scholarly journals Urine as a non-invasive alternative to blood for germline and somatic mutation detection in hepatocellular carcinoma

2021 ◽  
Author(s):  
Amy K. Kim ◽  
Selena Y. Lin ◽  
Surbhi Jain ◽  
Yixiao Cui ◽  
Terence Gade ◽  
...  
Keyword(s):  
Hepatocellular Carcinoma ◽  
Somatic Mutation ◽  
Liquid Biopsy ◽  
Mononuclear Cells ◽  
Cell Free Dna ◽  
Genome Coverage ◽  
Non Invasive ◽  
Free Dna ◽  
Genotype Information ◽  
Targeted Ngs

AbstractCell-free DNA (cfDNA) from blood has become a promising analyte for cancer genetic liquid biopsy. Urinary cfDNA has been shown to contain mutations associated with non-genitourologic cancers including hepatocellular carcinoma (HCC). In this study, we evaluate urine as a noninvasive alternative to blood-based liquid biopsy in both germline and circulating tumor DNA (ctDNA) genotyping in HCC. Using quantitative PCR (qPCR), whole-genome sequencing (WGS), and targeted NGS, DNA isolated from blood or urine of patients with HCC was analyzed for overall genome coverage, HCC hotspot coverage, and germline or somatic mutation concordance. Targeted NGS of plasma and urine cfDNA was also performed for detection of somatic variants. We found urine cfDNA, similar to plasma cfDNA, showed a major mononucleosomal species of 150-180 bp in both healthy individuals and patients with HCC. By WGS, overall genome coverage breadth was similar between urine and plasma cfDNA, with higher fraction of covered cancer-associated mutation hotspots in urine cfDNA. qPCR analyses of HCC-associated mutations (TP53, CTNNB1, and TERT) in 101 patients with HCC revealed 78% overall concordance between plasma and urine. Targeted NGS of HCC-associated gene regions in additional 15 HCC patients showed a 97% overall position-level concordance between plasma and urine cfDNA. Collectively, urine DNA can potentially be used as a completely noninvasive liquid biopsy for HCC.Significance StatementHepatocellular carcinoma (HCC) is the most common liver cancer worldwide and the fastest growing gastrointestinal cancer in the U.S. Cell-free DNA (cfDNA) which originates from various cells undergoing apoptosis or necrosis including tumor cells, is present in all body fluids levels including urine. Urinary cfDNA isolated from patients with HCC showed a similar fragment size distribution, overall genome coverage, and comparable sensitivity for detecting HCC-associated variants compared to plasma cfDNA. Urine was also determined to be a reliable source of germline genotype information, similar to peripheral blood mononuclear cells in blood-based liquid biopsies. Urine cfDNA can be used as a completely non-invasive liquid biopsy in HCC.

Potential clinical applications of circulating cell-free DNA in ovarian cancer patients

2018 ◽  
Vol 20 ◽  
Author(s):  
Ana Barbosa ◽  
Ana Peixoto ◽  
Pedro Pinto ◽  
Manuela Pinheiro ◽  
Manuel R. Teixeira
Keyword(s):  
Ovarian Cancer ◽  
Cancer Patients ◽  
Liquid Biopsy ◽  
Clinical Applications ◽  
Epigenetic Alterations ◽  
Cell Free Dna ◽  
Non Invasive ◽  
Free Dna ◽  
Potential Use ◽  
Circulating Cell Free Dna

AbstractCirculating cell-free DNA (cfDNA) consists of small fragments of DNA that circulate freely in the bloodstream. In cancer patients, a fraction of cfDNA is derived from tumour cells, therefore containing the same genetic and epigenetic alterations, and is termed circulating cell-free tumour DNA. The potential use of cfDNA, the so-called ‘liquid biopsy’, as a non-invasive cancer biomarker has recently received a lot of attention. The present review will focus on studies concerning the potential clinical applications of cfDNA in ovarian cancer patients.

scholarly journals Somatic Mutations in Circulating Cell-Free DNA and Risk for Hepatocellular Carcinoma in Hispanics

2021 ◽  
Vol 22 (14) ◽  
pp. 7411
Author(s):  
Jingjing Jiao ◽  
Jessica I. Sanchez ◽  
Erika J. Thompson ◽  
Xizeng Mao ◽  
Joseph B. McCormick ◽  
...  
Keyword(s):  
Hepatocellular Carcinoma ◽  
Overall Survival ◽  
Liver Fibrosis ◽  
Somatic Mutations ◽  
Advanced Fibrosis ◽  
Cell Free Dna ◽  
Non Invasive ◽  
Free Dna ◽  
Significant Difference ◽  
Advanced Liver Fibrosis

Hispanics are disproportionally affected by liver fibrosis and hepatocellular carcinoma (HCC). Advanced liver fibrosis is a major risk factor for HCC development. We aimed at identifying somatic mutations in plasma cell-free DNA (cfDNA) of Hispanics with HCC and Hispanics with advanced liver fibrosis but no HCC. Targeted sequencing of over 262 cancer-associated genes identified nonsynonymous mutations in 22 of the 27 HCC patients. Mutations were detected in known HCC-associated genes (e.g., CTNNB1, TP53, NFE2L2, and ARID1A). No difference in cfDNA concentrations was observed between patients with mutations and those without detectable mutations. HCC patients with higher cfDNA concentrations or higher number of mutations had a shorter overall survival (p < 0.001 and p = 0.045). Nonsynonymous mutations were also identified in 17 of the 51 subjects with advanced liver fibrosis. KMT2C was the most commonly mutated gene. Nine genes were mutated in both subjects with advanced fibrosis and HCC patients. Again, no significant difference in cfDNA concentrations was observed between subjects with mutations and those without detectable mutations. Furthermore, higher cfDNA concentrations and higher number of mutations correlated with a death outcome in subjects with advanced fibrosis. In conclusion, cfDNA features are promising non-invasive markers for HCC risk prediction and overall survival.

scholarly journals A serum-based DNA methylation assay provides accurate detection of glioma

2021 ◽  
Author(s):  
Thais Sabedot ◽  
Tathiane Malta ◽  
James Snyder ◽  
Kevin Nelson ◽  
Michael Wells ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Liquid Biopsy ◽  
Somatic Mutations ◽  
Methylation Status ◽  
Experimental Treatment ◽  
Cell Free Dna ◽  
Invasive Approach ◽  
Non Invasive ◽  
Free Dna

Abstract Background The detection of somatic mutations in cell-free DNA (cfDNA) from liquid biopsy has emerged as a non-invasive tool to monitor the follow-up of cancer patients. However, the significance of cfDNA clinical utility remains uncertain in patients with brain tumors, primarily because of the limited sensitivity cfDNA has to detect real tumor-specific somatic mutations. This unresolved challenge has prevented accurate follow-up of glioma patients with non-invasive approaches. Methods Genome-wide DNA methylation profiling of tumor tissue and serum cell-free DNA of glioma patients. Results Here, we developed a non-invasive approach to profile the DNA methylation status in the serum of patients with gliomas and identified a cfDNA-derived methylation signature that is associated with the presence of gliomas and related immune features. By testing the signature in an independent discovery and validation cohorts, we developed and verified a score metric (the “glioma epigenetic liquid biopsy score” or GeLB) that optimally distinguished patients with or without glioma (sensitivity: 100%, specificity: 97.78%). Furthermore, we found that changes in GeLB score reflected clinicopathological changes during surveillance (e.g., progression, pseudoprogression or response to standard or experimental treatment). Conclusions Our results suggest that the GeLB score can be used as a complementary approach to diagnose and follow up patients with glioma.

A pilot study of next generation sequencing–liquid biopsy on cell-free DNA as a novel non-invasive diagnostic tool for Klippel–Trenaunay syndrome

Vascular ◽  
2020 ◽  
pp. 170853812093642
Author(s):  
Maria Palmieri ◽  
Anna Maria Pinto ◽  
Laura di Blasio ◽  
Aurora Currò ◽  
Valentina Monica ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Liquid Biopsy ◽  
Somatic Mutations ◽  
Causative Role ◽  
Next Generation ◽  
Cell Free Dna ◽  
Non Invasive ◽  
Free Dna ◽  
Klippel Trenaunay Syndrome ◽  
Generation Sequencing

Objectives Somatic mosaicism of PIK3CA gene is currently recognized as the molecular driver of Klippel–Trenaunay syndrome. However, given the limitation of the current technologies, PIK3CA somatic mutations are detected only in a limited proportion of Klippel–Trenaunay syndrome cases and tissue biopsy remains an invasive high risky, sometimes life-threatening, diagnostic procedure. Next generation sequencing liquid biopsy using cell-free DNA has emerged as an innovative non-invasive approach for early detection and monitoring of cancer. This approach, overcoming the space-time profile constraint of tissue biopsies, opens a new scenario also for others diseases caused by somatic mutations. Methods In the present study, we performed a comprehensive analysis of seven patients (four females and three males) with Klippel–Trenaunay syndrome. Blood samples from both peripheral and efferent vein from malformation were collected and cell-free DNA was extracted from plasma. Tissue biopsies from vascular lesions were also collected when available. Cell-free DNA libraries were performed using Oncomine™ Pan-Cancer Cell-Free Assay. Ion Proton for sequencing and Ion Reporter Software for analysis were used (Life Technologies, Carlsbad, CA, USA). Results Cell-free circulating DNA analysis revealed pathogenic mutations in PIK3CA gene in all patients. The mutational load was higher in plasma obtained from the efferent vein at lesional site (0.81%) than in the peripheral vein (0.64%) leading to conclude for a causative role of the identified variants. Tissue analysis, available for one amputated patient, confirmed the presence of the mutation at the malformation site at a high molecular frequency (14–25%), confirming its causative role. Conclusions Our data prove for the first time that the cell-free DNA-next generation sequencing–liquid biopsy, which is currently used exclusively in an oncologic setting, is indeed the most effective tool for Klippel–Trenaunay syndrome diagnosis and tailored personalized treatment.

scholarly journals Circulating Cell-Free DNA-Based Liquid Biopsy Markers for the Non-Invasive Prognosis and Monitoring of Metastatic Pancreatic Cancer

Cancers ◽  
2020 ◽  
Vol 12 (7) ◽  
pp. 1754 ◽  
Author(s):  
Marta Toledano-Fonseca ◽  
M. Teresa Cano ◽  
Elizabeth Inga ◽  
Rosa Rodríguez-Alonso ◽  
M. Auxiliadora Gómez-España ◽  
...  
Keyword(s):  
Liquid Biopsy ◽  
Hepatic Metastases ◽  
Progression Free Survival ◽  
The Body ◽  
Ductal Adenocarcinoma ◽  
Cell Free Dna ◽  
Ras Mutation ◽  
Non Invasive ◽  
Free Dna ◽  
Circulating Cell Free Dna

Liquid biopsy may assist in the management of cancer patients, which can be particularly applicable in pancreatic ductal adenocarcinoma (PDAC). In this study, we investigated the utility of circulating cell-free DNA (cfDNA)-based markers as prognostic tools in metastatic PDAC. Plasma was obtained from 61 metastatic PDAC patients, and cfDNA levels and fragmentation were determined. BEAMing technique was used for quantitative determination of RAS mutation allele fraction (MAF) in cfDNA. We found that the prognosis was more accurately predicted by RAS mutation detection in plasma than in tissue. RAS mutation status in plasma was a strong independent prognostic factor for both overall survival (OS) and progression-free survival (PFS). Moreover, RAS MAF in cfDNA was also an independent risk factor for poor OS, and was strongly associated with primary tumours in the body/tail of the pancreas and liver metastases. Higher cfDNA levels and fragmentation were also associated with poorer OS and shorter PFS, body/tail tumors, and hepatic metastases, whereas cfDNA fragmentation positively correlated with RAS MAF. Remarkably, the combination of CA19-9 with MAF, cfDNA levels and fragmentation improved the prognostic stratification of patients. Furthermore, dynamics of RAS MAF better correlated with patients’ outcome than standard CA19-9 marker. In conclusion, our study supports the use of cfDNA-based liquid biopsy markers as clinical tools for the non-invasive prognosis and monitoring of metastatic PDAC patients.

scholarly journals Clinical Application Value of Circulating Cell-free DNA in Hepatocellular Carcinoma

2021 ◽  
Vol 8 ◽  
Author(s):  
Yuyuan Zhang ◽  
Zaoqu Liu ◽  
Kun Ji ◽  
Xin Li ◽  
Caihong Wang ◽  
...  
Keyword(s):  
Hepatocellular Carcinoma ◽  
Liquid Biopsy ◽  
Clinical Decision Making ◽  
Early Stage ◽  
Predictive Biomarker ◽  
Intrahepatic Metastasis ◽  
Genetic Profile ◽  
Cell Free Dna ◽  
Free Dna ◽  
Systemic Treatments

Hepatocellular carcinoma (HCC) is one of the most common cancers worldwide and a leading cause of cancer-related deaths. Due to late diagnosis, early intrahepatic metastasis and nonresponse to systemic treatments, surgical resection and/or biopsy specimens remain the gold standard for disease staging, grading and clinical decision-making. Since only a small amount of tissue was obtained in a needle biopsy, the conventional tissue biopsy is unable to represent tumor heterogeneity in HCC. For this reason, it is imperative to find a new non-invasive and easily available diagnostic tool to detect HCC at an early stage and to monitor HCC recurrence. The past decade has witnessed considerable evolution in the development of liquid biopsy technologies with the emergence of next-generation sequencing. As a liquid biopsy approach, molecular analysis of cell-free DNA (cfDNA), characterized by noninvasiveness and real-time analysis, may accurately represent the tumor burden and comprehensively reflect genetic profile of HCC. Therefore, cfDNA may be used clinically as a predictive biomarker in early diagnosis, outcome assessment, and even molecular typing. In this review, we provide an update on the recent advances made in clinical applications of cfDNA in HCC.

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