Evidence map›Paper›PMID 40164811›Full record

ArticleScientific reports2025

Comparison of nanopore with illumina whole genome assemblies of the Epstein-Barr virus in Burkitt lymphoma.

Isaac E Kim, Abebe A Fola, Enrique Puig, Titus Kipkemboi Maina, Sin Ting Hui, Hongyu Ma, Kaleb Zuckerman, Eddy O Agwati, Alec Leonetti, Rebecca Crudale and 4 more

Abstract readComparative Study
PubMed Full text at PMC Publisher
In one paragraph

Article in Scientific reports, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 3 papers.

0numbers the graph read from it
0cells of the map it votes in
3citing 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

3 citing papers in PubMed.

  1. Article
  2. Article
  3. Review
4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

14 authors.

Isaac E KimCenter for Computational Molecular Biology, Brown University, Box G-E5, Providence, 02912, RI, USA.
Abebe A FolaCenter for Computational Molecular Biology, Brown University, Box G-E5, Providence, 02912, RI, USA.
Enrique PuigCenter for Computational Molecular Biology, Brown University, Box G-E5, Providence, 02912, RI, USA.
Titus Kipkemboi MainaDepartment of Pathology and Laboratory Medicine, Brown University, Providence, RI, USA.
Sin Ting HuiDepartment of Pathology and Laboratory Medicine, Brown University, Providence, RI, USA.
Hongyu MaDepartment of Pathology and Laboratory Medicine, Brown University, Providence, RI, USA.
Kaleb ZuckermanCenter for Computational Molecular Biology, Brown University, Box G-E5, Providence, 02912, RI, USA.
Eddy O AgwatiDepartment of Zoology, Maseno University, Maseno, Kenya.
Alec LeonettiDepartment of Pathology and Laboratory Medicine, Brown University, Providence, RI, USA.
Rebecca CrudaleDepartment of Pathology and Laboratory Medicine, Brown University, Providence, RI, USA.
Micah A LuftigDepartment of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC, USA.
Ann M MoormannDivision of Infectious Diseases and Immunology, Department of Medicine, University of Massachusetts Chan Medical School, Worcester, MA, USA.
Cliff OduorDepartment of Pathology and Laboratory Medicine, Brown University, Providence, RI, USA.
Jeffrey A BaileyCenter for Computational Molecular Biology, Brown University, Box G-E5, Providence, 02912, RI, USA. jeffrey_bailey@brown.edu.

Funding

Impact of malaria on shaping immunity to EBV in the etiology of Burkitt lymphomaR01CA189806 · NCI · UNIV OF MASSACHUSETTS MED SCH WORCESTER · PI MOORMANN, ANN M · 2014 to 2024
$5.7M
Blavatnik Family Foundation Brown University Blavatnik Family Graduate Fellowship in Biology and MedicineNCI NIH HHS R01 CA189806NIH HHS R01 CA189806
6 · The paper itself

Abstract

Endemic Burkitt lymphoma (eBL) is one of the most prevalent cancer in children in sub-Saharan Africa, and while prior studies have found that Epstein-Barr virus (EBV) type and variation may alter the tumor driver genes necessary for tumor survival, the precise relationship between EBV variation and EBV-associated tumorigenesis remains unclear due to lack of scalable, cost-effective, viral whole-genome sequencing from tumor samples. This study introduces a rapid and cost-effective method of enriching, sequencing, and assembling accurate EBV genomes in BL tumor cell lines through a combination of selective whole genome amplification (sWGA) and subsequent 2-tube multiplex polymerase chain reaction along with long-read sequencing with a portable sequencer. The method was optimized across a range of parameters to yield a high percentage of EBV reads and sufficient coverage across the EBV genome except for large repeat regions. After optimization, we applied our method to sequence 18 cell lines and 3 patient tumors from fine needle biopsies and assembled them with median coverages of 99.62 and 99.68%, respectively. The assemblies showed high concordance (99.61% similarity) to available Illumina-based assemblies. The improved method and assembly pipeline will allow for better understanding of EBV variation in relation to BL and is applicable more broadly for translational research studies, especially useful for laboratories in Africa where eBL is most widespread.

Indexed as

Burkitt LymphomaEpstein-Barr Virus InfectionsGenome, ViralHerpesvirus 4, HumanNanoporesWhole Genome SequencingCell Line, TumorHigh-Throughput Nucleotide SequencingHumansNanopore SequencingBurkitt lymphomaEpstein-Barr virusLong-read sequencingOxford nanopore technologiesSelective whole genome amplification

Identifiers

PMID40164811
PMCPMC11958722

What OpenQuestion holds

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LicenceCC BY
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Registered trials

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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.