2015
DOI: 10.1186/1471-2164-16-s13-s1
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Non-random fragmentation patterns in circulating cell-free DNA reflect epigenetic regulation

Abstract: BackgroundThe assessment of cell-free circulating DNA fragments, also known as a "liquid biopsy" of the patient's plasma, is an important source for the discovery and subsequent non-invasive monitoring of cancer and other pathological conditions. Although the nucleosome-guided fragmentation patterns of cell-free DNA (cfDNA) have not yet been studied in detail, non-random representation of cfDNA sequencies may reflect chromatin features in the tissue of origin at gene-regulation level.ResultsIn this study, we i… Show more

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Cited by 160 publications
(147 citation statements)
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“…2C, inset); the GC content of the super-100 bp group was 40.9%, while that of the sub-100 bp group was 43.5%. We hypothesized that the sub-100 bp nuclear cfDNA may be derived from coding regions of genes, which are known to be GC-rich (Vinogradov 2003; Ivanov et al 2015). These observations indicate that a considerable amount of nuclear genomic cfDNA is not nucleosome protected and, thus, subject to degradation by nucleases in the blood.…”
Section: Resultsmentioning
confidence: 99%
“…2C, inset); the GC content of the super-100 bp group was 40.9%, while that of the sub-100 bp group was 43.5%. We hypothesized that the sub-100 bp nuclear cfDNA may be derived from coding regions of genes, which are known to be GC-rich (Vinogradov 2003; Ivanov et al 2015). These observations indicate that a considerable amount of nuclear genomic cfDNA is not nucleosome protected and, thus, subject to degradation by nucleases in the blood.…”
Section: Resultsmentioning
confidence: 99%
“…More recent studies illustrate how NSG mice grafted with HLA mismatched patient AML cells and healthy human control hematopoietic cells can further refine the study of BM interactions . Moreover, the PDX model allows for the development of translational biomarker platforms where peripheral blood can be analyzed to track cancer‐specific signatures such as cell‐free DNA , or miRNA contained in exosomes . While PDX models provide useful in vivo context, insufficient or heterotopic engraftment has proven to be a significant barrier.…”
Section: Prospective Modeling Of Leukemia In Murine Modelsmentioning
confidence: 99%
“…Several approaches have been used to investigate this question, including i) identification of tissue-specific patterns of promoter methylation; [52][53][54][55] ii) analysis of tissue-specific modifications in circulating nucleosomes, per se; 18,19 and iii) identification of tissue-specific DNA fragmentation patterns or nucleosome occupancy. 53,56,57 In cancer, all these approaches could aid in defining the cfDNA tissue of origin without requiring a preliminary search for genetic differences. 27 It can be postulated that circulating tumor cells are not the main source of cfDNA.…”
Section: Introductionmentioning
confidence: 99%