Multilayered VBC score predicts sgRNAs that efficiently generate loss-of-function alleles.

Nature Methods
Georg MichlitsUlrich Elling

Abstract

CRISPR-Cas9 screens have emerged as a transformative approach to systematically probe gene functions. The quality and success of these screens depends on the frequencies of loss-of-function alleles, particularly in negative-selection screens widely applied for probing essential genes. Using optimized screening workflows, we performed essentialome screens in cancer cell lines and embryonic stem cells and achieved dropout efficiencies that could not be explained by common frameshift frequencies. We find that these superior effect sizes are mainly determined by the impact of in-frame mutations on protein function, which can be predicted based on amino acid composition and conservation. We integrate protein features into a 'Bioscore' and fuse it with improved predictors of single-guide RNA activity and indel formation to establish a score that captures all relevant processes in CRISPR-Cas9 mutagenesis. This Vienna Bioactivity CRISPR score (www.vbc-score.org) outperforms previous prediction tools and enables the selection of sgRNAs that effectively produce loss-of-function alleles.

References

Oct 21, 1999·Experimental Cell Research·M KoteckiB H Cochran
Apr 3, 2004·Genome Research·Mathieu BlanchetteWebb Miller
May 24, 2007·Bioinformatics·John A Capra, Mona Singh
Apr 1, 2010·Nature Methods·Ivan A AdzhubeiShamil R Sunyaev
Jun 13, 2012·Nucleic Acids Research·Ngak-Leng SimPauline C Ng
Dec 18, 2013·Science·Tim WangEric S Lander
Dec 18, 2013·Science·Ophir ShalemFeng Zhang
Jul 31, 2014·Nature Methods·Neville E SanjanaFeng Zhang
Sep 4, 2014·Nature Biotechnology·John G DoenchDavid E Root
Nov 28, 2014·Nucleic Acids Research·Kate R RosenbloomW James Kent
May 12, 2015·Nature Biotechnology·Junwei ShiChristopher R Vakoc
Oct 17, 2015·Science·Vincent A BlomenThijn R Brummelkamp
Dec 18, 2015·Nucleic Acids Research·Robert D FinnAlex Bateman
Jan 19, 2016·Nature Biotechnology·John G DoenchDavid E Root
Jun 5, 2016·Cancer Discovery·Andrew J AguirreWilliam C Hahn
Oct 30, 2016·Bioinformatics·Jian MaXiaole Shirley Liu
Aug 9, 2016·Molecular Cell·Megan van OverbeekAndrew P May
Oct 30, 2016·Nucleic Acids Research·Benedikt RauscherMichael Boutros
Feb 2, 2017·ACS Synthetic Biology·Raj ChariGeorge M Church
Jul 13, 2017·Cell Reports·Timothy D MartinStephen J Elledge
Oct 19, 2017·Nature Methods·Georg MichlitsUlrich Elling
Dec 22, 2017·Nucleic Acids Research·Maurice LabuhnDirk Heckl
Mar 13, 2018·Molecular Cell·Yusuke TarumotoChristopher R Vakoc
Jun 28, 2018·Genome Biology·Guohui ChuaiQi Liu
Oct 26, 2018·Nucleic Acids Research·Sara El-GebaliRobert D Finn
Nov 28, 2018·Nature Biotechnology·Felicity AllenLeopold Parts
Dec 18, 2018·Molecular Cell·Anob M ChakrabartiPaola Scaffidi
Dec 24, 2018·Nature Communications·Kendall R SansonJohn G Doench
Apr 12, 2019·Nature·Fiona M BehanMathew J Garnett
Sep 8, 2019·Nature Communications·Rubina TuladharLawrence Lum
Oct 6, 2019·Nature Communications·Daeseong ChoeJung-Woo Yoo

❮ Previous
Next ❯

Citations

May 30, 2020·Life Science Alliance·Petra van der LelijMark Petronczki
Nov 7, 2020·Nature Methods·Vivien Marx
Feb 2, 2021·Frontiers in Physiology·Kyle E SimpsonTom W Claydon
Jun 23, 2021·Scientific Reports·Benjamin LindnerMichael Schuler
Jul 15, 2021·Cell Death & Disease·Jiashuo ZhengMarcus Conrad

❮ Previous
Next ❯

Methods Mentioned

BETA
targeted mutations
gene-trap
PCR
chip
fluorescence-activated cell sorting
FCS
transfection
FACS

Software Mentioned

Bioscore
scipy1
Scorer
StandardScaler
intellicyte iQue screener
QuantileTransformer
MinMaxScaler
phastCons
custom
learn

Related Concepts

Related Feeds

CRISPR (general)

Clustered regularly interspaced short palindromic repeats (CRISPR) are DNA sequences in the genome that are recognized and cleaved by CRISPR-associated proteins (Cas). CRISPR-Cas system enables the editing of genes to create or correct mutations. Discover the latest research on CRISPR here.

CRISPR for Genome Editing

Genome editing technologies enable the editing of genes to create or correct mutations. Clustered regularly interspaced short palindromic repeats (CRISPR) are DNA sequences in the genome that are recognized and cleaved by CRISPR-associated proteins (Cas). Here is the latest research on the use of CRISPR-Cas system in gene editing.