spin that removed blood cells and prevents cell lysis, that is then followed by a quick higher speed spin that removes unwanted debris ( Sorber et al, 2019 ). Adding a third centrifugation step does not significantly change the cfDNA yield, and as such, is not typically conducted ( Till et al, 2021 ).…”

Section: Liquid Biopsy Techniques and Applications For Vm Carementioning

confidence: 99%

The expansion of liquid biopsies to vascular care: an overview of existing principles, techniques and potential applications to vascular malformation diagnostics

Mansur,

Radovanovic

2024

Front. Genet.

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Vascular malformations are congenital lesions that occur due to mutations in major cellular signalling pathways which govern angiogenesis, cell proliferation, motility, and cell death. These pathways have been widely studied in oncology and are substrates for various small molecule inhibitors. Given their common molecular biology, there is now a potential to repurpose these cancer drugs for vascular malformation care; however, a molecular diagnosis is required in order to tailour specific drugs to the individual patient’s mutational profile. Liquid biopsies (LBs), emerging as a transformative tool in the field of oncology, hold significant promise in this feat. This paper explores the principles and technologies underlying LBs and evaluates their potential to revolutionize the management of vascular malformations. The review begins by delineating the fundamental principles of LBs, focusing on the detection and analysis of circulating biomarkers such as cell-free DNA, circulating tumor cells, and extracellular vesicles. Subsequently, an in-depth analysis of the technological advancements driving LB platforms is presented. Lastly, the paper highlights the current state of research in applying LBs to various vascular malformations, and uses the aforementioned principles and techniques to conceptualize a liquid biopsy framework that is unique to vascular malformation research and clinical care.

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“…Other preanalytical factors include the delay before centrifugation and protocols for plasma separation, and plasma storage conditions [26]. For example, two-step centrifugation reduces contamination by genomic DNA thanks to reduced white blood cell lysis, compared to one-step centrifugation [27]. Moreover, some DNA extraction platforms, such as Maxwell and QIAsymphony, preferentially isolate short fragments over long ones [28].…”

Section: Introductionmentioning

confidence: 99%

Alleviating cell-free DNA sequencing biases with optimal transport

Passemiers,

Jatsenko,

Vanderstichele

et al. 2024

Preprint

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Cell-free DNA (cfDNA) is a rich source of biomarkers for various (patho)physiological conditions. Recent developments have used Machine Learning on large cfDNA data sets to enhance the detection of cancers and immunological diseases. Preanalytical variables, such as the library preparation protocol or sequencing platform, are major confounders that influence such data sets and lead to domain shifts (i.e., shifts in data distribution as those confounders vary across time or space). Here, we present a domain adaptation method that builds on the concept of optimal transport, and explicitly corrects for the effect of such preanalytical variables. Our approach can be used to merge cohorts representative of the same population but separated by technical biases. Moreover, we also demonstrate that it improves cancer detection via Machine Learning by alleviating the sources of variation that are not of biological origin. Our method also improves over the widely used GC-content bias correction, both in terms of bias removal and cancer signal isolation. These results open perspectives for the downstream analysis of larger data sets through the integration of cohorts produced by different sequencing pipelines or collected in different centers. Notably, the approach is rather general with the potential for application to many other genomic data analysis problems.

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Optimization of Sources of Circulating Cell-Free DNA Variability for Downstream Molecular Analysis

Cited by 9 publications

References 28 publications

The utility of cfDNA in TGCT patient management: a systematic review

The utility of cfDNA in TGCT patient management: a systematic review

The expansion of liquid biopsies to vascular care: an overview of existing principles, techniques and potential applications to vascular malformation diagnostics

Alleviating cell-free DNA sequencing biases with optimal transport

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