Cell-free DNA as a post-treatment surveillance strategy: current status

Burgener, Justin M.; Rostami, Ariana; Carvalho, Daniel D. De; Bratman, Scott V.

doi:10.1053/j.seminoncol.2018.01.009

Cited by 23 publications

(25 citation statements)

References 124 publications

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“…In recent years, great strides have been made to identify mutations in either whole exome or specifically selected clinically relevant genes . Assays such as allele‐specific qPCR (AS‐qPCR), Scorpion/ARMS‐PCR, PNAClamp PCR, droplet or bead‐based digital PCR, are currently being used or developed to detect genetic alterations in the plasma sample.…”

Section: Discussionmentioning

confidence: 99%

“…10 Assays such as allele-specific qPCR (AS-qPCR), Scorpion/ARMS-PCR, PNAClamp PCR, droplet or bead-based digital PCR, 9,[34][35][36] are currently being used or developed to detect genetic alterations in the plasma sample. These techniques can reach the high sensitivity of 0.01-1%, 10 however they are only able to detect known mutations in known genes, and their throughput are usually low. 37 Nextgeneration sequencing based assays have high throughput, high sensitivity and can detect new mutations.…”

Section: Discussionmentioning

confidence: 99%

“…For both diagnosis and treatment, there is growing evidence of the clinical usefulness of cfDNA . Along with being noninvasive, cfDNA‐based assays have among their advantages real‐time processing that allows timely detection of drug resistance and disease monitoring, thus making it an extremely useful tool to individualize treatment . Circulating tumor DNA (ctDNA) refers to DNA fragments that are released from primary tumors, circulating tumor cells, micrometastasis or overt metastases in the cancer patient .…”

Section: Introductionmentioning

confidence: 99%

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Using plasma cell‐free DNA to monitor the chemoradiotherapy course of cervical cancer

Tian

Geng

et al. 2019

Intl Journal of Cancer

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The liquid biopsy is being integrated into cancer diagnostics and surveillance. However, critical questions still remain, such as how to precisely evaluate cancer mutation burden and interpret the corresponding clinical implications. Herein, we evaluated the role of peripheral blood cell‐free DNA (cfDNA) in characterizing the dynamic mutation alterations of 48 cancer driver genes from cervical cancer patients. We performed targeted deep sequencing on 93 plasma cfDNA from 57 cervical cancer patients and from this developed an algorithm, allele fraction deviation (AFD), to monitor in an unbiased manner the dynamic changes of genomic aberrations. Differing treatments, including chemotherapy (n = 22), radiotherapy (n = 14) and surgery (n = 15), led to a significant decrease in AFD values (Wilcoxon, p = 0.029). The decrease of cfDNA AFD values was accompanied by shrinkage in the size of the tumor in most patients. However, in a subgroup of patients where cfDNA AFD values did not reflect a reduction in tumor size, there was a detection of progressive disease (metastasis). Furthermore, a low AFD value at diagnosis followed a later increase of AFD value also successfully predicted relapse. These results show that plasma cfDNA, together with targeted deep sequencing, may help predict treatment response and disease development in cervical cancer.

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Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Using plasma cell‐free DNA to monitor the chemoradiotherapy course of cervical cancer

Tian

Geng

et al. 2019

Intl Journal of Cancer

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“…Liquid biopsy procedures have been developed to identify oncologic biomarkers in several body fluids such as blood, plasma, cerebrospinal liquid, seminal fluid, saliva and urine. (Ulrich and Paweletz, 2018;Burgener et al, 2017) The concept that body fluids may reveal the presence of several systemic diseases dates back to ancient Greek and Indian history. The development of humoral theory was attributed to Hippocrates (ca.…”

Section: Introductionmentioning

confidence: 99%

“…The presence of DNA within the non-cellular fraction of peripheral blood, termed cell-free DNA (cfDNA), was initially identified more than 50 years ago. (Ulrich and Paweletz, 2018;Burgener et al, 2017) Decades passed before cfDNA levels were found to be elevated within the serum of cancer patients, with at least a portion of the cfDNA being tumor-derived (ctDNA). The advantage of ctDNA analysis from liquids other than blood is the collection of targeted information from a body fluid directly in contact with the tumor source (eg.…”

Section: Introductionmentioning

confidence: 99%

Non-blood sources of cell-free DNA for cancer molecular profiling in clinical pathology and oncology

Ponti

Manfredini

Tomasi

2019

Critical Reviews in Oncology/Hematology

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Liquid biopsy can quantify and qualify cell-free (cfDNA) and tumour-derived (ctDNA) DNA fragments in the bloodstream. CfDNA quantification and mutation analysis can be applied to diagnosis, follow-up and therapeutic management as novel oncologic biomarkers. However, some tumor-types release a low amount of DNA into the bloodstream, hampering diagnosis through standard liquid biopsy procedures. Several tumors, as such as brain, kidney, prostate, and thyroid cancer, are in direct contact with other body fluids and may be alternative sources for cfDNA and ctDNA. Non-blood sources of cfDNA/ctDNA useful as novel oncologic biomarkers include cerebrospinal fluids, urine, sputum, saliva, pleural effusion, stool and seminal fluid. Seminal plasma cfDNA, which can be analyzed with cost-effective procedures, may provide powerful information capable to revolutionize prostate cancer (PCa) patient diagnosis and management. In the near future, cfDNA analysis from non-blood biological liquids will become routine clinical practice for cancer patient diagnosis and management.

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Potential utility of longitudinal somatic mutation and methylation profiling for predicting molecular residual disease in postoperative non‐small cell lung cancer patients

et al. 2021

Cancer Medicine

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Growing efforts are being invested in investigating various molecular approaches to detect minimal residual disease (MRD) and predict disease recurrence. In our study, we investigated the utility of parallel longitudinal analysis of mutation and DNA methylation profiles for predicting MRD in postoperative non‐small‐cell lung cancer (NSCLC) patients. Tumor tissues and longitudinal blood samples were obtained from 65 patients with resected stage IA‐IIIB NSCLC. Somatic mutation and DNA methylation profiling were performed using ultra‐deep targeted sequencing and targeted bisulfite sequencing, respectively. Dynamic changes in plasma‐based mutation and tumor‐informed methylation profiles, reflected as MRD score, were observed from before surgery (baseline) to postoperative follow‐up, reflecting the decrease in tumor burden of the patients with resected NSCLC. Mutations were detected from plasma samples in 63% of the patients at baseline, which significantly reduced to 23‐25% during post‐operative follow‐ups. MRD score positive rate was 95.7% at baseline, which reduced to 74% at the first and 70% at the second follow‐up. Among the 5 relapsed patients with parallel longitudinal analysis of mutation and methylation profile, elevated MRD score was observed at follow‐up between 0.5‐7 months prior to radiologic recurrence for all 5 patients. Of them, 4 patients also had concomitant increase in allelic fraction of mutations in at least 1 follow‐up time point, but one patient had no mutation detected throughout all follow‐ups. Our results demonstrate that longitudinal profiling of mutation and DNA methylation may have potential for detecting MRD and predicting recurrence in postoperative NSCLC patients.

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Cell-free DNA as a post-treatment surveillance strategy: current status

Cited by 23 publications

References 124 publications

Using plasma cell‐free DNA to monitor the chemoradiotherapy course of cervical cancer

Using plasma cell‐free DNA to monitor the chemoradiotherapy course of cervical cancer

Non-blood sources of cell-free DNA for cancer molecular profiling in clinical pathology and oncology

Potential utility of longitudinal somatic mutation and methylation profiling for predicting molecular residual disease in postoperative non‐small cell lung cancer patients

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