Characterizing the Cancer Genome in Blood

Dawson, Sarah-Jane

doi:10.1101/cshperspect.a026880

Cited by 10 publications

(5 citation statements)

References 112 publications

(161 reference statements)

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“…Using the same method that is commonly used for isolating ccfDNA (see material and methods section for details) from human plasma, we have thus investigated the presence of ccfDNA in mussels. Our results revealed that we indeed found ccfDNA in hemolymph of Mytilus edulis ( Table 2 ) at in a range of concentrations (nanograms/ml) that were similar to that found in humans [32]. Similar results were obtained for M .…”

Section: Resultssupporting

confidence: 86%

“…while it can increase by 5–10 times in patients with malignant disease or stress conditions [36]. Future studies will be needed to determine whether measuring ccfDNA levels in mussels can be used as a rapid stress biomarker as it does in humans [32, 36, 37]. Analysis of ccfDNA is also perfectly adaptable for serial samplings of DNA abnormalities, gene expression analysis, point mutations, chromosome translocations, miRegulome, epigenetic changes, etc.…”

Section: Discussionmentioning

confidence: 99%

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Liquid biopsies for omics-based analysis in sentinel mussels

Caza¹,

Boissel²,

Villemur³

et al. 2019

PLoS ONE

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Liquid biopsy of plasma is a simple and non-invasive technology that holds great promise in biomedical research. It is based on the analysis of nucleic acid-based biomarkers with predictive potential. In the present work, we have combined this concept with the FTA technology for sentinel mussels. We found that hemocytes collected from liquid biopsies can be readily fixed on FTA cards and used for long-term transcriptome analysis. We also showed that liquid biopsy is easily adaptable for metagenomic analysis of bacterial profiles of mussels. We finally provide evidence that liquid biopsies contained circulating cell-free DNA (ccfDNA) which can be used as an easily accessible genomic reservoir. Sampling of FTA-fixed circulating nucleic acids is stable at room temperature and does not necessitate a cold-chain protection. It showed comparable performance to frozen samples and is ideally adapted for sampling in remote areas, most notably in polar regions threatened by anthropogenic activities. From an ethical point of view, this minimally-invasive and non-lethal approach further reduces incidental mortality associated with conventional tissue sampling. This liquid biopsy-based approach should thus facilitate biobanking activities and development of omics-based biomarkers in mussels to assess the quality of aquatic ecosystems.

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Section: Resultssupporting

confidence: 86%

Section: Discussionmentioning

confidence: 99%

Liquid biopsies for omics-based analysis in sentinel mussels

Caza¹,

Boissel²,

Villemur³

et al. 2019

PLoS ONE

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“…Whole genome sequencing may also be used in a tumor-naïve fashion allowing the use of other biomarkers besides mutations, including epigenetic alterations (eg, methylation) or fragmentomic analysis of ctDNA to capture tumor derived ctDNA signals. [82][83][84][85] Sampling considerations for MRD testing It is important that all sites in a clinical study follow standardized protocols for sample collection (eg, blood collection in the specific collection tube that will be used with the final market ready assay), storage, timing of sample collection, and processing and handling, for consistent measurement of ctDNA across patients. 3 Since the shedding of ctDNA is affected by histology, grade, stage, and size of the tumor, a baseline pretreatment sample allows for consideration of the impact of variation in tumor shedding rates on assay performance and interpretation of results from the post-treatment sample for study Open access enrolment.…”

Section: Assay Considerations Mrd Test Considerationsmentioning

confidence: 99%

Regulatory implications of ctDNA in immuno-oncology for solid tumors

Vellanki

Ghosh

Pathak

et al. 2023

J Immunother Cancer

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In the era of precision oncology, use of circulating tumor DNA (ctDNA) is emerging as a minimally invasive approach for the diagnosis and management of patients with cancer and as an enrichment tool in clinical trials. In recent years, the US Food and Drug Administration has approved multiple ctDNA-based companion diagnostic assays for the safe and effective use of targeted therapies and ctDNA-based assays are also being developed for use with immuno-oncology-based therapies. For early-stage solid tumor cancers, ctDNA may be particularly important to detect molecular residual disease (MRD) to support early implementation of adjuvant or escalated therapy to prevent development of metastatic disease. Clinical trials are also increasingly using ctDNA MRD for patient selection and stratification, with an ultimate goal of improving trial efficiency through use of an enriched patient population. Standardization and harmonization of ctDNA assays and methodologies, along with further clinical validation of ctDNA as a prognostic and predictive biomarker, are necessary before ctDNA may be considered as an efficacy-response biomarker to support regulatory decision making.

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“…The detection of rare somatic mutations from such limited genomic material input is highly challenging [39]. Target enrichment, either by hybrid capture or amplicon methods, with extensive PCR amplification, is generally required to successfully capture the tumor genomic profile from the small quantity of cfDNA [102,103]. However, the small size of cfDNA fragments can restrict target enrichment and reduce the accuracy of alignment to the human reference genome [39,104].…”

Section: Technical Limitations Leading To False Positive and Negative...mentioning

confidence: 99%

Circulating Tumor DNA-Based Genomic Profiling Assays in Adult Solid Tumors for Precision Oncology: Recent Advancements and Future Challenges

Chan

Chin

Low

2022

Cancers

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Genomic profiling using tumor biopsies remains the standard approach for the selection of approved molecular targeted therapies. However, this is often limited by its invasiveness, feasibility, and poor sample quality. Liquid biopsies provide a less invasive approach while capturing a contemporaneous and comprehensive tumor genomic profile. Recent advancements in the detection of circulating tumor DNA (ctDNA) from plasma samples at satisfactory sensitivity, specificity, and detection concordance to tumor tissues have facilitated the approval of ctDNA-based genomic profiling to be integrated into regular clinical practice. The recent approval of both single-gene and multigene assays to detect genetic biomarkers from plasma cell-free DNA (cfDNA) as companion diagnostic tools for molecular targeted therapies has transformed the therapeutic decision-making procedure for advanced solid tumors. Despite the increasing use of cfDNA-based molecular profiling, there is an ongoing debate about a ‘plasma first’ or ‘tissue first’ approach toward genomic testing for advanced solid malignancies. Both approaches present possible advantages and disadvantages, and these factors should be carefully considered to personalize and select the most appropriate genomic assay. This review focuses on the recent advancements of cfDNA-based genomic profiling assays in advanced solid tumors while highlighting the major challenges that should be tackled to formulate evidence-based guidelines in recommending the ‘right assay for the right patient at the right time’.

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Characterizing the Cancer Genome in Blood

Cited by 10 publications

References 112 publications

Liquid biopsies for omics-based analysis in sentinel mussels

Liquid biopsies for omics-based analysis in sentinel mussels

Regulatory implications of ctDNA in immuno-oncology for solid tumors

Circulating Tumor DNA-Based Genomic Profiling Assays in Adult Solid Tumors for Precision Oncology: Recent Advancements and Future Challenges

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