Circle-Seq-based eccDNA Identification

Introduction Services Highlights Samples Q&As Resource

Creative Biolabs has organized a staff of outstanding scientists who are proficient in providing high-quality next generation sequencing (NGS) solutions for cancer research. We provide comprehensive circle-seq services from sample preparation to reliable data delivery to help global customers to analyze and identify novel eccDNAs in tumor cells, facilitating cancer marker identification and tumorigenesis research.

Introduction of eccDNA

eccDNAs (extrachromosomal circular DNA elements) refer to extrachromosomal circular DNA that is widely present in eukaryotic cells including humans. eccDNAs are usually released or shed from the normal genome and free from the chromosomal genome. The whole genome sequence analysis of eccDNA from yeast, nematodes, ciliates and mammals found that the size of eccDNA ranges from dozens of bases to hundreds of thousands of base pairs. eccDNAs not only carry complete or partial genes, but also harbor intergenic sequences, and part of it contains the initiation point of replication, which can complete replication independently. In many human tumor cells, a large amount of extrachromosomal circular DNAs have been detected. Recently, a study reported the major oncogene transcripts were directly derived from eccDNAs. The eccDNA chromatin is highly open and can express large amounts of oncogenes. At the same time, it lacks centromeres and cannot follow Mendelian laws of inheritance. This feature makes eccDNA an important mechanism for driving tumor heterogeneity. Thus it can be seen eccDNA can not only be used as a novel and specific tumor marker, but also play a significant potential value in the study of the mechanism of tumor occurrence and development. It is foreseeable that eccDNA will quickly become a new research hotspot, and will even bring a revolutionary impact on traditional genetics and genomics.

Fig.1 ecDNA drives high levels of RNA expression. (Wu, 2019)

Our Capacibility

Creative Biolabs’ eccDNA sequencing service (also known as Circle-seq, circular DNA sequencing) uses a variety of methods to efficiently enrich and amplify eccDNA, which greatly improves the detection rate of eccDNA. After enrichment, NGS sequencing is used to detect all eccDNA molecules in the cell with high throughput. And through the rigorous eccDNA bioinformatics analysis process, accurate identification of eccDNA and detailed gene annotation are realized.

Fig.2 Workflow of eccDNA sequencing.

Highlights

One-stop service: we provide the entire service process of eccDNA enrichment, library preparation, Circle-seq to data analysis for you.

High detection rate of eccDNA: a variety of powerful methods are used to efficiently enrich and detect eccDNA.

Professional bioinformatics analysis: our professional bioinformatics team has developed an algorithm for high-efficiency identification and analysis of eccDNA to meet various in-depth data analysis needs of customers.

Sample Requirement

Sample Type

Cells, tissues, genomic DNA. Please inquire for other types of samples.

Sample size

Cell: ~2×10⁷
Tissue: ~100 mg
DNA: ≥10 µg, dissolved in sterile water or TE (pH=8); OD 260/280=1.7~2.0; RNA should be removed and no other individuals or DNA contamination of other species.

Sample transportation and storage

The sample should be place in a 1.5mL Eppendorf tube, sealed with a parafilm, and transported on dry ice. DNA can be transported in an ice bag.

Cell samples or fresh tissue pieces were cut and frozen in liquid nitrogen at -80℃. DNA samples can be -20℃ in a short period of time to avoid repeated freezing and thawing.

If you are interested in our services, please feel free to contact us for more details.

Q&As

Q: How does Circle-Seq enhance the detection of low-abundance eccDNA?

A: Circle-Seq employs specialized enrichment techniques to isolate and amplify low-abundance eccDNA molecules. This enhances the sensitivity of detection, allowing researchers to identify rare eccDNA elements that may play critical roles in disease mechanisms and drug resistance.

Q: How does Circle-Seq contribute to the study of genomic instability?

A: Circle-Seq can detect eccDNA, which is often associated with genomic instability in cancer cells. By analyzing these elements, researchers can understand how genomic instability contributes to cancer progression and identify potential therapeutic targets to stabilize the genome.

Q: What role does Circle-Seq play in studying gene amplification?

A: Circle-Seq identifies eccDNA that often contains amplified oncogenes or drug resistance genes. Studying these amplified genes helps researchers understand the mechanisms of gene amplification in cancers and develop therapies that specifically target these amplified regions.

Q: What are the challenges in Circle-Seq-based eccDNA Identification?

A: Challenges include the efficient enrichment and isolation of eccDNA, managing large volumes of sequencing data, and accurately mapping circular DNA elements back to the genome. Advanced bioinformatics tools are essential to overcome these challenges and provide precise identification and characterization of eccDNA.

Q: How does Circle-Seq improve the understanding of cancer mechanisms?

A: Circle-Seq allows for the detection of eccDNA, which often harbors oncogenes and drug resistance genes. By analyzing these circular DNA elements, researchers can gain insights into the mechanisms driving cancer progression and resistance, leading to better-targeted therapies.

Reference

Wu, S.; et al. Circular ecDNA promotes accessible chromatin and high oncogene expression. Nature. 2019, 575(6): 1330-1341

Introduction of NGS

A brief introduction of NGS related information.

Learn More