The primary focus of the lab is to develop tools for studying gene function on a genome wide scale. We have recently shifted our mutagenesis efforts from random retroviral integration mutagenesis to using the bacterial CRISPR/Cas9 gene-targeting technique. This provides us with a cost effective way to efficiently target gene KO's in zebrafish. We have developed a streamlined pipeline for gene targeting using CRISPR/Cas9 where we use fluorescent PCR and the ABI capillary sequencer to rapidly identify insertions or deletions caused by CRISPR/Cas9 induced double stranded breaks. We can verify mutations using MiSeq data and specialized software we wrote. Using this pipeline we have already targeted over 500 genomic locations and identified the mutations transmitted through the germline. We will continue to develop high-throughput techniques to generate approximately 2,000 targeted gene KO's in the next 3 years. These mutations will feed into other ongoing projects in the lab. In addition, we are now focused on improving CRISPR-based alterations in the genome that are not specifically gene-inactivating, including targeted transgene integration and SNP knock-ins.

Project Start
Project End
Budget Start
Budget End
Support Year
18
Fiscal Year
2018
Total Cost
Indirect Cost
Name
Human Genome Research
Department
Type
DUNS #
City
State
Country
Zip Code
Giannelou, Angeliki; Wang, Hongying; Zhou, Qing et al. (2018) Aberrant tRNA processing causes an autoinflammatory syndrome responsive to TNF inhibitors. Ann Rheum Dis 77:612-619
Tseng, Wei-Chia; Loeb, Hannah E; Pei, Wuhong et al. (2018) Modeling Niemann-Pick disease type C1 in zebrafish: a robust platform for in vivo screening of candidate therapeutic compounds. Dis Model Mech 11:
Pei, Wuhong; Xu, Lisha; Huang, Sunny C et al. (2018) Guided genetic screen to identify genes essential in the regeneration of hair cells and other tissues. NPJ Regen Med 3:11
Watkins-Chow, Dawn E; Varshney, Gaurav K; Garrett, Lisa J et al. (2017) Highly Efficient Cpf1-Mediated Gene Targeting in Mice Following High Concentration Pronuclear Injection. G3 (Bethesda) 7:719-722
Crawford, Nicholas G; Kelly, Derek E; Hansen, Matthew E B et al. (2017) Loci associated with skin pigmentation identified in African populations. Science 358:
Li, Huiqing; Pei, Wuhong; Vergarajauregui, Sivia et al. (2017) Novel degenerative and developmental defects in a zebrafish model of mucolipidosis type IV. Hum Mol Genet 26:2701-2718
Burgess, Shawn (2016) Genomics: A matched set of frog sequences. Nature 538:320-321
Vrljicak, Pavle; Tao, Shijie; Varshney, Gaurav K et al. (2016) Genome-Wide Analysis of Transposon and Retroviral Insertions Reveals Preferential Integrations in Regions of DNA Flexibility. G3 (Bethesda) 6:805-17
Chandler, Randy J; LaFave, Matthew C; Varshney, Gaurav K et al. (2016) Genotoxicity in Mice Following AAV Gene Delivery: A Safety Concern for Human Gene Therapy? Mol Ther 24:198-201
Varshney, Gaurav K; Burgess, Shawn M (2016) DNA-guided genome editing using structure-guided endonucleases. Genome Biol 17:187

Showing the most recent 10 out of 48 publications