Thread by @thatdnaguy

#ASHG21 AT: Adelaide Tovar.
A modular massively parallel reporter assay uncovers context-specific allelic activity of GWAS variants.

#ASHG21 AT: GWAS hits often not in coding sequence [though plenty are in gene bodies] and suggests that the promoter / enhancer / other non-coding sites may affect gene regulation and therefore disease risk.

#ASHG21 AT: MPRA assay activity depends on context (genomic context, episomes versus integrated, promoter/enhancer compatibility)

#ASHG21 AT: How do promoter sequence and proximity affect activity of type 2 diabetes (T2D) associated risk variants?

#ASHG21 AT: 13,230 allele pairs. 79,380 GWAS oligos. Rat insulinoma cells.

#ASHG21 AT: Both the positioning and the promoter affect the activity of the inserted GWAS variants.

#ASHG21 AT: Joint modeling to quantify activity per insert and including the position and promoter used as covariates.

#ASHG21 AT: Looking just at significant effects about equal number of inserts biased toward having further or closer positioning. More in the insulin promoter plasmids versus SCP1 plasmids.

#ASHG21 AT: Used lasso regression to predict the bias based on genomic annotation and transcription factor motifs. Identified features. The highest coefficient was for active TSS motif being close to promoter. Enhancer like do better downstream.

#ASHG21 AT: [ i.e. they seem to do better if the positioning is similar to their genomic context. If you're testing enhancers, they should be further away. Promoters should be closer. ]

#ASHG21 AT: Top 3 TF motif coefficients they see HNF1alpha, which is known to regulate glucose metabolishm.

#ASHG21 AT: Previously documented allele effects are only detected using a tissue-specific promoter, not a general promoter.

#ASHG21 AT: Overall context is important in MPRA. Need the right cell type. The right types of promoters. And the right positioning, which is context-dependent on the type of element being tested.