Evaluating intra- and inter-individual variation in the human placental transcriptome
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- dc.contributor.author Hughes, Davidca
- dc.contributor.author Kircher, Martinca
- dc.contributor.author He, Zhisongca
- dc.contributor.author Guo, Songtaoca
- dc.contributor.author Fairbrother, Genevieveca
- dc.contributor.author Moreno, Carlosca
- dc.contributor.author Khaitovich, Philippca
- dc.contributor.author Stoneking, Markca
- dc.date.accessioned 2015-12-16T14:19:43Z
- dc.date.available 2015-12-16T14:19:43Z
- dc.date.issued 2015ca
- dc.description.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./nResults. 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 each 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 demonstrate 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 exhibits expression profiles consistent with neutrality; the remainder are consistent with stabilizing selection, directional selection, or diversifying selection./nConclusions. 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.
- dc.description.sponsorship The Max Planck Society and a grant for visiting young scientists from the Chinese Academy of Science (2009YB1-12) funded the project. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
- dc.format.mimetype application/pdfca
- dc.identifier.citation Hughes D, Kircher M, He Z, Guo S, Fairbrother G, Moreno C, Khaitovich P, Stoneking M. Evaluating intra- and inter-individual variation in the human placental transcriptome. Genome Biology. 2015;16:54. DOI: 10.1186/s13059-015-0627-zca
- dc.identifier.doi http://dx.doi.org/10.1186/s13059-015-0627-z
- dc.identifier.issn 1465-6906ca
- dc.identifier.uri http://hdl.handle.net/10230/25444
- dc.language.iso engca
- dc.publisher BioMed Centralca
- dc.relation.ispartof Genome Biology. 2015;16:54
- dc.rights © 2015 Hughes et al.; licensee BioMed Central. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited.ca
- dc.rights.accessRights info:eu-repo/semantics/openAccessca
- dc.rights.uri http://creativecommons.org/licenses/by/4.0
- dc.subject.other Placenta
- dc.title Evaluating intra- and inter-individual variation in the human placental transcriptomeca
- dc.type info:eu-repo/semantics/articleca
- dc.type.version info:eu-repo/semantics/publishedVersionca