Highly sensitive fusion detection using plasma cell‐free RNA in non‐small‐cell lung cancers

Hasegawa, Naoto; Kurokawa, Kana; Shinno, Yuki; Nakamura, Ikuko; Ueno, Toshihide; Kojima, Shinya; Kawazu, Masahito; Suehara, Yoshiyuki; Ishijima, Muneaki; Goto, Yasushi; Kojima, Yoshiyuki; Yonemori, Kan; Hayashi, Takuo; Saito, Tsuyoshi; Shukuya, Takehito; Takahashi, Fumiyuki; Takahashi, Kazuhisa; Mano, Hiroyuki

doi:10.1111/cas.15084

Cited by 32 publications

(21 citation statements)

References 39 publications

(81 reference statements)

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“…At such low rates, ct DNA detections will need to improve significantly and be specialized to reduce the chance of error. A similar situation is true for cf RNA because blood contains mRNA, miRNA, and RNA fragments, which act as noise and contribute to the false detection of RNA [ 69 ]. In addition, the shorter half-life of ct DNA and cf RNA is another challenge that causes a range of problems, from tracking tumor heterogeneity to precision treatment.…”

Section: Applications Of Cf Dna and Cf ...mentioning

confidence: 99%

“…The diagnosis of cancer through cf RNA can also be conducted by using a urine analysis; Kim et al reported that the urine of bladder cancer patients has higher levels of cf RNA compared to healthy persons. Multiple studies have shown the effective diagnostic capabilities of cf RNA in different cancer types, including breast cancer [ 67 ], colorectal cancer [ 68 ], lung cancer [ 69 ], and many others.…”

Section: Applications Of Cf Dna and Cf ...mentioning

confidence: 99%

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Diagnostic and Therapeutic Potential of Circulating-Free DNA and Cell-Free RNA in Cancer Management

et al. 2022

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Over time, molecular biology and genomics techniques have been developed to speed up the early diagnosis and clinical management of cancer. These therapies are often most effective when administered to the subset of malignancies harboring the target identified by molecular testing. Important advances in applying molecular testing involve circulating-free DNA (cfDNA)- and cell-free RNA (cfRNA)-based liquid biopsies for the diagnosis, prognosis, prediction, and treatment of cancer. Both cfDNA and cfRNA are sensitive and specific biomarkers for cancer detection, which have been clinically proven through multiple randomized and prospective trials. These help in cancer management based on the noninvasive evaluation of size, quantity, and point mutations, as well as copy number alterations at the tumor site. Moreover, personalized detection of ctDNA helps in adjuvant therapeutics and predicts the chances of recurrence of cancer and resistance to cancer therapy. Despite the controversial diagnostic values of cfDNA and cfRNA, many clinical trials have been completed, and the Food and Drug Administration has approved many multigene assays to detect genetic alterations in the cfDNA of cancer patients. In this review, we underpin the recent advances in the physiological roles of cfDNA and cfRNA, as well as their roles in cancer detection by highlighting recent clinical trials and their roles as prognostic and predictive markers in cancer management.

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Section: Applications Of Cf Dna and Cf ...mentioning

confidence: 99%

Section: Applications Of Cf Dna and Cf ...mentioning

confidence: 99%

Diagnostic and Therapeutic Potential of Circulating-Free DNA and Cell-Free RNA in Cancer Management

et al. 2022

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“…However, one of the most relevant issues to address is the assessment of gene fusions in liquid biopsy. Their detection by the NGS-based cfDNA analysis is challenging and the sensitivity of detecting in cfDNA is currently debated [ 66 , 67 ]. Moreover, recent reports describe an incidence of detection of gene fusions in plasma samples lower than expected in NSCLC [ 68 , 69 ].…”

Section: Liquid Biopsy As the Challenge Of Todaymentioning

confidence: 99%

“…In fact, analysis of cfRNA in circulation or embedded in vesicles or tumour-educated platelets (TEPs) has shown widely applicability in the detection of several cancer-associated aberrations [ 73 , 74 ]. The sensitivity of cfRNA-based assays could reach over 77% [ 67 ]; however, its clinical implementation is to be improved and needs standardisation of liquid biopsy workflow and optimisation of pre-analytical conditions.…”

Section: Liquid Biopsy As the Challenge Of Todaymentioning

confidence: 99%

Liquid biopsy and non-small cell lung cancer: are we looking at the tip of the iceberg?

et al. 2022

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The possibility to analyse the tumour genetic material shed in the blood is undoubtedly one of the main achievements of translational research in the latest years. In the modern clinical management of advanced non-small cell lung cancer, molecular characterisation plays an essential role. In parallel, immunotherapy is widely employed, but reliable predictive markers are not available yet. Liquid biopsy has the potential to face the two issues and to increase its role in advanced NSCLC in the next future. The aim of this review is to summarise the main clinical applications of liquid biopsy in advanced non-small cell lung cancer, underlining both its potential and limitations from a clinically driven perspective.

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“…In contrast to cfDNA, cfRNA-based assays are not affected by intronic regions and only identify expressed fusion genes [117]. In a recent exploratory study, the authors demonstrated that a cfRNA-based NGS assay has an overall higher sensitivity to detect ALK, ROS1, and RET fusions than a cfDNA-based NGS system (78% and 33%, respectively) [122]. Furthermore, amplicon-based NGS panels that analyze gene fusions at the ctRNA level and gene alterations at the ctDNA level may also hold promise in improving fusion detection [89,123].…”

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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Highly sensitive fusion detection using plasma cell‐free RNA in non‐small‐cell lung cancers

Abstract: This is an open access article under the terms of the Creat ive Commo ns Attri butio n-NonCo mmerc ial-NoDerivs License, which permits use and distribution in any medium, provided the original work is properly cited, the use is non-commercial and no modifications or adaptations are made.

Cited by 32 publications

References 39 publications

Diagnostic and Therapeutic Potential of Circulating-Free DNA and Cell-Free RNA in Cancer Management

Diagnostic and Therapeutic Potential of Circulating-Free DNA and Cell-Free RNA in Cancer Management

Liquid biopsy and non-small cell lung cancer: are we looking at the tip of the iceberg?

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

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