Title |
Genetic Drivers of Epigenetic and Transcriptional Variation in Human Immune Cells
|
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Published in |
Cell, November 2016
|
DOI | 10.1016/j.cell.2016.10.026 |
Pubmed ID | |
Authors |
Lu Chen, Bing Ge, Francesco Paolo Casale, Louella Vasquez, Tony Kwan, Diego Garrido-Martín, Stephen Watt, Ying Yan, Kousik Kundu, Simone Ecker, Avik Datta, David Richardson, Frances Burden, Daniel Mead, Alice L. Mann, Jose Maria Fernandez, Sophia Rowlston, Steven P. Wilder, Samantha Farrow, Xiaojian Shao, John J. Lambourne, Adriana Redensek, Cornelis A. Albers, Vyacheslav Amstislavskiy, Sofie Ashford, Kim Berentsen, Lorenzo Bomba, Guillaume Bourque, David Bujold, Stephan Busche, Maxime Caron, Shu-Huang Chen, Warren Cheung, Oliver Delaneau, Emmanouil T. Dermitzakis, Heather Elding, Irina Colgiu, Frederik O. Bagger, Paul Flicek, Ehsan Habibi, Valentina Iotchkova, Eva Janssen-Megens, Bowon Kim, Hans Lehrach, Ernesto Lowy, Amit Mandoli, Filomena Matarese, Matthew T. Maurano, John A. Morris, Vera Pancaldi, Farzin Pourfarzad, Karola Rehnstrom, Augusto Rendon, Thomas Risch, Nilofar Sharifi, Marie-Michelle Simon, Marc Sultan, Alfonso Valencia, Klaudia Walter, Shuang-Yin Wang, Mattia Frontini, Stylianos E. Antonarakis, Laura Clarke, Marie-Laure Yaspo, Stephan Beck, Roderic Guigo, Daniel Rico, Joost H.A. Martens, Willem H. Ouwehand, Taco W. Kuijpers, Dirk S. Paul, Hendrik G. Stunnenberg, Oliver Stegle, Kate Downes, Tomi Pastinen, Nicole Soranzo |
Abstract |
Characterizing the multifaceted contribution of genetic and epigenetic factors to disease phenotypes is a major challenge in human genetics and medicine. We carried out high-resolution genetic, epigenetic, and transcriptomic profiling in three major human immune cell types (CD14(+) monocytes, CD16(+) neutrophils, and naive CD4(+) T cells) from up to 197 individuals. We assess, quantitatively, the relative contribution of cis-genetic and epigenetic factors to transcription and evaluate their impact as potential sources of confounding in epigenome-wide association studies. Further, we characterize highly coordinated genetic effects on gene expression, methylation, and histone variation through quantitative trait locus (QTL) mapping and allele-specific (AS) analyses. Finally, we demonstrate colocalization of molecular trait QTLs at 345 unique immune disease loci. This expansive, high-resolution atlas of multi-omics changes yields insights into cell-type-specific correlation between diverse genomic inputs, more generalizable correlations between these inputs, and defines molecular events that may underpin complex disease risk. |
X Demographics
Geographical breakdown
Country | Count | As % |
---|---|---|
United States | 12 | 14% |
United Kingdom | 10 | 12% |
Australia | 6 | 7% |
Canada | 5 | 6% |
Spain | 5 | 6% |
Germany | 3 | 3% |
Switzerland | 1 | 1% |
Russia | 1 | 1% |
France | 1 | 1% |
Other | 7 | 8% |
Unknown | 35 | 41% |
Demographic breakdown
Type | Count | As % |
---|---|---|
Members of the public | 43 | 50% |
Scientists | 40 | 47% |
Science communicators (journalists, bloggers, editors) | 2 | 2% |
Practitioners (doctors, other healthcare professionals) | 1 | 1% |
Mendeley readers
Geographical breakdown
Country | Count | As % |
---|---|---|
United States | 6 | <1% |
United Kingdom | 6 | <1% |
Germany | 2 | <1% |
Sweden | 2 | <1% |
Spain | 2 | <1% |
South Africa | 1 | <1% |
Netherlands | 1 | <1% |
Mexico | 1 | <1% |
France | 1 | <1% |
Other | 2 | <1% |
Unknown | 771 | 97% |
Demographic breakdown
Readers by professional status | Count | As % |
---|---|---|
Researcher | 183 | 23% |
Student > Ph. D. Student | 182 | 23% |
Student > Master | 71 | 9% |
Student > Bachelor | 54 | 7% |
Student > Doctoral Student | 39 | 5% |
Other | 136 | 17% |
Unknown | 130 | 16% |
Readers by discipline | Count | As % |
---|---|---|
Biochemistry, Genetics and Molecular Biology | 243 | 31% |
Agricultural and Biological Sciences | 199 | 25% |
Immunology and Microbiology | 58 | 7% |
Medicine and Dentistry | 53 | 7% |
Computer Science | 31 | 4% |
Other | 62 | 8% |
Unknown | 149 | 19% |