Journal article

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

Drew Neavin, Quan Nguyen, Maciej S Daniszewski, Helena H Liang, Han Sheng Chiu, Yong Kiat Wee, Anne Senabouth, Samuel W Lukowski, Duncan E Crombie, Grace E Lidgerwood, Damian Hernandez, James C Vickers, Anthony L Cook, Nathan J Palpant, Alice Pebay, Alex W Hewitt, Joseph E Powell

Genome Biology | BMC | Published : 2021

Abstract

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 development and population genetics studies. Gene expression plays a critical role in complex disease risk and therapeutic response. However, while the genetic background of reprogrammed cell lines has been shown to strongly influence gene expression, the effect has not been evaluated at the level of individual cells which would provide significant resolution. By integrating single cell RNA-sequencing (scRNA-seq) and population genetics, we apply a framework in which to evaluate cell type-specific effects of genetic va..

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Grants

Awarded by National Health and Medical Research Council (NHMRC)


Awarded by Australian Research Council


Awarded by NHMRC Investigator grant


Awarded by NHMRC Senior Practitioner Fellowship


Awarded by Australian Research Council Future Fellowship


Awarded by NHMRC Senior Research Fellowship


Awarded by Australian Heart Foundation


Funding Acknowledgements

This work was supported by grants from the National Health and Medical Research Council (NHMRC) project grant (APP1143163) and Australian Research Council discovery project (DP180101405). JEP is supported by an NHMRC Investigator grant (APP1175781). AWH is supported by an NHMRC Senior Practitioner Fellowship (APP1195444). AP is supported by an Australian Research Council Future Fellowship (FT140100047) and an NHMRC Senior Research Fellowship (APP1154389). NJP is supported by a Fellowship from the Australian Heart Foundation (101889). MD was supported by an International Postgraduate Research Scholarship & Research Training Program Scholarship. This work is also supported by a special initiative from the Australian Research Council (SR1101002), the Joan and Peter Clemenger Foundation, the Ophthalmic Research Institute of Australia, Stem Cells Australia -the Australian Research Council Special Research Initiative in Stem Cell Science, the University of Melbourne and Operational Infrastructure Support from the Victorian Government.