Evidence map›Paper›PMID 37503289›Full record

ArticleResearch square2023

Multi-Faceted Attributes of Salivary Cell-free DNA as Liquid Biopsy Biomarkers for Gastric Cancer Detection.

Neeti Swarup, Jordan Cheng, Irene Choi, You Jeong Heo, Misagh Kordi, Feng Li, Mohammad Aziz, David Chia, Fang Wei, David Elashoff and 4 more

Open access · greenAbstract readPreprint
PubMed Full text at PMC Publisher
In one paragraph

Article in Research square, 2023. 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, 1 citations in OpenAlex.

No citing paper in PubMed yet.

4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

14 authors at 2 institutions in 3 countries.

Neeti SwarupSchool of Dentistry, University of California, Los Angeles, Los Angeles, CA, 90095, USA.
Jordan ChengSchool of Dentistry, University of California, Los Angeles, Los Angeles, CA, 90095, USA.
Irene ChoiSchool of Dentistry, University of California, Los Angeles, Los Angeles, CA, 90095, USA.
You Jeong HeoThe Samsung Advanced Institute for Health Sciences & Technology (SAIHST), Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul 06355, Republic of Korea.
Misagh KordiSchool of Dentistry, University of California, Los Angeles, Los Angeles, CA, 90095, USA.
Feng LiSchool of Dentistry, University of California, Los Angeles, Los Angeles, CA, 90095, USA.
Mohammad AzizSchool of Dentistry, University of California, Los Angeles, Los Angeles, CA, 90095, USA.
David ChiaDepartment of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, 90095, USA.
Fang WeiSchool of Dentistry, University of California, Los Angeles, Los Angeles, CA, 90095, USA.
David ElashoffDepartment of Medicine, Biostatistics and Computational Medicine, University of California Los Angeles, Los Angeles, CA, 90095, USA.
Liying ZhangDepartment of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, 90095, USA.
Sung KimDepartment of Surgery, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul 06355, South Korea.
Yong KimSchool of Dentistry, University of California, Los Angeles, Los Angeles, CA, 90095, USA.
David T W WongSchool of Dentistry, University of California, Los Angeles, Los Angeles, CA, 90095, USA.
University of California, Los Angeles · USSamsung Medical Center · KR

Funding

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
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
Local and Systemic Multi-Omics of TMJ DisordersUH2DE032208 · NIDCR · UNIVERSITY OF CALIFORNIA LOS ANGELES · PI ARONOVICH, SHARON, BHUTANI, NIDHI · 2022 to 2022
$420k
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
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
NCI NIH HHS F99 CA264398NCI NIH HHS K00 CA264398NCI NIH HHS R21 CA239052NCI NIH HHS U01 CA233370NCI NIH HHS UH3 CA206126NIDCR NIH HHS R90 DE031531NIDCR NIH HHS UH2 DE032208
6 · The paper itself

Abstract

Background: Recent advances in circulating cell-free DNA (cfDNA) analysis from biofluids have opened new avenues for liquid biopsy (LB). However, current cfDNA LB assays are limited by the availability of existing information on established genotypes associated with tumor tissues. Certain cancers present with a limited list of established mutated cfDNA biomarkers, and thus, nonmutated cfDNA characteristics along with alternative biofluids are needed to broaden the available cfDNA targets for cancer detection. Saliva is an intriguing and accessible biofluid that has yet to be fully explored for its clinical utility for cancer detection. Methods: In this report, we employed a low-coverage single stranded (ss) library NGS pipeline "Broad-Range cell-free DNA-Seq" (BRcfDNA-Seq) using saliva to comprehensively investigate the characteristics of salivary cfDNA (ScfDNA). The identification of cfDNA features has been made possible by applying novel cfDNA processing techniques that permit the incorporation of ultrashort, ss, and jagged DNA fragments. As a proof of concept using 10 gastric cancer (GC) and 10 noncancer samples, we examined whether ScfDNA characteristics, including fragmentomics, end motif profiles, microbial contribution, and human chromosomal mapping, could differentiate between these two groups. Results: Individual and integrative analysis of these ScfDNA features demonstrated significant differences between the two cohorts, suggesting that disease state may affect the ScfDNA population by altering nuclear cleavage or the profile of contributory organism cfDNA to total ScfDNA. We report that principal component analysis integration of several aspects of salivary cell-free DNA fragmentomic profiles, genomic element profiles, end-motif sequence patterns, and distinct oral microbiome populations can differentiate the two populations with a p value of < 0.0001 (PC1). Conclusion: These novel features of ScfDNA characteristics could be clinically useful for improving saliva-based LB detection and the eventual monitoring of local or systemic diseases.

Indexed as

Cell-free DNAFragmentomicsLiquid BiopsySalivary Cell-free DNA

Identifiers

PMID37503289
PMCPMC10371094
OpenAlexW4384301286

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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.