Functional dynamic genetic effects on gene regulation are specific to particular cell types and environmental conditions

AS Findley, A Monziani, AL Richards, K Rhodes… - Elife, 2021 - elifesciences.org
Genetic effects on gene expression and splicing can be modulated by cellular and
environmental factors; yet interactions between genotypes, cell type, and treatment have not …

[HTML][HTML] Genotype-environment interactions reveal causal pathways that mediate genetic effects on phenotype

J Gagneur, O Stegle, C Zhu, P Jakob, MM Tekkedil… - PLoS …, 2013 - journals.plos.org
Unraveling the molecular processes that lead from genotype to phenotype is crucial for the
understanding and effective treatment of genetic diseases. Knowledge of the causative …

Dynamic genetic regulation of gene expression during cellular differentiation

BJ Strober, R Elorbany, K Rhodes, N Krishnan… - Science, 2019 - science.org
Genetic regulation of gene expression is dynamic, as transcription can change during cell
differentiation and across cell types. We mapped expression quantitative trait loci (eQTLs) …

Impact of regulatory variation across human iPSCs and differentiated cells

NE Banovich, YI Li, A Raj, MC Ward… - Genome …, 2018 - genome.cshlp.org
Induced pluripotent stem cells (iPSCs) are an essential tool for studying cellular
differentiation and cell types that are otherwise difficult to access. We investigated the use of …

[HTML][HTML] Single cell eQTL analysis identifies cell type-specific genetic control of gene expression in fibroblasts and reprogrammed induced pluripotent stem cells

D Neavin, Q Nguyen, MS Daniszewski, HH Liang… - Genome biology, 2021 - Springer
Background The discovery that somatic cells can be reprogrammed to induced pluripotent
stem cells (iPSCs) has provided a foundation for in vitro human disease modelling, drug …

[HTML][HTML] Patterns of Cis Regulatory Variation in Diverse Human Populations

BE Stranger, SB Montgomery, AS Dimas, L Parts… - PLoS …, 2012 - journals.plos.org
The genetic basis of gene expression variation has long been studied with the aim to
understand the landscape of regulatory variants, but also more recently to assist in the …

[PDF][PDF] Analysis of transcriptional variability in a large human iPSC library reveals genetic and non-genetic determinants of heterogeneity

I Carcamo-Orive, GE Hoffman, P Cundiff… - Cell stem cell, 2017 - cell.com
Variability in induced pluripotent stem cell (iPSC) lines remains a concern for disease
modeling and regenerative medicine. We have used RNA-sequencing analysis and linear …

Inputs drive cell phenotype variability

J Park, A Brureau, K Kernan, A Starks, S Gulati… - Genome …, 2014 - genome.cshlp.org
What is the significance of the extensive variability observed in individual members of a
single-cell phenotype? This question is particularly relevant to the highly differentiated …

[HTML][HTML] A village in a dish model system for population-scale hiPSC studies

DR Neavin, AM Steinmann, N Farbehi, HS Chiu… - Nature …, 2023 - nature.com
The mechanisms by which DNA alleles contribute to disease risk, drug response, and other
human phenotypes are highly context-specific, varying across cell types and different …

Local genetic effects on gene expression across 44 human tissues

F Aguet, AA Brown, SE Castel, JR Davis… - BioRxiv, 2016 - biorxiv.org
Expression quantitative trait locus (eQTL) mapping provides a powerful means to identify
functional variants influencing gene expression and disease pathogenesis. We report the …