Recent advances in genome sciences have allowed for early applications of precision medicine. While the genes causing over 4,000 Mendelian diseases have been identified, many leading to new diagnostics and therapeutics, most diseases prove more complicated. For over a decade, researchers have looked for genetic variation that is linked to these more complex diseases through genome wide association studies. While this avenue of research has generated over 18,000 unique variants linked to disease, the interpretation of these variants, and therefore their application to clinical medicine, remains unresolved. Recently, several groups have identified that many of these variants overlap enhancer elements, regions of DNA responsible for the spatiotemporal expression of genes. In this proposal, I aim to functionally validate and interpret the roles of thousands of these variants in complex disease. To do so, I am developing novel technologies with broad application to genome sciences and proteomics. I am developing methods to generate complex libraries of DNA to test, in which I can program specific variation. This same technology has been adopted by others to design proteins with novel functions. I am also developing a novel assay to test the effects of thousands of these variants on enhancer function with unprecedented sequence and chromosomal context. Together, these methods permit the simultaneous analysis of thousands of predefined enhancer variants. This study will provide insight into the genetic basis of complex traits and may guide the development of novel diagnostics and therapeutics.

Public Health Relevance

Approximately 96% of variation linked to disease does not code for protein and is difficult to interpret. This study aims to characterize thousands of these variants overlapping with enhancer elements, which control expression of genes. The study will validate disease-causing variants, uncover new disease pathways and improve our understanding of non-coding variation's role in gene expression.

Agency
National Institute of Health (NIH)
Institute
National Human Genome Research Institute (NHGRI)
Type
Individual Predoctoral NRSA for M.D./Ph.D. Fellowships (ADAMHA) (F30)
Project #
5F30HG009479-03
Application #
9612415
Study Section
Special Emphasis Panel (ZRG1)
Program Officer
Gatlin, Christine L
Project Start
2016-12-16
Project End
2020-12-15
Budget Start
2018-12-16
Budget End
2019-12-15
Support Year
3
Fiscal Year
2019
Total Cost
Indirect Cost
Name
University of Washington
Department
Genetics
Type
Schools of Medicine
DUNS #
605799469
City
Seattle
State
WA
Country
United States
Zip Code
98195
Klein, Jason C; Keith, Aidan; Agarwal, Vikram et al. (2018) Functional characterization of enhancer evolution in the primate lineage. Genome Biol 19:99
Klein, Jason C; Chen, Wei; Gasperini, Molly et al. (2018) Identifying Novel Enhancer Elements with CRISPR-Based Screens. ACS Chem Biol 13:326-332