Evidence map›Paper›PMID 30575746›Full record

ArticleNature communications2018

Optimized libraries for CRISPR-Cas9 genetic screens with multiple modalities.

Kendall R Sanson, Ruth E Hanna, Mudra Hegde, Katherine F Donovan, Christine Strand, Meagan E Sullender, Emma W Vaimberg, Amy Goodale, David E Root, Federica Piccioni and 1 more

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Nature communications, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 677 papers.

0numbers the graph read from it
0cells of the map it votes in
677citing 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

677 citing papers in PubMed.

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617 more citing papers are in PubMed but not listed here.

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

11 authors.

Kendall R SansonBroad Institute of Harvard and MIT, 75 Ames Street, Cambridge, MA, 02142, USA.
Ruth E HannaBroad Institute of Harvard and MIT, 75 Ames Street, Cambridge, MA, 02142, USA.
Mudra HegdeBroad Institute of Harvard and MIT, 75 Ames Street, Cambridge, MA, 02142, USA.ORCID http://orcid.org/0000-0003-4530-4633
Katherine F DonovanBroad Institute of Harvard and MIT, 75 Ames Street, Cambridge, MA, 02142, USA.
Christine StrandBroad Institute of Harvard and MIT, 75 Ames Street, Cambridge, MA, 02142, USA.ORCID http://orcid.org/0000-0001-5783-6667
Meagan E SullenderBroad Institute of Harvard and MIT, 75 Ames Street, Cambridge, MA, 02142, USA.ORCID http://orcid.org/0000-0001-6666-8650
Emma W VaimbergBroad Institute of Harvard and MIT, 75 Ames Street, Cambridge, MA, 02142, USA.
Amy GoodaleBroad Institute of Harvard and MIT, 75 Ames Street, Cambridge, MA, 02142, USA.
David E RootBroad Institute of Harvard and MIT, 75 Ames Street, Cambridge, MA, 02142, USA.
Federica PiccioniBroad Institute of Harvard and MIT, 75 Ames Street, Cambridge, MA, 02142, USA.ORCID http://orcid.org/0000-0003-1210-3210
John G DoenchBroad Institute of Harvard and MIT, 75 Ames Street, Cambridge, MA, 02142, USA. jdoench@broadinstitute.org.ORCID http://orcid.org/0000-0002-3707-9889

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

The creation of genome-wide libraries for CRISPR knockout (CRISPRko), interference (CRISPRi), and activation (CRISPRa) has enabled the systematic interrogation of gene function. Here, we show that our recently-described CRISPRko library (Brunello) is more effective than previously published libraries at distinguishing essential and non-essential genes, providing approximately the same perturbation-level performance improvement over GeCKO libraries as GeCKO provided over RNAi. Additionally, we present genome-wide libraries for CRISPRi (Dolcetto) and CRISPRa (Calabrese), and show in negative selection screens that Dolcetto, with fewer sgRNAs per gene, outperforms existing CRISPRi libraries and achieves comparable performance to CRISPRko in detecting essential genes. We also perform positive selection CRISPRa screens and demonstrate that Calabrese outperforms the SAM approach at identifying vemurafenib resistance genes. We further compare CRISPRa to genome-scale libraries of open reading frames (ORFs). Together, these libraries represent a suite of genome-wide tools to efficiently interrogate gene function with multiple modalities.

Indexed as

CRISPR-Cas SystemsGenomic LibraryCRISPR-Associated Protein 9Streptococcus pyogenesCas9 endonuclease Streptococcus pyogenesCRISPR-Associated Protein 9

Identifiers

PMID30575746
PMCPMC6303322

What OpenQuestion holds

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LicenceCC BY
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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.