Evidence map›Paper›PMID 38877540›Full record

ArticleGenome biology2024

LABS: linear amplification-based bisulfite sequencing for ultrasensitive cancer detection from cell-free DNA.

Xiao-Long Cui, Ji Nie, Houxiang Zhu, Krissana Kowitwanich, Alana V Beadell, Diana C West-Szymanski, Zhou Zhang, Urszula Dougherty, Akushika Kwesi, Zifeng Deng and 19 more

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Genome biology, 2024. 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
–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

9 citing papers in PubMed.

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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

29 authors.

Xiao-Long Cui *Department of Chemistry, Department of Biochemistry and Molecular Biology, Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL, USA.
Ji Nie *Department of Chemistry, Department of Biochemistry and Molecular Biology, Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL, USA.
Houxiang Zhu *Department of Medicine, The University of Chicago, Chicago, IL, USA.
Krissana KowitwanichDepartment of Chemistry, Department of Biochemistry and Molecular Biology, Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL, USA.
Alana V BeadellDepartment of Chemistry, Department of Biochemistry and Molecular Biology, Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL, USA.
Diana C West-SzymanskiDepartment of Chemistry, Department of Biochemistry and Molecular Biology, Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL, USA.
Zhou ZhangDepartment of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA.
Urszula DoughertyDepartment of Medicine, The University of Chicago, Chicago, IL, USA.
Akushika KwesiDepartment of Medicine, The University of Chicago, Chicago, IL, USA.
Zifeng DengDepartment of Medicine, The University of Chicago, Chicago, IL, USA.
Yan LiDepartment of Medicine, The University of Chicago, Chicago, IL, USA.
Danqing MengDepartment of Molecular Biosciences, Northwestern University, Evanston, IL, USA.
Kevin RogginDepartment of Surgery, The University of Chicago, Chicago, IL, USA.
Teresa BarryDepartment of Medicine, The University of Chicago, Chicago, IL, USA.
Ryan OwyangDepartment of Chemistry, Department of Biochemistry and Molecular Biology, Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL, USA.
Ben FeffermanDepartment of Chemistry, Department of Biochemistry and Molecular Biology, Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL, USA.
Chang ZengDepartment of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA.
Lu GaoDepartment of Chemistry, Department of Biochemistry and Molecular Biology, Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL, USA.
Carolyn W T ZhaoDepartment of Chemistry, Department of Biochemistry and Molecular Biology, Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL, USA.
Yuri MalinaDepartment of Chemistry, Department of Biochemistry and Molecular Biology, Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL, USA.
Jiangbo WeiDepartment of Chemistry, Department of Biochemistry and Molecular Biology, Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL, USA.
Melanie WeigertDepartment of Obstetrics and Gynecology/Section of Gynecologic Oncology, The University of Chicago, Chicago, IL, USA.
Wenjun KangDepartment of Medicine, The University of Chicago, Chicago, IL, USA.
Ajay GoelCity of Hope Comprehensive Cancer Center, Duarte, CA, USA.
Brian C-H ChiuDepartment of Public Health Sciences, The University of Chicago, Chicago, IL, USA.
Marc BissonnetteDepartment of Medicine, The University of Chicago, Chicago, IL, USA.
Wei Zhang *Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA. wei.zhang1@northwestern.edu.
Mengjie Chen *Department of Medicine, The University of Chicago, Chicago, IL, USA. mengjiechen@uchicago.edu.
Chuan He *Department of Chemistry, Department of Biochemistry and Molecular Biology, Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL, USA. chuanhe@uchicago.edu.

Funding

Labeling and sequencing of 5hmC and 5mC in DNA-RenewalR01HG006827 · NHGRI · UNIVERSITY OF CHICAGO · PI HE, CHUAN · 2012 to 2025
$7.2M
Development of 5hmC and 5mC biomarkers in cell-free circulating DNA for sensitive colon cancer detection and prognosisU01CA217078 · NCI · UNIVERSITY OF CHICAGO · PI BISSONNETTE, BRUCE MARC, ZHANG, WEI · 2017 to 2021
$3.2M
New directions in single cell genomics method developmentR01GM126553 · NIGMS · UNIVERSITY OF CHICAGO · PI Mengjie Chen · 2017 to 2026
$2.9M
Develop new bioinformatics infrastructures and computational tools for epitranscriptomics dataR01HG012927 · NHGRI · UNIVERSITY OF CHICAGO · PI Mengjie Chen · 2023 to 2026
$1.6M
Developing new computational tools for spatial transcriptomics dataR01HG011883 · NHGRI · UNIVERSITY OF CHICAGO · PI CHEN, MENGJIE, ZHOU, XIANG · 2021 to 2024
$1.5M
A highly sensitive linear amplification based DNA methylation profiling technique for clinical cancer researchR33CA269100 · NCI · UNIVERSITY OF CHICAGO · PI CHIU, BRIAN C-H, ZHANG, WEI · 2022 to 2024
$1.2M
NCI NIH HHS R33 CA269100NCI NIH HHS U01 CA217078NHGRI NIH HHS R01 HG006827NHGRI NIH HHS R01 HG011883NHGRI NIH HHS R01 HG012927NIGMS NIH HHS R01 GM126553
6 · The paper itself

Abstract

Methylation-based liquid biopsies show promises in detecting cancer using circulating cell-free DNA; however, current limitations impede clinical application. Most assays necessitate substantial DNA inputs, posing challenges. Additionally, underrepresented tumor DNA fragments may go undetected during exponential amplification steps of traditional sequencing methods. Here, we report linear amplification-based bisulfite sequencing (LABS), enabling linear amplification of bisulfite-treated DNA fragments in a genome-wide, unbiased fashion, detecting cancer abnormalities with sub-nanogram inputs. Applying LABS to 100 patient samples revealed cancer-specific patterns, copy number alterations, and enhanced cancer detection accuracy by identifying tissue-of-origin and immune cell composition.

Indexed as

DNA MethylationNeoplasmsSequence Analysis, DNASulfitesCell-Free Nucleic AcidsCirculating Tumor DNADNA Copy Number VariationsDNA, NeoplasmHumansNucleic Acid Amplification TechniquesCell-Free Nucleic AcidsCirculating Tumor DNADNA, Neoplasmhydrogen sulfiteSulfitesBisulfite sequencingCancer detectionCell-free DNALinear amplificationLow-input DNA

Identifiers

PMID38877540
PMCPMC11177480

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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.