2023-09-18

Presentation by Scott Adamson

Pre-mRNA splicing can be important in interpreting functional interpretation of GWAS associations.

Proposed experiments:

• Aim 1. Use colocalization / ML predictions to find splicing relevant variants in GWAS associated variants of hematological phenotype. (sQTLs, SpliceAI high delta score, RNAprot high delta score)
• Aim 2. Assay effects on splicing. CRiSPR based editing \(\rightarrow\) scRNA-seq library \(\rightarrow\) hybrid capture of specific junctions and gRNAs \(\rightarrow\) identify splice-altering variants \(\rightarrow\) validation of splice-altering variants on isoforms with ONT and mass spectrometry.

Experimental considerations:

How many cells? How many guides? How good the editing needs to be done?

Population scale scRNA-seq enables discovery of cell type specific eQTLs. Also see splatPOP – scRNA-seq simulation. How to simulate scRNA-seq sQTL?

Scott used simulations to identify and implement reasonable default parameters, e,g. read count parameters, transcript-end read bias, technology specificity.

Estimating base editing efficiency

Scott also developed a method for measuring editing efficiency.