Evidence map›Paper›PMID 40672269›Full record

ArticlebioRxiv : the preprint server for biology2025

An Enhancement of Extrachromosomal Circular DNA Enrichment and Amplification to Address the Extremely Low Overlap Between Replicates.

Charles M Burnham, Alongkorn Kurilung, Visanu Wanchai, Birgritte Regenberg, Jesus Delgado-Calle, Alexei G Basnakian, Intawat Nookaew

Abstract readPreprint
PubMed Full text at PMC Publisher
In one paragraph

Article in bioRxiv : the preprint server for biology, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

0numbers the graph read from it
0cells of the map it votes in
0citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

0 citing papers in PubMed.

No citing paper in PubMed yet.

4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

7 authors.

Charles M BurnhamDepartment of Biomedical Informatics, College of Medicine, University of Arkansas for Medical Sciences, Little Rock, AR, USA.
Alongkorn KurilungDepartment of Biomedical Informatics, College of Medicine, University of Arkansas for Medical Sciences, Little Rock, AR, USA.
Visanu WanchaiDepartment of Biomedical Informatics, College of Medicine, University of Arkansas for Medical Sciences, Little Rock, AR, USA.
Birgritte RegenbergDepartment of Biology, University of Copenhagen, Copenhagen, Denmark.
Jesus Delgado-CalleDepartment of Physiology and Cell Biology, University of Arkansas for Medical Sciences, Little Rock, AR, USA.ORCID 0000-0002-2083-2774
Alexei G BasnakianDepartment of Pharmacology and Toxicology, College of Medicine, University of Arkansas for Medical Sciences.
Intawat NookaewDepartment of Biomedical Informatics, College of Medicine, University of Arkansas for Medical Sciences, Little Rock, AR, USA.ORCID 0000-0001-8901-1088

Funding

Understanding the Negative Prognostic Impact of Intraosseous Focal Lesions in Multiple MyelomaP20GM125503 · NIGMS · UNIV OF ARKANSAS FOR MED SCIS · PI CHARLES A O'BRIEN · 2018 to 2026
$23.0M
Bone-Targeted Therapies to Improve Bone Health and Prevent Relapse in Multiple MyelomaR37CA251763 · NCI · UNIV OF ARKANSAS FOR MED SCIS · PI DELGADO-CALLE, JESUS · 2020 to 2025
$2.6M
Systems Pharmacology and Toxicology Training ProgramT32GM106999 · NIGMS · UNIV OF ARKANSAS FOR MED SCIS · PI PRATHER, PAUL L · 2013 to 2022
$1.4M
BLRD VA I01 BX002425BLRD VA IK6 BX006184NCI NIH HHS R37 CA251763NIGMS NIH HHS P20 GM125503NIGMS NIH HHS T32 GM106999
6 · The paper itself

Abstract

Extrachromosomal circular DNA (eccDNA) of chromosomal origin is present in all eukaryotic organisms and tissues that have been tested. Populations of eccDNA exhibit immense diversity and a characteristically low degree of overlap between samples, suggesting low inheritance of eccDNA between cells or a deficiency in the methods by which eccDNA is detected. This study revisits the Circle-seq approach for enrichment of eccDNA to address these limitations, hypothesizing that experimental procedures significantly contribute to the observed low eccDNA overlap. We optimized the protocol by reducing the time needed to complete the procedure. Linear DNA is digested by increasing Exonuclease V activity. We employed CRISPR-Cas9 for mitochondrial linearization, which proved superior to using restriction enzymes. A key finding is the critical role of random hexamer primer concentration and genomic DNA input in Rolling circle amplification (RCA) for generating high-quality long amplicons from eccDNA (concatemeric tandem copy [CTC]), essential for confident

Indexed as

CRISPR-Cas9Exonuclease VExtrachromosomal circular DNA (eccDNA)Long-read sequencingOverlapPrimerRolling Circle Amplification (RCA)

Identifiers

PMID40672269
PMCPMC12265738

What OpenQuestion holds

Textmetadata
LicenceCC BY-NC-ND
Read underepoch 390

Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.