Advances in sequencing-based studies of microDNA and ecDNA: Databases, identification methods, and integration with single-cell analysis

Yang, Manqiu; Zhang, Shufan; Huang, Moli

doi:10.1016/j.csbj.2023.05.017

Cited by 7 publications

(6 citation statements)

References 65 publications

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“…Although there are inconsistencies in the definitions of ecDNA and eccDNA used by various studies [ 12 , 22 , 43 ], it does not affect the results obtained from eccDNA-pipe. In general, we take those eccDNAs obtained from AA with length >10 kb as ecDNAs.…”

Section: Discussionmentioning

confidence: 99%

eccDNA-pipe: an integrated pipeline for identification, analysis and visualization of extrachromosomal circular DNA from high-throughput sequencing data

Fang,

Luo

et al. 2024

Briefings in Bioinformatics

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Extrachromosomal circular DNA (eccDNA) is currently attracting considerable attention from researchers due to its significant impact on tumor biogenesis. High-throughput sequencing (HTS) methods for eccDNA identification are continually evolving. However, an efficient pipeline for the integrative and comprehensive analysis of eccDNA obtained from HTS data is still lacking. Here, we introduce eccDNA-pipe, an accessible software package that offers a user-friendly pipeline for conducting eccDNA analysis starting from raw sequencing data. This dataset includes data from various sequencing techniques such as whole-genome sequencing (WGS), Circle-seq and Circulome-seq, obtained through short-read sequencing or long-read sequencing. eccDNA-pipe presents a comprehensive solution for both upstream and downstream analysis, encompassing quality control and eccDNA identification in upstream analysis and downstream tasks such as eccDNA length distribution analysis, differential analysis of genes enriched with eccDNA and visualization of eccDNA structures. Notably, eccDNA-pipe automatically generates high-quality publication-ready plots. In summary, eccDNA-pipe provides a comprehensive and user-friendly pipeline for customized analysis of eccDNA research.

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Section: Discussionmentioning

confidence: 99%

eccDNA-pipe: an integrated pipeline for identification, analysis and visualization of extrachromosomal circular DNA from high-throughput sequencing data

Fang,

Luo

et al. 2024

Briefings in Bioinformatics

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“…We defined ecDNA as eccDNA colocalizing with genome copy number-amplified regions 11 , due to the putative gene amplification effect of ecDNA. Other studies may use size thresholds to define ecDNA 23,24 . Establishing a consensus definition is crucial for harmonizing research findings in this rapidly evolving field.…”

Section: Discussionmentioning

confidence: 99%

Comparative analysis of methodologies for detecting extrachromosomal circular DNA

Gao,

Liu,

Luo

et al. 2023

Preprint

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Extrachromosomal circular DNA (eccDNA) is crucial in oncogene amplification, gene transcription regulation, and intratumor heterogeneity. While various analysis pipelines and experimental methods have been developed for eccDNA identification, their detection efficiencies have not been systematically assessed. To address this, we evaluated the performance of 7 analysis pipelines using three simulated datasets, in terms of accuracy, similarity, duplication rate, and computational resource consumption. We also compared the eccDNA detection efficiency of 7 experimental methods through twenty-one real sequencing datasets. Our results identified Circle-Map and CReSIL as the most effective pipelines for eccDNA detection through short-read and long-read sequencing data, respectively. Moreover, third-generation sequencing-based Circle-Seq showed superior efficiency in detecting copy number-amplified eccDNA over 10 kb in length. These results offer valuable insights for researchers in choosing the most suitable methods for eccDNA research.

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“…According to a number of recent studies, microDNAs can express functional small regulatory RNAs, including micro RNAs (miRNAs) and novel si-like RNAs, to influence gene expression ( Paulsen et al, 2021 ; Yang et al, 2022 ). Furthermore, the discovery that tumor cells can release microDNAs into the bloodstream, and the differences and dynamic changes of microDNAs in tumor tissues versus normal tissues, as well as in the same tissues of patients before and after surgery ( Zhao et al, 2022 ; Jiang et al, 2023 ), suggest that microDNAs have the potential to be used as a non-invasive biomarker to monitor tumor progression and therapeutic efficacy ( Kumar et al, 2017 ; Zhu et al, 2018 ). Smalheiser suggested that microDNA, which is mobile and stable circular DNA, might have a role in regulating memory and communication in CNS neurons ( Smalheiser, 2023 ).…”

Section: Characteristics and Diverse Capabilities Of Eccdnamentioning

confidence: 99%

“…In Deshpande’s benchmarking, AA had an error rate of <11% ( Deshpande et al, 2019 ). However, for complex amplicons like BFBs, AA may fail to capture their fine structures, leaving various possible reconstruction options ( Jiang et al, 2023 ). As a result, Luebeck’s team developed the AmpliconReconstructor (AR) ( Luebeck et al, 2020 ), based on AmpliconArchitect, which enables OM of large fragments (>150 kb) using NGS to resolve eccDNA at single-nucleotide resolution.…”

Section: Computational Identification and Prediction For Eccdnamentioning

confidence: 99%

Characterization, biogenesis model, and current bioinformatics of human extrachromosomal circular DNA

Zhou,

Tang,

et al. 2024

Front. Genet.

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Human extrachromosomal circular DNA, or eccDNA, has been the topic of extensive investigation in the last decade due to its prominent regulatory role in the development of disorders including cancer. With the rapid advancement of experimental, sequencing and computational technology, millions of eccDNA records are now accessible. Unfortunately, the literature and databases only provide snippets of this information, preventing us from fully understanding eccDNAs. Researchers frequently struggle with the process of selecting algorithms and tools to examine eccDNAs of interest. To explain the underlying formation mechanisms of the five basic classes of eccDNAs, we categorized their characteristics and functions and summarized eight biogenesis theories. Most significantly, we created a clear procedure to help in the selection of suitable techniques and tools and thoroughly examined the most recent experimental and bioinformatics methodologies and data resources for identifying, measuring and analyzing eccDNA sequences. In conclusion, we highlighted the current obstacles and prospective paths for eccDNA research, specifically discussing their probable uses in molecular diagnostics and clinical prediction, with an emphasis on the potential contribution of novel computational strategies.

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Advances in sequencing-based studies of microDNA and ecDNA: Databases, identification methods, and integration with single-cell analysis

Cited by 7 publications

References 65 publications

eccDNA-pipe: an integrated pipeline for identification, analysis and visualization of extrachromosomal circular DNA from high-throughput sequencing data

eccDNA-pipe: an integrated pipeline for identification, analysis and visualization of extrachromosomal circular DNA from high-throughput sequencing data

Comparative analysis of methodologies for detecting extrachromosomal circular DNA

Characterization, biogenesis model, and current bioinformatics of human extrachromosomal circular DNA

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