With the rapid advances in DNA sequencing, we now have a near-complete human genome, a fairly comprehensive catalog of germline and somatic variants, as well as rich annotations of functional genomic elements. The next challenge in the field is to obtain a complete functional annotation of genetic variants and genomic elements at the cellular and organismal levels. Genome editing technology, in particularly the CRISPR/Cas9 system, has allowed rapid and precise modifications of the genome and connecting of these to functional outcomes. However, all current high-throughput screening approaches rely on phenotypes that can be coupled to cell survival, cell imaging, fluorescent cell sorting, or affinity enrichments. Genetic variants that have more subtle phenotypic consequences, which might represent the majority, are not amenable to such screens. Furthermore, screening of natural genetic variation via assaying of individual cell lines under in vitro culture conditions also has limited throughput and might miss functional differences that depend on specific physiological contexts. In this project we seek to develop a next-generation functional genetic screening method that can overcome these current limitations. Utilizing induced pluripotent stem cell differentiation as an exemplar model system, we will develop and demonstrate our integrated experimental and computational methodology to enable comprehensive and en masse functional screening of coding and non-coding genomic elements. We expect our platform will greatly accelerate the functional annotation of genetic variants, including many variants of unknown significance, across various normal and diseased cell types and tissues.

Public Health Relevance

In this proposal we will seek to develop a next-generation functional genetic screening method to enable high-throughput, information-rich, multi-dimensional study of genomic elements. We expect our approach will greatly accelerate the functional annotation of genetic variants, including many variants of unknown significance, across various normal and diseased cell types and tissues. We anticipate this understanding will also enable us to program the genome for future medicinal and technological purposes.

Agency
National Institute of Health (NIH)
Institute
National Human Genome Research Institute (NHGRI)
Type
Research Project (R01)
Project #
1R01HG009285-01A1
Application #
9379760
Study Section
Special Emphasis Panel (ZRG1)
Program Officer
Pazin, Michael J
Project Start
2017-08-25
Project End
2021-07-31
Budget Start
2017-08-25
Budget End
2018-07-31
Support Year
1
Fiscal Year
2017
Total Cost
Indirect Cost
Name
University of California San Diego
Department
Engineering (All Types)
Type
Schools of Arts and Sciences
DUNS #
804355790
City
La Jolla
State
CA
Country
United States
Zip Code
92093