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Elucidation of Genotype-Phenotype Relationships Using Human Stem Cell Models

Our goal of this work is to determine how natural human genetic variation influences molecular and cellular phenotypes using human pluripotent stem cell (hPSC) cells and their derivatives.

This project utilizes the “cell village” approach in which hPSCs (or their derivatives) from many different genetically-distinct donors are pooled together in shared in vitro environments for high throughput multi-modal phenotyping. Genotypes for each donor are collected prior to village construction using whole genome sequencing or SNP array profiling followed by whole genome imputation. Molecular phenotypes for each donor are ascertained via single-cell RNA sequencing followed by Dropulation-based donor de-multiplexing. Finally, cellular phenotypes are quantified using low coverage (0.5-1X) whole genome sequencing of the village followed by Census-seq computation of donor proportions. By capturing genetic, molecular, and cellular phenotyping heterogeneity in a uniform environment, we can detect relationships among alleles, molecules, and cellular traits.

The project data registered with the study includes assessments of cell fitness, defined as a cell's ability to proliferate and survive:

(1) Low coverage (0.5X-1x) whole genome sequencing data from a human embryonic stem cell (hESC)-derived neural progenitor cell village consisting of 38 donors that was harvested at multiple time points (Day 0, 1, 5, 6, and 10) to quantify differential baseline growth rates among donors.

(2) Low coverage (0.5X-1x) whole genome sequencing data from a human embryonic stem cell (hESC)-derived neural progenitor cell village consisting of 38 donors that was harvested at multiple time points (Day 0, 4, and 7) after exposure to a vehicle control, 3 uM, or 10 uM lead (Pb) acetate to quantify differential Pb sensitivities across donors.

(3) Low coverage (0.5X-1x) whole genome sequencing data from a human induced pluripotent stem cell (hiPSC)-derived neural progenitor cell village composed of eleven neurotypical controls and twelve 16p11.2 deletion patients harvested at multiple time points (Day 0, 1, 5, 6, 10) to quantify case-control differences in baseline growth rates.