Evidence map›Paper›PMID 32160537›Full record

ArticleCell reports2020

Detection of Marker-Free Precision Genome Editing and Genetic Variation through the Capture of Genomic Signatures.

Pierre Billon, Tarun S Nambiar, Samuel B Hayward, Maria P Zafra, Emma M Schatoff, Koichi Oshima, Andrew Dunbar, Marco Breinig, Young C Park, Han S Ryu and 6 more

Open access · goldAbstract read
In one paragraph

Article in Cell reports, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.

0numbers the graph read from it
0cells of the map it votes in
10citing papers in PubMed
0.6field-weighted citation impact, top 36% 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

10 citing papers in PubMed, 15 citations in OpenAlex.

  1. Article
  2. Article
  3. Article
  4. Article
  5. Article
  6. Current advancement in the application of prime editing.Frontiers in bioengineering and biotechnology · 2023
    Review
  7. Review
  8. Precise genome engineering inProceedings of the National Academy of Sciences of the United States of America · 2021
    Article
  9. Review
  10. 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

16 authors at 7 institutions in 2 countries.

Pierre BillonDepartment of Genetics and Development, Columbia University Irving Medical Center, New York, NY 10032, USA; Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA.
Tarun S NambiarDepartment of Genetics and Development, Columbia University Irving Medical Center, New York, NY 10032, USA; Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA.
Samuel B HaywardDepartment of Genetics and Development, Columbia University Irving Medical Center, New York, NY 10032, USA; Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA.
Maria P ZafraSandra and Edward Meyer Cancer Center, Department of Medicine, Weill Cornell Medicine, New York, NY 10065, USA.
Emma M SchatoffSandra and Edward Meyer Cancer Center, Department of Medicine, Weill Cornell Medicine, New York, NY 10065, USA; Weill Cornell/Rockefeller/Sloan Kettering Tri-Institutional MD-PhD Program, New York, NY 10065, USA.
Koichi OshimaDepartment of Pediatrics, Columbia University Irving Medical Center, New York, NY 10032, USA; Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY 10032, USA; Department of Systems Biology, Columbia University Irving Medical Center, New York, NY 10032, USA; Institute for Cancer Genetics, Columbia University Irving Medical Center, New York, NY 10032, USA.
Andrew DunbarHuman Oncology and Pathogenesis Program, Center for Hematological Malignancies, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA.
Marco BreinigHelmholtz-University Group "Cell Plasticity and Epigenetic Remodeling", German Cancer Research Center (DKFZ) and Institute of Pathology University Hospital, 69120 Heidelberg, Germany.
Young C ParkHuman Oncology and Pathogenesis Program, Center for Hematological Malignancies, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA.
Han S RyuDepartment of Genetics and Development, Columbia University Irving Medical Center, New York, NY 10032, USA; Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA.
Darjus F TschaharganehHelmholtz-University Group "Cell Plasticity and Epigenetic Remodeling", German Cancer Research Center (DKFZ) and Institute of Pathology University Hospital, 69120 Heidelberg, Germany.
Ross L LevineHuman Oncology and Pathogenesis Program, Center for Hematological Malignancies, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA.
Richard BaerDepartment of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY 10032, USA; Institute for Cancer Genetics, Columbia University Irving Medical Center, New York, NY 10032, USA; Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA.
Adolfo FerrandoDepartment of Pediatrics, Columbia University Irving Medical Center, New York, NY 10032, USA; Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY 10032, USA; Department of Systems Biology, Columbia University Irving Medical Center, New York, NY 10032, USA; Institute for Cancer Genetics, Columbia University Irving Medical Center, New York, NY 10032, USA.
Lukas E DowSandra and Edward Meyer Cancer Center, Department of Medicine, Weill Cornell Medicine, New York, NY 10065, USA.
Alberto CicciaDepartment of Genetics and Development, Columbia University Irving Medical Center, New York, NY 10032, USA; Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA. Electronic address: ac3685@cumc.columbia.edu.
Columbia University Irving Medical Center · USMemorial Sloan Kettering Cancer Center · USCornell University · USColumbia University · USHeidelberg University · DEUniversity Hospital Heidelberg · DEWeill Cornell Medicine · US

Funding

X-RAY CRYSTALLOGRAPHYP30CA008748 · NCI · SLOAN-KETTERING INSTITUTE FOR CANCER RES · PI Hongbiao Carl Lekaye · 1985 to 2026
$347.4M
Tumor Biology and Microenvironment ProgramP30CA013696 · NCI · COLUMBIA UNIV NEW YORK MORNINGSIDE · PI Anil K Rustgi · 1985 to 2026
$115.3M
The Role of CTIP in Lymphocyte Development and LymphomagenesisP01CA174653 · NCI · COLUMBIA UNIVERSITY HEALTH SCIENCES · PI ZHA, SHAN · 2014 to 2024
$17.6M
Molecular pathways and targeted therapies in human leukemiaR35CA210065 · NCI · COLUMBIA UNIVERSITY HEALTH SCIENCES · PI FERRANDO, ADOLFO A. · 2017 to 2021
$4.7M
Replication fork remodeling and genomic stabilityR01CA197774 · NCI · COLUMBIA UNIVERSITY HEALTH SCIENCES · PI Alberto Ciccia · 2016 to 2026
$4.2M
Molecular characterization and targeting of NT5C2 mutations in acute lymphoblastic leukemiaR01CA216981 · NCI · COLUMBIA UNIVERSITY HEALTH SCIENCES · PI FERRANDO, ADOLFO A., STOCKWELL, BRENT R. · 2017 to 2021
$1.9M
The BARD1 tumor suppressor and breast cancerR01CA172272 · NCI · COLUMBIA UNIVERSITY HEALTH SCIENCES · PI BAER, RICHARD J · 2013 to 2017
$1.7M
Transcriptional regulation by the DNA damage responseR01GM117064 · NIGMS · COLUMBIA UNIVERSITY HEALTH SCIENCES · PI CICCIA, ALBERTO · 2016 to 2019
$1.2M
Targeting the WNT Pathway in Colorectal CancerF31CA224800 · NCI · WEILL MEDICAL COLL OF CORNELL UNIV · PI SCHATOFF, EMMA M · 2017 to 2020
$179k
NCI NIH HHS F31 CA224800NCI NIH HHS P01 CA174653NCI NIH HHS P30 CA008748NCI NIH HHS P30 CA013696NCI NIH HHS R01 CA172272NCI NIH HHS R01 CA197774NCI NIH HHS R01 CA216981NCI NIH HHS R35 CA210065NIGMS NIH HHS R01 GM117064
6 · The paper itself

Abstract

Genome editing technologies have transformed our ability to engineer desired genomic changes within living systems. However, detecting precise genomic modifications often requires sophisticated, expensive, and time-consuming experimental approaches. Here, we describe DTECT (Dinucleotide signaTurE CapTure), a rapid and versatile detection method that relies on the capture of targeted dinucleotide signatures resulting from the digestion of genomic DNA amplicons by the type IIS restriction enzyme AcuI. DTECT enables the accurate quantification of marker-free precision genome editing events introduced by CRISPR-dependent homology-directed repair, base editing, or prime editing in various biological systems, such as mammalian cell lines, organoids, and tissues. Furthermore, DTECT allows the identification of oncogenic mutations in cancer mouse models, patient-derived xenografts, and human cancer patient samples. The ease, speed, and cost efficiency by which DTECT identifies genomic signatures should facilitate the generation of marker-free cellular and animal models of human disease and expedite the detection of human pathogenic variants.

Indexed as

Gene EditingGenetic VariationGenomicsAnimalsBase SequenceBRCA1 ProteinBRCA2 ProteinDisease Models, AnimalDNAGenetic LociGenetic MarkersGenotypeHEK293 CellsHumansMiceMutationBRCA1 ProteinBRCA2 ProteinDNAGenetic MarkersNucleotidesbase editingCRISPRdetection methoddinucleotide signaturesgenetic variationhomology-directed repairhuman pathogenic variantsprecision genome editingprime editingtype IIS restriction endonucleases

Identifiers

PMID32160537
PMCPMC7108696
OpenAlexW3012036607

What OpenQuestion holds

Textmetadata
LicenceCC BY-NC-ND
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.