Evidence map›Paper›PMID 37191802›Full record

ArticleMethods in molecular biology (Clifton, N.J.)2023

Circle Damage Sequencing for Whole-Genome Analysis of DNA Damage.

Seung-Gi Jin, Jennifer Johnson, Gerd P Pfeifer

Abstract read
PubMed Publisher
In one paragraph

Article in Methods in molecular biology (Clifton, N.J.), 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1 paper.

0numbers the graph read from it
0cells of the map it votes in
1citing 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

1 citing paper in PubMed.

  1. 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

3 authors.

Seung-Gi JinDepartment of Epigenetics, Van Andel Institute, Grand Rapids, MI, USA.
Jennifer JohnsonDepartment of Epigenetics, Van Andel Institute, Grand Rapids, MI, USA.
Gerd P PfeiferDepartment of Epigenetics, Van Andel Institute, Grand Rapids, MI, USA. gerd.pfeifer@vai.org.

Funding

Mechanisms of cancer mutationsR01CA276031 · NCI · VAN ANDEL RESEARCH INSTITUTE · PI Gerd P Pfeifer · 2023 to 2026
$1.9M
Etheno Adducts in Liver CancerR21CA228089 · NCI · VAN ANDEL RESEARCH INSTITUTE · PI PFEIFER, GERD P · 2018 to 2019
$448k
NCI NIH HHS R01 CA276031NCI NIH HHS R21 CA228089
6 · The paper itself

Abstract

There are many sources of endogenous and exogenous DNA damage. Damaged bases represent a threat to genome integrity and may interfere with normal cellular processes such as replication and transcription. To understand the specificity and biological consequences of DNA damage, it is essential to employ methods that are sensitive enough to detect damaged DNA bases at the level of single nucleotide resolution and genome-wide. Here we describe in detail a method we developed for this purpose, circle damage sequencing (CD-seq). This method is based on the circularization of genomic DNA that contains damaged bases and conversion of the damaged sites into double-strand breaks using specific DNA repair enzymes. Library sequencing of the opened circles yields the precise positions of the DNA lesions that are present. CD-seq can be adopted to various types of DNA damage as long as a specific cleavage scheme can be designed.

Indexed as

DNA DamageGenomeDNADNA RepairDNA ReplicationDNACD-seq sequencing libraryCircle damage sequencing (CD-seq)Circularization of genomic DNADNA damageDouble strand breakWhole-genome

Identifiers

PMID37191802

What OpenQuestion holds

Textmetadata
Read underepoch 390

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.