Evidence map›Paper›PMID 38260558›Full record

ArticlebioRxiv : the preprint server for biology2024

FinaleMe: Predicting DNA methylation by the fragmentation patterns of plasma cell-free DNA.

Yaping Liu, Sarah C Reed, Christopher Lo, Atish D Choudhury, Heather A Parsons, Daniel G Stover, Gavin Ha, Gregory Gydush, Justin Rhoades, Denisse Rotem and 7 more

Abstract readPreprint
PubMed Full text at PMC Publisher
In one paragraph

Article in bioRxiv : the preprint server for biology, 2024. 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

17 authors.

Yaping LiuDepartment of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611.ORCID 0000-0003-4165-7693
Sarah C ReedBroad Institute of MIT and Harvard, Cambridge, MA 02142.
Christopher LoBroad Institute of MIT and Harvard, Cambridge, MA 02142.
Atish D ChoudhuryBroad Institute of MIT and Harvard, Cambridge, MA 02142.
Heather A ParsonsDana-Farber Cancer Institute, Boston, MA, USA.
Daniel G StoverDana-Farber Cancer Institute, Boston, MA, USA.
Gavin HaBroad Institute of MIT and Harvard, Cambridge, MA 02142.
Gregory GydushBroad Institute of MIT and Harvard, Cambridge, MA 02142.
Justin RhoadesBroad Institute of MIT and Harvard, Cambridge, MA 02142.
Denisse RotemBroad Institute of MIT and Harvard, Cambridge, MA 02142.
Samuel FreemanBroad Institute of MIT and Harvard, Cambridge, MA 02142.
David KatzDepartment of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611.
Ravi BandaruDepartment of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611.
Haizi ZhengDivision of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229.
Hailu FuDepartment of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611.
Viktor A AdalsteinssonUniversity of Cincinnati Center for Environmental Genetics, Cincinnati, OH 45229.
Manolis KellisUniversity of Cincinnati Center for Environmental Genetics, Cincinnati, OH 45229.ORCID 0000-0001-7113-9630

Funding

Inferring 1D and 3D epigenomes by cell-free DNA fragmentation patterns.R56HG012360 · NHGRI · NORTHWESTERN UNIVERSITY AT CHICAGO · PI LIU, YAPING · 2022 to 2022
$569k
NHGRI NIH HHS R56 HG012360
6 · The paper itself

Abstract

Analysis of DNA methylation in cell-free DNA (cfDNA) reveals clinically relevant biomarkers but requires specialized protocols and sufficient input material that limits its applicability. Millions of cfDNA samples have been profiled by genomic sequencing. To maximize the gene regulation information from the existing dataset, we developed FinaleMe, a non-homogeneous Hidden Markov Model (HMM), to predict DNA methylation of cfDNA and, therefore, tissues-of-origin directly from plasma whole-genome sequencing (WGS). We validated the performance with 80 pairs of deep and shallow-coverage WGS and whole-genome bisulfite sequencing (WGBS) data.

Indexed as

Cell-free DNADNA methylationfragmentationtissues-of-originwhole-genome sequencing

Identifiers

PMID38260558
PMCPMC10802291

What OpenQuestion holds

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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.