Evidence map›Paper›PMID 37191787›Full record

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

Genome-Wide Analysis of Palindrome Formation with Next-Generation Sequencing (GAPF-Seq) and a Bioinformatics Pipeline for Assessing De Novo Palindromes in Cancer Genomes.

Michael M Murata, Armando E Giuliano, Hisashi Tanaka

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
4.6field-weighted citation impact, top 4% 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

1 citing paper in PubMed, 3 citations in OpenAlex.

  1. Review
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 at 1 institution in 1 country.

Michael M MurataDepartment of Surgery, Cedars-Sinai Medical Center, West Hollywood, CA, USA. michael.murata@cshs.org.
Armando E GiulianoDepartment of Surgery, Cedars-Sinai Medical Center, West Hollywood, CA, USA.
Hisashi TanakaDepartment of Surgery, Cedars-Sinai Medical Center, West Hollywood, CA, USA. hisashi.tanaka@cshs.org.
Cedars-Sinai Medical Center · US

Funding

Mechanisms of gene amplification in human cancersR01CA149385 · NCI · CLEVELAND CLINIC LERNER COM-CWRU · PI TANAKA, HISASHI · 2010 to 2022
$3.4M
6 · The paper itself

Abstract

DNA palindromes are a type of chromosomal aberration that appears frequently during tumorigenesis. They are characterized by sequences of nucleotides that are identical to their reverse complements and often arise due to illegitimate repair of DNA double-strand breaks, fusion of telomeres, or stalled replication forks, all of which are common adverse early events in cancer. Here, we describe the protocol for enriching palindromes from genomic DNA sources with low-input DNA amounts and detail a bioinformatics tool for assessing the enrichment and location of de novo palindrome formation from low-coverage whole-genome sequencing data.

Indexed as

Gene AmplificationNeoplasmsComputational BiologyDNAHigh-Throughput Nucleotide SequencingHumansDNABioinformaticsBreakage–fusion–bridge (BFB) cyclesDNA palindromesFold-back inversionsGenomic amplificationGenomic instabilityInverted repeatsLarge chromosomal aberrationsNext-generation sequencing

Identifiers

PMID37191787
OpenAlexW4376643477

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.