eccDNA Sequencing for Biomarker Discovery and Cancer Research
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| Extrachromosomal circular DNA (eccDNA) is a class of double-stranded circular DNA molecules present outside of regular chromosomal DNA, functionally regulating diverse molecular and physiological processes (Fig 1). According to the lengths, eccDNA can be classified into two main categories : eccDNA(<10 kb) and ecDNA(>=10 kb)[1]. |
eccDNA:
Superior biomarker potential, owing to their many desired characteristics, e.g. long, circular, and strong resistant to exonuclease digestion[2].
ecDNA:
Major breakthroughs and research hotspots in recent cancer research, owing to their harboring oncogenes, drug resistance genes or mobile super-enhancers to provide an evolutionary advantage for cancers[2-6].
Arraystar has developed eccDNA sequencing with maximal eccDNA enrichment. The service not only dramatically increases eccDNA reads, but also provides a broad coverage, which simultaneously profiles both of eccDNA and ecDNA. Meanwhile, the data analysis part of the service provides rich annotation, genome browser track visualization, publication-ready graphics for biologists and clinicians.
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Fig.1 eccDNAs regulate diverse molecular and physiological processes.
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References
[1] Hung, K. L., et al. (2022) "Gene regulation on extrachromosomal DNA" Nat Struct Mol Biol 29(8):736-744 [PMID: 35948767]
[2] Yang, L., et al. (2022) "Extrachromosomal circular DNA: biogenesis, structure, functions and diseases" Signal Transduct Target Ther 7(1):342 [PMID: 36184613]
[3] Noorani, I., et al. (2022) "Leveraging extrachromosomal DNA to fine-tune trials of targeted therapy for glioblastoma: opportunities and challenges" Nat Rev Clin Oncol 19(11):733-743 [PMID: 36131011]
[4] Nathanson, D. A., et al. (2014) "Targeted therapy resistance mediated by dynamic regulation of extrachromosomal mutant EGFR DNA" Science 343(6166):72-6 [PMID: 24310612]
[5] Zhao, Y., et al. (2022) "Extrachromosomal circular DNA: Current status and future prospects" Elife 11([PMID: 36256570]
[6] Zhu, Y., et al. (2021) "Oncogenic extrachromosomal DNA functions as mobile enhancers to globally amplify chromosomal transcription" Cancer Cell 39(5):694-707 e7 [PMID: 33836152]
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Selected Publications
• Epitranscriptomic Array
[PMID: 38355624]
Xiong YW, et al.
(2024) Nature Communications
• Small RNA Modification Array
[PMID: 38747146]
Zhang J, et al.
(2024) Circulation Research
• Circular RNA Array
[PMID: 39695693]
Hu Y, et al.
(2024) Molecular Cancer
• tRNA Sequencing
[PMID: 38519786]
Wu X, et al.
(2024) Nature Cancer
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