CrispRVariants Charts the Mutation Spectrum of Genome Engineering Experiments

Overview

Journal Nat Biotechnol

Specialty Biotechnology

Date 2016 Jul 13

PMID 27404876

Citations 80

Authors

Helen Lindsay

Alexa Burger

Berthin Biyong

Anastasia Felker

Christopher Hess

Jonas Zaugg

Elena Chiavacci

Carolin Anders

Martin Jinek

Christian Mosimann

Mark D Robinson

Affiliations

Soon will be listed here.

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References

Ran F, Hsu P, Lin C, Gootenberg J, Konermann S, Trevino A . Double nicking by RNA-guided CRISPR Cas9 for enhanced genome editing specificity. Cell. 2013; 154(6):1380-9. PMC: 3856256. DOI: 10.1016/j.cell.2013.08.021. View

Kent W . BLAT--the BLAST-like alignment tool. Genome Res. 2002; 12(4):656-64. PMC: 187518. DOI: 10.1101/gr.229202. View

Shah A, Davey C, Whitebirch A, Miller A, Moens C . Rapid reverse genetic screening using CRISPR in zebrafish. Nat Methods. 2015; 12(6):535-40. PMC: 4667794. DOI: 10.1038/nmeth.3360. View

Li H . Toward better understanding of artifacts in variant calling from high-coverage samples. Bioinformatics. 2014; 30(20):2843-51. PMC: 4271055. DOI: 10.1093/bioinformatics/btu356. View

Guell M, Yang L, Church G . Genome editing assessment using CRISPR Genome Analyzer (CRISPR-GA). Bioinformatics. 2014; 30(20):2968-70. PMC: 4184265. DOI: 10.1093/bioinformatics/btu427. View

Cho S, Kim S, Kim Y, Kweon J, Kim H, Bae S . Analysis of off-target effects of CRISPR/Cas-derived RNA-guided endonucleases and nickases. Genome Res. 2013; 24(1):132-41. PMC: 3875854. DOI: 10.1101/gr.162339.113. View

Burger A, Lindsay H, Felker A, Hess C, Anders C, Chiavacci E . Maximizing mutagenesis with solubilized CRISPR-Cas9 ribonucleoprotein complexes. Development. 2016; 143(11):2025-37. DOI: 10.1242/dev.134809. View

ORawe J, Jiang T, Sun G, Wu Y, Wang W, Hu J . Low concordance of multiple variant-calling pipelines: practical implications for exome and genome sequencing. Genome Med. 2013; 5(3):28. PMC: 3706896. DOI: 10.1186/gm432. View

Yoshimi K, Kaneko T, Voigt B, Mashimo T . Allele-specific genome editing and correction of disease-associated phenotypes in rats using the CRISPR-Cas platform. Nat Commun. 2014; 5:4240. PMC: 4083438. DOI: 10.1038/ncomms5240. View

10.

Varshney G, Pei W, LaFave M, Idol J, Xu L, Gallardo V . High-throughput gene targeting and phenotyping in zebrafish using CRISPR/Cas9. Genome Res. 2015; 25(7):1030-42. PMC: 4484386. DOI: 10.1101/gr.186379.114. View

11.

Hsu P, Lander E, Zhang F . Development and applications of CRISPR-Cas9 for genome engineering. Cell. 2014; 157(6):1262-1278. PMC: 4343198. DOI: 10.1016/j.cell.2014.05.010. View

12.

Gagnon J, Valen E, Thyme S, Huang P, Akhmetova L, Ahkmetova L . Efficient mutagenesis by Cas9 protein-mediated oligonucleotide insertion and large-scale assessment of single-guide RNAs. PLoS One. 2014; 9(5):e98186. PMC: 4038517. DOI: 10.1371/journal.pone.0098186. View

13.

Huber W, Carey V, Gentleman R, Anders S, Carlson M, Carvalho B . Orchestrating high-throughput genomic analysis with Bioconductor. Nat Methods. 2015; 12(2):115-21. PMC: 4509590. DOI: 10.1038/nmeth.3252. View

14.

Yen S, Zhang M, Deng J, Usman S, Smith C, Parker-Thornburg J . Somatic mosaicism and allele complexity induced by CRISPR/Cas9 RNA injections in mouse zygotes. Dev Biol. 2014; 393(1):3-9. PMC: 4166609. DOI: 10.1016/j.ydbio.2014.06.017. View

15.

Moreno-Mateos M, Vejnar C, Beaudoin J, Fernandez J, Mis E, Khokha M . CRISPRscan: designing highly efficient sgRNAs for CRISPR-Cas9 targeting in vivo. Nat Methods. 2015; 12(10):982-8. PMC: 4589495. DOI: 10.1038/nmeth.3543. View

16.

McCarthy D, Humburg P, Kanapin A, Rivas M, Gaulton K, Cazier J . Choice of transcripts and software has a large effect on variant annotation. Genome Med. 2014; 6(3):26. PMC: 4062061. DOI: 10.1186/gm543. View

17.

Lawrence M, Huber W, Pages H, Aboyoun P, Carlson M, Gentleman R . Software for computing and annotating genomic ranges. PLoS Comput Biol. 2013; 9(8):e1003118. PMC: 3738458. DOI: 10.1371/journal.pcbi.1003118. View

18.

Zetsche B, Gootenberg J, Abudayyeh O, Slaymaker I, Makarova K, Essletzbichler P . Cpf1 is a single RNA-guided endonuclease of a class 2 CRISPR-Cas system. Cell. 2015; 163(3):759-71. PMC: 4638220. DOI: 10.1016/j.cell.2015.09.038. View

19.

Charpentier E, Doudna J . Biotechnology: Rewriting a genome. Nature. 2013; 495(7439):50-1. DOI: 10.1038/495050a. View