scholarly journals Quick assessment of cell-free DNA in seminal fluid and fragment size for early non-invasive prostate cancer diagnosis

2019 ◽  
Vol 497 ◽  
pp. 76-80 ◽  
Author(s):  
Giovanni Ponti ◽  
Monia Maccaferri ◽  
Marco Manfredini ◽  
Salvatore Micali ◽  
Federica Torricelli ◽  
...  
2013 ◽  
Vol 2013 ◽  
pp. 1-5 ◽  
Author(s):  
Valentina Casadio ◽  
Daniele Calistri ◽  
Samanta Salvi ◽  
Roberta Gunelli ◽  
Elisa Carretta ◽  
...  

Circulating cell-free DNA has been recognized as an accurate marker for the diagnosis of prostate cancer, whereas the role of urine cell-free DNA (UCF DNA) has never been evaluated in this setting. It is known that normal apoptotic cells produce highly fragmented DNA while cancer cells release longer DNA. We thus verified the potential role of UCF DNA integrity for early prostate cancer diagnosis. UCF DNA was isolated from 29 prostate cancer patients and 25 healthy volunteers. Sequences longer than 250 bp (c-Myc,BCAS1, andHER2) were quantified by real-time PCR to verify UCF DNA integrity. Receiver operating characteristic (ROC) curve analysis revealed an area under the curve of 0.7959 (95% CI 0.6729–0.9188). At the best cut-off value of 0.04 ng/μL, UCF DNA integrity analysis showed a sensitivity of 0.79 (95% CI 0.62–0.90) and a specificity of 0.84 (95% CI 0.65–0.94). These preliminary findings indicate that UCF DNA integrity could be a promising noninvasive marker for the early diagnosis of prostate cancer and pave the way for further research into this area.


2021 ◽  
Vol 39 (15_suppl) ◽  
pp. 3058-3058
Author(s):  
Jacob Carey ◽  
Bryan Chesnick ◽  
Denise Butler ◽  
Michael Rongione ◽  
Giovanni Parmigiani ◽  
...  

3058 Background: Circulating cell-free DNA (cfDNA) is largely nucleosomal in origin with typical fragment lengths of 167 base-pairs reflecting the length of DNA wrapped around-the histone and H1 linker. Given the nucleosomal origin of cfDNA, we have previously used low coverage whole genome sequencing to evaluate DNA fragmentation profiles to sensitively and specifically detect tumor-derived DNA with altered fragment lengths or coverage. Methods: Here we evaluate the use of Bayesian finite mixtures to model the fragment length distribution and demonstrate how the parameters from these models can be useful to distinguish between individuals with and without cancer. We examined the number of cfDNA fragments by size ranging from 100-220bp and approximated the mixture component location, scale, and weight using Markov Chain Monte Carlo. The performance of the method was determined using a ten-fold, ten repeat cross-validation of Gradient Boosted Machine model using 1) our previously described genome-wide fragmentation profile approach, 2) the parameters from the mixture model and 3) a combination of approaches 1) and 2) as features. Results: In this study of 215 cancer patients and 208 cancer-free individuals, we observed cross-validated AUCs of 1) 0.94, 2) 0.95, and 3) 0.97 among the three approaches. Conclusions: Our findings indicate that parsimonious mixture models may improve detection of cancer in conjunction with fragmentation profile analyses across the genome.


2017 ◽  
Vol 18 (1) ◽  
Author(s):  
Shuli Kang ◽  
Qingjiao Li ◽  
Quan Chen ◽  
Yonggang Zhou ◽  
Stacy Park ◽  
...  

2020 ◽  
Author(s):  
Emmalyn Chen ◽  
Clinton L. Cario ◽  
Lancelote Leong ◽  
Karen Lopez ◽  
César P. Márquez ◽  
...  

AbstractPurposeProstate cancer is the most commonly diagnosed neoplasm in American men. Although existing biomarkers may detect localized prostate cancer, additional strategies are necessary for improving detection and identifying aggressive disease that may require further intervention. One promising, minimally invasive biomarker is cell-free DNA (cfDNA), which consist of short DNA fragments released into circulation by dying or lysed cells that may reflect underlying cancer. Here we investigated whether differences in cfDNA concentration and cfDNA fragment size could improve the sensitivity for detecting more advanced and aggressive prostate cancer.Materials and MethodsThis study included 268 individuals: 34 healthy controls, 112 men with localized prostate cancer who underwent radical prostatectomy (RP), and 122 men with metastatic castration-resistant prostate cancer (mCRPC). Plasma cfDNA concentration and fragment size were quantified with the Qubit 3.0 and the 2100 Bioanalyzer. The potential relationship between cfDNA concentration or fragment size and localized or mCRPC prostate cancer was evaluated with descriptive statistics, logistic regression, and area under the curve analysis with cross-validation.ResultsPlasma cfDNA concentrations were elevated in mCRPC patients in comparison to localized disease (OR5 ng/mL = 1.34, P = 0.027) or to being a control (OR5 ng/mL = 1.69, P = 0.034). Decreased average fragment size was associated with an increased risk of localized disease compared to controls (OR5bp = 0.77, P = 0.0008).ConclusionThis study suggests that cfDNA concentration and average cfDNA fragment size may provide a quick, cost-effective approach to help determine which patients will benefit most from further screening and/or disease monitoring to help improve prostate cancer outcomes.


Lab on a Chip ◽  
2020 ◽  
Vol 20 (24) ◽  
pp. 4632-4637
Author(s):  
Yanlin Wang ◽  
Qiaoyu Li ◽  
Haimei Shi ◽  
Keqi Tang ◽  
Liang Qiao ◽  
...  

Tumor-derived exosomes, which contain RNA, DNA, and proteins, are a potentially rich non-invasive source of biomarkers.


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