Evidence map›Paper›PMID 29162844›Full record

ArticleNature communications2017

DNA nanomapping using CRISPR-Cas9 as a programmable nanoparticle.

Andrey Mikheikin, Anita Olsen, Kevin Leslie, Freddie Russell-Pavier, Andrew Yacoot, Loren Picco, Oliver Payton, Amir Toor, Alden Chesney, James K Gimzewski and 2 more

Open access · goldAbstract read
In one paragraph

Article in Nature communications, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.

0numbers the graph read from it
0cells of the map it votes in
13citing papers in PubMed
2.0field-weighted citation impact, top 13% 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

13 citing papers in PubMed, 37 citations in OpenAlex.

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  12. [Progress in the applications of high-speed atomic force microscopy in cell biology].Nan fang yi ke da xue xue bao = Journal of Southern Medical University · 2018
    Review
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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

12 authors at 6 institutions in 2 countries.

Andrey MikheikinDepartment of Physics, Virginia Commonwealth University, Richmond, 23284, VA, USA.
Anita OlsenDepartment of Physics, Virginia Commonwealth University, Richmond, 23284, VA, USA.
Kevin LeslieDepartment of Physics, Virginia Commonwealth University, Richmond, 23284, VA, USA.
Freddie Russell-PavierNational Physical Laboratory, Hampton Road, Teddington, TW11 0LW, Middlesex, UK.
Andrew YacootNational Physical Laboratory, Hampton Road, Teddington, TW11 0LW, Middlesex, UK.
Loren PiccoInterface Analysis Centre, H. H. Wills Physics Laboratory, Tyndall Avenue, Bristol, BS8 1TL, UK.
Oliver PaytonInterface Analysis Centre, H. H. Wills Physics Laboratory, Tyndall Avenue, Bristol, BS8 1TL, UK.
Amir ToorDepartment of Internal Medicine, VCU School of Medicine, Richmond, 23284, VA, USA.
Alden ChesneyVCU Massey Cancer Center, Richmond, 23284, VA, USA.
James K GimzewskiDepartment of Chemistry and Biochemistry, UCLA, Los Angeles, 90095, CA, USA.ORCID http://orcid.org/0000-0003-4333-6957
Bud MishraDepartments of Computer Science and Mathematics, Courant Institute of Mathematical Sciences, New York University, New York, 10012, NY, USA.
Jason ReedDepartment of Physics, Virginia Commonwealth University, Richmond, 23284, VA, USA. jcreed@vcu.edu.
Virginia Commonwealth University · USInterface (United Kingdom) · GBNational Physical Laboratory · GBVirginia Cancer Institute · USCourant Institute of Mathematical Sciences · USUniversity of California, Los Angeles · US

Funding

Virus Vector Shared ResourceP30CA016059 · NCI · VIRGINIA COMMONWEALTH UNIVERSITY · PI Keri R Maher · 1985 to 2026
$51.0M
(PQD5) Mass Profiling Melanoma Responses to Improve Therapy Choices and PrognosisR01CA185189 · NCI · UNIVERSITY OF CALIFORNIA LOS ANGELES · PI REED, JASON C, TEITELL, MICHAEL A · 2014 to 2017
$1.9M
Nanotechnologies for Determining Gene Expression Patterns from Single CellsR01GM094388 · NIGMS · VIRGINIA COMMONWEALTH UNIVERSITY · PI REED, JASON C · 2010 to 2013
$1.3M
NCI NIH HHS P30 CA016059NCI NIH HHS R01 CA185189NIGMS NIH HHS R01 GM094388
6 · The paper itself

Abstract

Progress in whole-genome sequencing using short-read (e.g., <150 bp), next-generation sequencing technologies has reinvigorated interest in high-resolution physical mapping to fill technical gaps that are not well addressed by sequencing. Here, we report two technical advances in DNA nanotechnology and single-molecule genomics: (1) we describe a labeling technique (CRISPR-Cas9 nanoparticles) for high-speed AFM-based physical mapping of DNA and (2) the first successful demonstration of using DVD optics to image DNA molecules with high-speed AFM. As a proof of principle, we used this new "nanomapping" method to detect and map precisely BCL2-IGH translocations present in lymph node biopsies of follicular lymphoma patents. This HS-AFM "nanomapping" technique can be complementary to both sequencing and other physical mapping approaches.

Indexed as

CRISPR-Cas SystemsNanoparticlesChromosome MappingDNAGenomicsHigh-Throughput Nucleotide SequencingHumansImage Processing, Computer-AssistedImmunoglobulin Heavy ChainsLymphoma, FollicularMicroscopy, Atomic ForceNanotechnologyProto-Oncogene Proteins c-bcl-2Translocation, GeneticDNAImmunoglobulin Heavy ChainsProto-Oncogene Proteins c-bcl-2

Identifiers

PMID29162844
PMCPMC5698298
OpenAlexW2769503935

What OpenQuestion holds

Textmetadata
LicenceCC BY
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.