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Gene editing approaches (including but not limited to: CRISPR, LNP, AAV, RNAi etc.) for the medical specialty of interventional genomics require (1) determination of the clinical relevance of genomic variants and (2) systematic evaluation of the 'editability' of those variants. Here, we seek to use in silico and in vitro analyses of genomic, cellular, and clinical data/specimens to (1) identify novel pathogenic variants underlying diseases and (2) examine the specificity and efficacy of various gene editing components across the entire human genomic landscape.
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| Label | Type | Description | Intervention Names |
|---|---|---|---|
| Center for Genome Surgery Case Series Discussion | |||
| Enrollment in Registry and Biobank |
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| Measure | Description | Time Frame |
|---|---|---|
| Improve our understanding of how specific mutations lead to dysfunction and cause disease | Up to 25 years | |
| Empirically assess the edibility of individual participant genomic variants in silico and in patient-derived cells for the purpose of bespoke genomic therapies. | Up to 25 years |
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| Measure | Description | Time Frame |
|---|---|---|
| Support preclinical investigations of gene therapies specific to participants | Up to 25 years |
Inclusion Criteria:
For initial screening and discussion at huddle call:
For enrollment into registry or biobanking:
Exclusion Criteria:
For initial screening and discussion at huddle call:
For enrollment into registry or biobanking:
-Any participant that the IGB agrees is inappropriate for enrollment in the registry and biobanking portion of this protocol.
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Any individual diagnosed with a genetic disorder that may be amenable to gene therapy.
| Name | Role | Phone | Extension | |
|---|---|---|---|---|
| Emma Canepa | Contact | (415) 476-7255 | Emma.Canepa@ucsf.edu |
| Name | Affiliation | Role |
|---|---|---|
| Tippi Mackenzie, MD | University of California, San Francisco | Principal Investigator |
| Facility | Status | City | State | ZIP | Country | Contacts |
|---|---|---|---|---|---|---|
| University of California, San Francisco | San Francisco | California | 94143 | United States |
| PubMed Identifier | Type | Citation | Retractions |
|---|---|---|---|
| 25513782 | Background | Tsai SQ, Zheng Z, Nguyen NT, Liebers M, Topkar VV, Thapar V, Wyvekens N, Khayter C, Iafrate AJ, Le LP, Aryee MJ, Joung JK. GUIDE-seq enables genome-wide profiling of off-target cleavage by CRISPR-Cas nucleases. Nat Biotechnol. 2015 Feb;33(2):187-197. doi: 10.1038/nbt.3117. Epub 2014 Dec 16. | |
| 32541958 | Background |
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De-identified specimens and data may be shared with other researchers
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| Lazzarotto CR, Malinin NL, Li Y, Zhang R, Yang Y, Lee G, Cowley E, He Y, Lan X, Jividen K, Katta V, Kolmakova NG, Petersen CT, Qi Q, Strelcov E, Maragh S, Krenciute G, Ma J, Cheng Y, Tsai SQ. CHANGE-seq reveals genetic and epigenetic effects on CRISPR-Cas9 genome-wide activity. Nat Biotechnol. 2020 Nov;38(11):1317-1327. doi: 10.1038/s41587-020-0555-7. Epub 2020 Jun 15. |
| 27666373 | Background | Ioannidis NM, Rothstein JH, Pejaver V, Middha S, McDonnell SK, Baheti S, Musolf A, Li Q, Holzinger E, Karyadi D, Cannon-Albright LA, Teerlink CC, Stanford JL, Isaacs WB, Xu J, Cooney KA, Lange EM, Schleutker J, Carpten JD, Powell IJ, Cussenot O, Cancel-Tassin G, Giles GG, MacInnis RJ, Maier C, Hsieh CL, Wiklund F, Catalona WJ, Foulkes WD, Mandal D, Eeles RA, Kote-Jarai Z, Bustamante CD, Schaid DJ, Hastie T, Ostrander EA, Bailey-Wilson JE, Radivojac P, Thibodeau SN, Whittemore AS, Sieh W. REVEL: An Ensemble Method for Predicting the Pathogenicity of Rare Missense Variants. Am J Hum Genet. 2016 Oct 6;99(4):877-885. doi: 10.1016/j.ajhg.2016.08.016. Epub 2016 Sep 22. |