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August 28, 2019
Environmental Factor Estimate to Improve GWAS Power
September 4, 2019

Trans-eQTL Identification

Image Credit: Yao, Chen, et al. “Dynamic role of trans regulation of gene expression in relation to complex traits.” The American Journal of Human Genetics 100.4 (2017): 571-580.


Background:  The genes in our genomes encode the proteins that we need to live. Regulatory regions near the genes control how much of each protein is made by our cells. The regulatory regions fall into two areas, near by regulatory regions (cis-) and far away regions (trans-). Identifying cis-variants that influence gene expression is relatively straight forward. However, finding the trans-variants is very difficult because of the multiple testing burden when searching across an entire genome.


Hypothesis: Trans-variants may affect multiple genes. Therefore, we propose that we can first identify areas of the genome enriched for heritability across multiple genes for gene expression levels. Then we can search within the enriched regions for trans-eQTLs.


Project Progress:

Sept 4.

  1. Downloaded RHEmc and ran the test scripts
  2. Created scripts to split the GTEx genotype data into 10 Mb bins of SNPs with at least a minor allele frequency of 5%.
  3. Created scripts to create the annotation file and path file necessary as impute to RHEmc.
  4. Currently scripts running on Hoffman