Evidence map›Paper›PMID 37502948›Full record

ArticlebioRxiv : the preprint server for biology2023

High throughput PRIME editing screens identify functional DNA variants in the human genome.

Xingjie Ren, Han Yang, Jovia L Nierenberg, Yifan Sun, Jiawen Chen, Cooper Beaman, Thu Pham, Mai Nobuhara, Maya Asami Takagi, Vivek Narayan and 3 more

Open access · greenAbstract readPreprint
PubMed Full text at PMC Publisher
In one paragraph

Article in bioRxiv : the preprint server for biology, 2023. 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, 17 citations in OpenAlex.

No citing paper in PubMed yet.

4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

13 authors at 2 institutions in 1 country.

Xingjie RenInstitute for Human Genetics, University of California, San Francisco, San Francisco, CA, USA.
Han YangInstitute for Human Genetics, University of California, San Francisco, San Francisco, CA, USA.
Jovia L NierenbergDepartment of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA, USA.
Yifan SunInstitute for Human Genetics, University of California, San Francisco, San Francisco, CA, USA.
Jiawen ChenDepartment of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.
Cooper BeamanInstitute for Human Genetics, University of California, San Francisco, San Francisco, CA, USA.
Thu PhamPharmaceutical Sciences and Pharmacogenomics Graduate Program, University of California, San Francisco, San Francisco, CA, USA.
Mai NobuharaPharmaceutical Sciences and Pharmacogenomics Graduate Program, University of California, San Francisco, San Francisco, CA, USA.
Maya Asami TakagiInstitute for Human Genetics, University of California, San Francisco, San Francisco, CA, USA.
Vivek NarayanInstitute for Human Genetics, University of California, San Francisco, San Francisco, CA, USA.
Yun LiDepartment of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.
Elad ZivInstitute for Human Genetics, University of California, San Francisco, San Francisco, CA, USA.
Yin ShenInstitute for Human Genetics, University of California, San Francisco, San Francisco, CA, USA.
University of California, San Francisco · USUniversity of North Carolina at Chapel Hill · US

Funding

High throughput CRISPR-mediated functional validation of regulatory elementsUM1HG009402 · NHGRI · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI REN, BING, SHEN, YIN · 2017 to 2021
$8.4M
Polygenic risk scores for cardiometabolic disorders: the role of blood cells immune response and evolutionary adaptationU01HG011720 · NHGRI · UNIV OF NORTH CAROLINA CHAPEL HILL · PI Yun Li, ALEXANDER P REINER · 2021 to 2026
$5.4M
Functional characterization of Alzheimer's disease associated genetic variantsR01AG057497 · NIA · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI GAN, LI, SHEN, YIN · 2017 to 2021
$4.2M
Charting the 3D epigenome in human brain development and diseasesU01DA052713 · NIDA · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI KRIEGSTEIN, ARNOLD, SHEN, YIN · 2020 to 2024
$3.4M
Transcriptional regulation of BEST1 in retina pigment epithelium.R01EY027789 · NEI · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI SHEN, YIN · 2017 to 2021
$2.1M
Illumina NovaSeq 6000 Sequencing SystemS10OD028511 · OD · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI CHOW, ERIC D · 2020 to 2020
$583k
NEI NIH HHS R01 EY027789NHGRI NIH HHS U01 HG011720NHGRI NIH HHS UM1 HG009402NIA NIH HHS R01 AG057497NIDA NIH HHS U01 DA052713NIH HHS S10 OD028511
6 · The paper itself

Abstract

Despite tremendous progress in detecting DNA variants associated with human disease, interpreting their functional impact in a high-throughput and base-pair resolution manner remains challenging. Here, we develop a novel pooled prime editing screen method, PRIME, which can be applied to characterize thousands of coding and non-coding variants in a single experiment with high reproducibility. To showcase its applications, we first identified essential nucleotides for a 716 bp

Identifiers

PMID37502948
PMCPMC10370011
OpenAlexW4384205761

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.