|
| Status |
Public on Jun 15, 2015 |
| Title |
Massively parallel quantification of the regulatory effects of non-coding genetic variation |
| Organism |
Homo sapiens |
| Experiment type |
Other
|
| Summary |
We report a novel high-throughput method to empirically quantify individual-specific regulatory element activity at the population scale. The approach combines targeted DNA capture with a high-throughput reporter-gene expression assay. As demonstration, we have measured the activity of more than 100 putative regulatory elements from 95 individuals in a single experiment. We found that, in agreement with previous reports, most genetic variants have weak effects on distal regulatory element activity. Because haplotypes are typically maintained within but not between assayed regulatory elements, the approach can be used to identify likely causal regulatory haplotypes that contribute to human phenotypes. Finally, we demonstrate the utility of the method to functionally fine map causal regulatory variants in regions of high linkage disequilibrium identified by expression quantitative trait loci (eQTL) analyses.
|
| |
|
| Overall design |
104 candidate regulatory elements from 95 individuals were resequenced using Illumina custom amplicon sequencing. We then cloned the resulting DNA fragments into a massively parallel reporter assay to quantify allele-specific regulatory activity from that population.
SNP-fdr.txt contains output of significance evaluation
haplotype.fasta.gz contains the reference used to generate alignment files
|
| |
|
| Contributor(s) |
Vockley CM, Guo C, Majoros WH, Nodzenski M, Scholtens DM, Hayes MG, Lowe WL, Reddy TE |
| Citation(s) |
26084464 |
| Submission date |
Apr 28, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Christopher Vockley |
| E-mail(s) |
christopher.vockley@gmail.com
|
| Organization name |
Duke University
|
| Street address |
101 science drive rm 2193
|
| City |
Durham |
| State/province |
NC |
| ZIP/Postal code |
27708 |
| Country |
USA |
| |
|
| Platforms (1) |
|
| Samples (8)
|
|
| Relations |
| BioProject |
PRJNA282458 |
| SRA |
SRP057740 |
Less...
More...