Validation of Circulating Tumor DNA Assays for Detection of Metastatic Melanoma

Syeda, Mahrukh M.; Wiggins, Jennifer; Corless, Broderick C.; Spittle, Cindy; Karlin-Neumann, George; Polsky, David

doi:10.1007/978-1-4939-9773-2_7

Cited by 8 publications

(5 citation statements)

References 75 publications

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“…Nowadays, a great research effort is being put into the development of techniques that make it possible to detect DNA mutations that are strongly related to the early diagnosis of genetic disorders [21], with the aim of improving the quality of data obtained [6]. Among those techniques, PCR (polymerase chain reaction) and its modifications (such as qPCR, quantitative polymerase chain reaction, and ddPCR, droplet digital PCR), BEAMing [22], different types of blotting (e.g., Northern blot or Western blot) or next-generation sequencing [23] are mostly used to detect DNA mutations as part of cancer treatment [1].…”

Section: Currently Developed Methods For Detecting Dna Mutationsmentioning

confidence: 99%

“…There is strong interest in the development of new sensors for the sensitive identification of specific DNA fragments, for example, circulating free tumor DNA. Identifying circulating tumor DNA can be used to detect mutations in genes of predictive and prognostic importance for molecularly targeted therapies, and can therefore influence clinical decisions [1]. Currently, the most popular techniques for studying genetic predispositions for cancer are PCR (polymerase chain reaction) and NGS (next generation sequencing); however, the waiting time for the results of specific tests can be as long as 3 months, with a relatively high cost and a risk of false positive (contamination) or false negative (low sensitivity) results.…”

Section: Introductionmentioning

confidence: 99%

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Surface Enhanced Raman Spectroscopy for DNA Biosensors—How Far Are We?

et al. 2019

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A sensitive and accurate identification of specific DNA fragments (usually containing a mutation) can influence clinical decisions. Standard methods routinely used for this type of detection are PCR (Polymerase Chain Reaction, and its modifications), and, less commonly, NGS (Next Generation Sequencing). However, these methods are quite complicated, requiring time-consuming, multi-stage sample preparation, and specially trained staff. Usually, it takes weeks for patients to obtain their results. Therefore, different DNA sensors are being intensively developed by many groups. One technique often used to obtain an analytical signal from DNA sensors is Raman spectroscopy. Its modification, surface-enhanced Raman spectroscopy (SERS), is especially useful for practical analytical applications due to its extra low limit of detection. SERS takes advantage of the strong increase in the efficiency of Raman signal generation caused by a local electric field enhancement near plasmonic (typically gold and silver) nanostructures. In this condensed review, we describe the most important types of SERS-based nanosensors for genetic studies and comment on their potential for becoming diagnostic tools.

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Section: Currently Developed Methods For Detecting Dna Mutationsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Surface Enhanced Raman Spectroscopy for DNA Biosensors—How Far Are We?

et al. 2019

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“…Numerous studies have demonstrated a possible clinical usefulness of LB in patients with melanoma, both for the identification of BRAF and NRAS mutations to set up treatment (if tissue is not available), and for quantitative monitoring of ctDNA during treatment 67 , 68 , 69 , 70 , 71 ( Supplementary Figure S1 , available at https://doi.org/10.1016/j.esmoop.2021.100164 ).…”

Section: Lb In Clinical Settings: Current and Emerging Applicationsmentioning

confidence: 99%

The molecular profiling of solid tumors by liquid biopsy: a position paper of the AIOM–SIAPEC-IAP–SIBioC–SIC–SIF Italian Scientific Societies

Russo¹,

Incorvaia²,

Re³

et al. 2021

ESMO Open

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The term liquid biopsy (LB) refers to the use of various biological fluids as a surrogate for neoplastic tissue to achieve information for diagnostic, prognostic and predictive purposes. In the current clinical practice, LB is used for the identification of driver mutations in circulating tumor DNA derived from both tumor tissue and circulating neoplastic cells. As suggested by a growing body of evidence, however, there are several clinical settings where biological samples other than tissue could be used in the routine practice to identify potentially predictive biomarkers of either response or resistance to targeted treatments. New applications are emerging as useful clinical tools, and other blood derivatives, such as circulating tumor cells, circulating tumor RNA, microRNAs, platelets, extracellular vesicles, as well as other biofluids such as urine and cerebrospinal fluid, may be adopted in the near future. Despite the evident advantages compared with tissue biopsy, LB still presents some limitations due to both biological and technological issues. In this context, the absence of harmonized procedures corresponds to an unmet clinical need, ultimately affecting the rapid implementation of LB in clinical practice. In this position paper, based on experts’ opinions, the AIOM–SIAPEC-IAP–SIBIOC–SIF Italian Scientific Societies critically discuss the most relevant technical issues of LB, the current and emerging evidences, with the aim to optimizing the applications of LB in the clinical setting.

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“…When ddPCR became available in the laboratory, we tested tumors based on DNA availability to resolve mutational discordances between other methods (n ¼ 2) and explore the sensitivity of the methods with respect to allele fraction as measured by ddPCR (n ¼ 28). The ddPCR assays were performed according to the manufacturer's instructions (Bio-Rad Laboratories, Hercules, CA) and as previously described (Syeda et al, 2020).…”

Section: Mutational Analysismentioning

confidence: 99%

TERT, BRAF, and NRAS Mutational Heterogeneity between Paired Primary and Metastatic Melanoma Tumors

Chang

Wiggins

Corless

et al. 2020

Journal of Investigative Dermatology

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Mutational heterogeneity can contribute to therapeutic resistance in solid cancers. In melanoma, the frequencies of intertumoral and intratumoral heterogeneity are controversial. We examined mutational heterogeneity within individual patients with melanoma using multiplatform analysis of commonly mutated driver and nonpassenger genes. We analyzed paired primary and metastatic tumors from 60 patients and multiple metastatic tumors from 39 patients whose primary tumors were unavailable (n ¼ 271 tumors). We used a combination of multiplex SNaPshot assays, Sanger sequencing, mutation-specific PCR, or droplet digital PCR to determine the presence of BRAF V600 , NRAS Q61 , TERT e124C>T , and TERT e146C>T mutations. Mutations were detected in BRAF (39%), NRAS (21%), and/or TERT (78%). Thirteen patients had TERT mutant discordant tumors; seven of these had a single tumor with both TERT e124C>T and TERT e146C>T mutations present at different allele frequencies. Two patients had both BRAF and NRAS mutations; one had different tumors and the other had a single tumor with both mutations. One patient with a BRAF mutant primary lacked mutant BRAF in at least one of their metastases. Overall, we identified mutational heterogeneity in 18 of 99 patients (18%). These results suggest that some primary melanomas may be composed of subclones with differing mutational profiles. Such heterogeneity may be relevant to treatment responses and survival outcomes.

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Validation of Circulating Tumor DNA Assays for Detection of Metastatic Melanoma

Cited by 8 publications

References 75 publications

Surface Enhanced Raman Spectroscopy for DNA Biosensors—How Far Are We?

Surface Enhanced Raman Spectroscopy for DNA Biosensors—How Far Are We?

The molecular profiling of solid tumors by liquid biopsy: a position paper of the AIOM–SIAPEC-IAP–SIBioC–SIC–SIF Italian Scientific Societies

TERT, BRAF, and NRAS Mutational Heterogeneity between Paired Primary and Metastatic Melanoma Tumors

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