Evidence map›Paper›PMID 37725931›Full record

ArticleClinical chemistry2023

Distinct Features of Plasma Ultrashort Single-Stranded Cell-Free DNA as Biomarkers for Lung Cancer Detection.

Jordan Cheng, Neeti Swarup, Feng Li, Misagh Kordi, Chien-Chung Lin, Szu-Chun Yang, Wei-Lun Huang, Mohammad Aziz, Yong Kim, David Chia and 7 more

Open access · bronzeAbstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Clinical chemistry, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 papers.

0numbers the graph read from it
0cells of the map it votes in
9citing papers in PubMed
2.4field-weighted citation impact, top 11% of its field
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

9 citing papers in PubMed, 10 citations in OpenAlex.

  1. Article
  2. Article
  3. Review
  4. Article
  5. Article
  6. Review
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  8. Review
  9. Ultrashort plasma cell-free DNA: a novel non-invasive marker for cancer diagnostics.American journal of clinical and experimental immunology · 2024
    Article
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

17 authors at 3 institutions in 2 countries.

Jordan ChengSchool of Dentistry, University of California, Los Angeles, Los Angeles, CA, United States.ORCID 0000-0001-5352-4017
Neeti SwarupSchool of Dentistry, University of California, Los Angeles, Los Angeles, CA, United States.
Feng LiSchool of Dentistry, University of California, Los Angeles, Los Angeles, CA, United States.
Misagh KordiSchool of Dentistry, University of California, Los Angeles, Los Angeles, CA, United States.
Chien-Chung LinDepartment of Internal Medicine, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, Taiwan.
Szu-Chun YangDepartment of Internal Medicine, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, Taiwan.
Wei-Lun HuangCenter of Applied Nanomedicine, National Cheng Kung University, Tainan, Taiwan.
Mohammad AzizSchool of Dentistry, University of California, Los Angeles, Los Angeles, CA, United States.
Yong KimSchool of Dentistry, University of California, Los Angeles, Los Angeles, CA, United States.
David ChiaDepartment of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, United States.
Yu-Min YehCenter of Applied Nanomedicine, National Cheng Kung University, Tainan, Taiwan.
Fang WeiSchool of Dentistry, University of California, Los Angeles, Los Angeles, CA, United States.
David ZhengDepartment of Molecular, Cell and Developmental Biology, Life Sciences Division, University of California, Los Angeles, Los Angeles, CA, United States.ORCID 0000-0003-1161-6444
Liying ZhangDepartment of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, United States.ORCID 0000-0003-4517-0751
Matteo PellegriniDepartment of Molecular, Cell and Developmental Biology, Life Sciences Division, University of California, Los Angeles, Los Angeles, CA, United States.
Wu-Chou SuCenter of Applied Nanomedicine, National Cheng Kung University, Tainan, Taiwan.
David T W WongSchool of Dentistry, University of California, Los Angeles, Los Angeles, CA, United States.
University of California, Los Angeles · USNational Cheng Kung University Hospital · TWNational Cheng Kung University · TW

Funding

UCLA Clinical Translational Science InstituteUL1TR001881 · NCATS · UNIVERSITY OF CALIFORNIA LOS ANGELES · PI ARLEEN F. BROWN, ARASH NAEIM · 2016 to 2026
$118.1M
UCLA SPORE in Brain CancerP50CA211015 · NCI · UNIVERSITY OF CALIFORNIA LOS ANGELES · PI Robert M Prins · 2017 to 2026
$25.2M
EFIRM Liquid Biopsy Research Laboratory: Early Lung Cancer AssessmentU01CA233370 · NCI · UNIVERSITY OF CALIFORNIA LOS ANGELES · PI ABERLE, DENISE R., HSU, WILLIAM · 2018 to 2025
$8.0M
UCLA Dentist-Scientist and Oral Health-Researcher Training ProgramT90DE030860 · NIDCR · UNIVERSITY OF CALIFORNIA LOS ANGELES · PI TON-THAT, HUNG, WONG, DAVID T · 2021 to 2025
$2.1M
Advancing EFIRM-Liquid Biopsy (eLB) to a CLIA-Certified Laboratory Developed Test (eLB-LDT) for Detection of Actionable EGFR Mutations in NSCLC PatientsUH3CA206126 · NCI · UNIVERSITY OF CALIFORNIA LOS ANGELES · PI CHIA, DAVID S., SOO HOO, GUY · 2019 to 2021
$1.2M
UCLA Dentist-Scientist and Oral Health-Researcher Training ProgramR90DE031531 · NIDCR · UNIVERSITY OF CALIFORNIA LOS ANGELES · PI TON-THAT, HUNG, WONG, DAVID T · 2021 to 2025
$858k
Novel ultra-short cell free DNA biomarkers for early detection of non-small cell lung cancer.R21CA283665 · NCI · UNIVERSITY OF CALIFORNIA LOS ANGELES · PI LI, FENG, WONG, DAVID T · 2023 to 2024
$393k
Cell-free DNA Analysis for Liquid Biopsy of CancerK00CA264398 · NCI · STANFORD UNIVERSITY · PI Jordan C Cheng · 2023 to 2026
$389k
Ultra-short circulating tumor DNA (uctDNA) for liquid biopsy of non-small cell lung cancerR21CA239052 · NCI · UNIVERSITY OF CALIFORNIA LOS ANGELES · PI LI, FENG, WONG, DAVID T · 2019 to 2020
$373k
Advancing EFIRM-Liquid Biopsy (eLB) to a CLIA-Certified Laboratory Developed Test (eLB-LDT) for Detection of Actionable EGFR Mutations in NSCLC PatientsUH2CA206126 · NCI · UNIVERSITY OF CALIFORNIA LOS ANGELES · PI CHIA, DAVID S., DAS, KINGSHUK · 2017 to 2018
$368k
Predoctoral to Postdoctoral Research Training in ctDNA Biology for Liquid Biopsy of CancerF99CA264398 · NCI · UNIVERSITY OF CALIFORNIA LOS ANGELES · PI CHENG, JORDAN C · 2021 to 2022
$83k
NCATS NIH HHS UL1 TR001881NCI NIH HHS F99 CA264398NCI NIH HHS F99CA26498-02NCI NIH HHS K00 CA264398NCI NIH HHS P50 CA211015NCI NIH HHS R21 CA239052NCI NIH HHS R21 CA283665NCI NIH HHS U01 CA233370NCI NIH HHS UH2 CA206126NCI NIH HHS UH3 CA206126NIDCR NIH HHS R90 DE031531NIDCR NIH HHS T90 DE030860NIH HHS UH2/UH3 CA206126
6 · The paper itself

Abstract

backgroundUsing broad range cell-free DNA sequencing (BRcfDNA-Seq), a nontargeted next-generation sequencing (NGS) methodology, we previously identified a novel class of approximately 50 nt ultrashort single-stranded cell-free DNA (uscfDNA) in plasma that is distinctly different from 167 bp mononucleosomal cell-free DNA (mncfDNA). We hypothesize that uscfDNA possesses characteristics that are useful for disease detection.

methodsUsing BRcfDNA-Seq, we examined both cfDNA populations in the plasma of 18 noncancer controls and 14 patients with late-stage nonsmall cell lung carcinoma (NSCLC). In comparison to mncfDNA, we assessed whether functional element (FE) peaks, fragmentomics, end-motifs, and G-Quadruplex (G-Quad) signatures could be useful features of uscfDNA for NSCLC determination.

resultsIn noncancer participants, compared to mncfDNA, uscfDNA fragments showed a 45.2-fold increased tendency to form FE peaks (enriched in promoter, intronic, and exonic regions), demonstrated a distinct end-motif-frequency profile, and presented with a 4.9-fold increase in G-Quad signatures. Within NSCLC participants, only the uscfDNA population had discoverable FE peak candidates. Additionally, uscfDNA showcased different end-motif-frequency candidates distinct from mncfDNA. Although both cfDNA populations showed increased fragmentation in NSCLC, the G-Quad signatures were more discriminatory in uscfDNA. Compilation of cfDNA features using principal component analysis revealed that the first 5 principal components of both cfDNA subtypes had a cumulative explained variance of >80%.

conclusionsThese observations indicate that the distinct biological processes of uscfDNA and that FE peaks, fragmentomics, end-motifs, and G-Quad signatures are uscfDNA features with promising biomarker potential. These findings further justify its exploration as a distinct class of biomarker to augment pre-existing liquid biopsy approaches.

Indexed as

Carcinoma, Non-Small-Cell LungCell-Free Nucleic AcidsLung NeoplasmsBiomarkers, TumorDNA, Single-StrandedHumansLungBiomarkers, TumorCell-Free Nucleic AcidsDNA, Single-Stranded

Identifiers

PMID37725931
PMCPMC10644908
OpenAlexW4386864910

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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.