TP53, EGFR and PIK3CA gene variations observed as prominent biomarkers in breast and lung cancer by plasma cell-free DNA genomic testing

Savlı, Hakan; Sertdemir, Nilüfer; Aydın, Duygu; Dursun, Bilge; Kurtaş, Ömer; Reka, Seda; Sunnetci‐Akkoyunlu, Deniz; Eren-Keskin, Seda; Uygun, Kazım; Ercan, Ercan; Işik, Ulaş; Çabuk, Devrim; Demir, Gulhan; Guzdolu, Eda; Gökbayrak, Merve; Aksu, Maksut Görkem; Cantürk, Nuh Zafer; Çine, Naci

doi:10.1016/j.jbiotec.2019.05.005

Cited by 16 publications

(13 citation statements)

References 19 publications

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“…Therefore, medicine is moving toward a noninvasive genetic test for cancers (Méhes, 2019). Tumor profiles in plasma, urine, liquor and other body fluids that are useful for the detection and follow-up of specific genes by the several methods already discussed here provide a good alternative (Savli et al, 2019).…”

Section: Using Ctdna To Follow-up Cancer Treatment and Recurrencementioning

confidence: 99%

ctDNA as a Cancer Biomarker: A Broad Overview

Pessôa

Heringer²,

Ferrer

2020

Preprint

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Circulating tumor DNA (ctDNA) in fluids has gained attention because ctDNA seems to identify tumor-specific abnormalities, which could be used for diagnosis, follow-up of treatment, and prognosis: the so-called liquid biopsy. Liquid biopsy is a minimally invasive approach and presents the sum of ctDNA from primary and secondary tumor sites. It has been possible not only to quantify the amount of ctDNA but also to identify (epi)genetic changes. Specific mutations in genes have been identified in the plasma of patients with several types of cancer, which highlights ctDNA as a possible cancer biomarker. However, achieving detectable concentrations of ctDNA in body fluids is not an easy task. ctDNA fragments present a short half-life, and there are no cut-off values to discriminate high and low ctDNA concentrations. Here, we discuss the use of ctDNA as a cancer biomarker, the main methodologies, the inherent difficulties, and the clinical predictive value of ctDNA.

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Section: Using Ctdna To Follow-up Cancer Treatment and Recurrencementioning

confidence: 99%

ctDNA as a Cancer Biomarker: A Broad Overview

Pessôa

Heringer²,

Ferrer

2020

Preprint

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“…Frequencies of TP53 mutation reported in these studies agree with some recent ones reporting frequencies of 34% in tissue [ 44 , 45 ] and of 31% [ 46 ] and 32.5% [ 47 ] in plasma of primary breast cancer patients. Nevertheless, mutation frequency is higher in some other studies, showing a TP53 mutation prevalence of 41% [ 45 ], 50% [ 7 ] and 51.7% [ 24 ]. The fact that the reported variant allele fraction (VAF) of TP53 mutations in plasma has such wide ranges may make detection difficult when at low VAFs and may make it overestimated when at high VAFs, being a source of discordances with tissue.…”

Section: Variability Of Tp53 Status Between Liquid and Solid Biopsmentioning

confidence: 85%

“…Thus, the correlation between cfDNA and tissue samples for TP53 mutations is expected to be variable. In another study, TP53 mutations in cfDNA were only identified in 50% of the patients [ 47 ]; however, in another cohort of non-small cell lung cancer (NSCLC) patients, TP53 mutations were found in 71.7% (81/113) of patients [ 7 ], which again might be due to different inclusion criteria. High concordance was found in 10 patients comparing TP53 mutation status between tissue and cfDNA.…”

Section: Variability Of Tp53 Status Between Liquid and Solid Biopsmentioning

confidence: 99%

“…This facilitates the repetitive analysis of a particular biomarker to monitor the evolution of diseases like cancer, thus predicting their progression. The main types of liquid biopsies with a demonstrated prognostic role in several solid tumors are circulating tumor cells (CTCs) and cell-free DNA (cfDNA), particularly in advanced-stage tumors [ 6 , 7 , 8 , 9 ]. However, regarding diagnosis, and particularly at early stages, these biomarkers that need to be highly specific and sensitive have not yet proved their utility, although some studies suggest very low false positive rates [ 10 , 11 ].…”

Section: Introductionmentioning

confidence: 99%

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The Polemic Diagnostic Role of TP53 Mutations in Liquid Biopsies from Breast, Colon and Lung Cancers

Garrido-Navas

Garcia-Diaz

Molina-Vallejo

et al. 2020

Cancers

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Being minimally invasive and thus allowing repeated measures over time, liquid biopsies are taking over traditional solid biopsies in certain circumstances such as those for unreachable tumors, very early stages or treatment monitoring. However, regarding TP53 mutation status analysis, liquid biopsies have not yet substituted tissue samples, mainly due to the lack of concordance between the two types of biopsies. This needs to be examined in a study-dependent manner, taking into account the particular type of liquid biopsy analyzed, that is, circulating tumor cells (CTCs) or cell-free DNA (cfDNA), its involvement in the tumor biology and evolution and, finally, the technology used to analyze each biopsy type. Here, we review the main studies analyzing TP53 mutations in either CTCs or cfDNA in the three more prevalent solid tumors: breast, colon and lung cancers. We evaluate the correlation for mutation status between liquid biopsies and tumor tissue, suggesting possible sources of discrepancies, as well as evaluating the clinical utility of using liquid biopsies for the analysis of TP53 mutation status and the future actions that need to be undertaken to make liquid biopsy analysis a reality for the evaluation of TP53 mutations.

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“…9 Hakan et al reported a significant increase in isolation efficiency with very fresh blood samples of at least 15 milliliters which were processed in minutes. 48 Risberg et al investigated the potential preanalytical influential factors of ctDNA levels. The results revealed that using cell-stabilization tubes, storing at 4°C after collection for a short period, and performing the centrifugation in different types of centrifuges greatly improved the feasibility of collecting high-quality specimens.…”

Section: Pre-analytical Factorsmentioning

confidence: 99%

<p>Advances in the Detection Technologies and Clinical Applications of Circulating Tumor DNA in Metastatic Breast Cancer</p>

Liao¹,

Li²

2020

CMAR

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Breast cancer (BC) represents the most commonly diagnosed cancer among females worldwide. Although targeted therapy has greatly improved the efficacy of treating BC, a large proportion of BC patients eventually develop recurrence or metastasis. Traditional invasive tumor tissue biopsy is short of comprehensiveness in tumor assessment due to heterogeneity. Liquid biopsy, an attractive non-invasive approach mainly including circulating tumor cell and circulating tumor DNA (ctDNA), has been widely utilized in a variety of cancers with the advances of sequencing technologies in recent years. The ctDNA that is found circulating in body fluids refers to DNA released from tumor cells and has shown clinical utility in metastatic breast cancer (MBC). With the results of genomic variants detection, ctDNA could be used to predict clinical outcomes, monitor disease progression, and guide treatment for patients with MBC. Moreover, the drug resistance problem may be addressed by ctDNA detection. In this review, we summarized the technological developments and clinical applications of ctDNA in MBC.

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TP53, EGFR and PIK3CA gene variations observed as prominent biomarkers in breast and lung cancer by plasma cell-free DNA genomic testing

Cited by 16 publications

References 19 publications

ctDNA as a Cancer Biomarker: A Broad Overview

ctDNA as a Cancer Biomarker: A Broad Overview

The Polemic Diagnostic Role of TP53 Mutations in Liquid Biopsies from Breast, Colon and Lung Cancers

<p>Advances in the Detection Technologies and Clinical Applications of Circulating Tumor DNA in Metastatic Breast Cancer</p>

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