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Evaluating intra- and inter-individual variation in the human placental transcriptome

David A Hughes, Martin Kircher, Zhisong He, Song Guo, Genevieve L. Fairbrother, Carlos S. Moreno, Philipp Khaitovich, Mark Stoneking
doi: https://doi.org/10.1101/012468
David A Hughes
1Max-Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, Leipzig Germany 04103
2CAS-MPG Partner Institute for Computational Biology, 320 Yue Yang Road, Shanghai 200031, P.R. China
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Martin Kircher
1Max-Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, Leipzig Germany 04103
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Zhisong He
2CAS-MPG Partner Institute for Computational Biology, 320 Yue Yang Road, Shanghai 200031, P.R. China
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Song Guo
2CAS-MPG Partner Institute for Computational Biology, 320 Yue Yang Road, Shanghai 200031, P.R. China
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Genevieve L. Fairbrother
3Obstetrics and Gynecology of Atlanta, 1100 Johnson Ferry Rd NE Suite 800, Center 2, Atlanta, GA 30342, USA
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Carlos S. Moreno
4Department of Pathology and Laboratory Medicine and Department of Biomedical Informatics, Emory University, Atlanta, GA 30322, USA
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Philipp Khaitovich
2CAS-MPG Partner Institute for Computational Biology, 320 Yue Yang Road, Shanghai 200031, P.R. China
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Mark Stoneking
1Max-Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, Leipzig Germany 04103
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Abstract

Background Gene expression variation is a phenotypic trait of particular interest as it represents the initial link between genotype and other phenotypes. Analyzing how such variation apportions among and within groups allows for the evaluation of how genetic and environmental factors influence such traits. It also provides opportunities to identify genes and pathways that may have been influenced by non-neutral processes. Here we use a population genetics framework and next generation sequencing to evaluate how gene expression variation is apportioned among four human groups in a natural biological tissue, the placenta.

Results We estimate that on average, 33.2%, 58.9% and 7.8% of the placental transcriptome is explained by variation within individuals, among individuals and among human groups, respectively. Additionally, when technical and biological traits are included in models of gene expression they account for roughly 2% of total gene expression variation. Notably, the variation that is significantly different among groups is enriched in biological pathways associated with immune response, cell signaling and metabolism. Many biological traits demonstrated correlated changes in expression in numerous pathways of potential interest to clinicians and evolutionary biologists. Finally, we estimate that the majority of the human placental transcriptome (65% of expressed genes) exhibits expression profiles consistent with neutrality; the remainder are consistent with stabilizing selection (26%), directional selection (4.9%), or diversifying selection (4.8%).

Conclusion We apportion placental gene expression variation into individual, population and biological trait factors and identify how each influence the transcriptome. Additionally, we advance methods to associate expression profiles with different forms of selection.

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
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Posted December 08, 2014.
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Evaluating intra- and inter-individual variation in the human placental transcriptome
David A Hughes, Martin Kircher, Zhisong He, Song Guo, Genevieve L. Fairbrother, Carlos S. Moreno, Philipp Khaitovich, Mark Stoneking
bioRxiv 012468; doi: https://doi.org/10.1101/012468
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Evaluating intra- and inter-individual variation in the human placental transcriptome
David A Hughes, Martin Kircher, Zhisong He, Song Guo, Genevieve L. Fairbrother, Carlos S. Moreno, Philipp Khaitovich, Mark Stoneking
bioRxiv 012468; doi: https://doi.org/10.1101/012468

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