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Cited by 441

Identification of context-dependent expression quantitative trait loci in whole blood

Zhernakova, Daria V, Deelen, Patrick, Vermaat, Martijn, van Iterson, Maarten, van Galen, Michiel, Arindrarto, Wibowo, van 't Hof, Peter, Mei, Hailiang +39 more·2017·Nature Genetics
DOI 10.1038/ng.3737

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  • Previous analyses have prioritized ECHDC3, as it is upregulated in AD post-mortem brains and an eQTL for ECHDC3 was seen in whole blood, though it did not colocalize with the GWAS SNP.

    “Previous analyses have prioritized ECHDC3, as it is upregulated in AD post-mortem brains53,54, and an eQTL for ECHDC3 was seen in whole blood55, though it did not colocalize with the GWAS SNP23.”

    From Genetic analysis of the human microglial transcriptome across brain regions, aging and disease pathologies (2022) · cites this paper as [55]

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Research works printed but not linked: 17

  1. Deelen, P. et al. Calling genotypes from public RNA-sequencing data enables identification of genetic variants that affect gene-expression levels. Genome Med. 7, 30 (2015).
  2. Westra, H.-J. et al. Cell specific eQTL analysis without sorting cells. PLoS Genet. 11, e1005223 (2015).
  3. Fairfax, B.P. et al. Innate immune activity conditions the effect of regulatory variants upon monocyte gene expression. Science 343, 1246949 (2014).
  4. Çalıs ¸kan, M., Baker, S.W., Gilad, Y. & Ober, C. Host genetic variation influences gene expression response to rhinovirus infection. PLoS Genet. 11, e1005111 (2015).
  5. Lee, M.N. et al. Common genetic variants modulate pathogen-sensing responses in human dendritic cells. Science 343, 1246980 (2014).
  6. Barreiro, L.B. et al. Deciphering the genetic architecture of variation in the immune response to Mycobacterium tuberculosis infection. Proc. Natl. Acad. Sci. USA 109, 1204-1209 (2012).
  7. Tigchelaar, E.F. et al. Cohort profile: LifeLines DEEP, a prospective, general population cohort study in the northern Netherlands: study design and baseline characteristics. BMJ Open 5, e006772 (2015).
  8. Naranbhai, V. et al. Genomic modulators of gene expression in human neutrophils. Nat. Commun. 6, 7545 (2015).
  9. Hall, M.A. et al. The critical regulator of embryonic hematopoiesis, SCL, is vital in the adult for megakaryopoiesis, erythropoiesis, and lineage choice in CFU-S12. Proc. Natl. Acad. Sci. USA 100, 992-997 (2003).
  10. Heinrichs, S. et al. MYBL2 is a sub-haploinsufficient tumor suppressor gene in myeloid malignancy. eLife 2, e00825 (2013).
  11. McLeay, R.C. & Bailey, T.L. Motif Enrichment Analysis: a unified framework and an evaluation on ChIP data. BMC Bioinformatics 11, 165 (2010).
  12. Facchetti, F., Cella, M., Festa, S., Fremont, D.H. & Colonna, M. An unusual Fc receptor-related protein expressed in human centroblasts. Proc. Natl. Acad. Sci. USA 99, 3776-3781 (2002).
  13. Rosén, A. et al. Lymphoblastoid cell line with B1 cell characteristics established from a chronic lymphocytic leukemia clone by in vitro EBV infection. OncoImmunology 1, 18-27 (2012). Reprints and permissions information is available online at http://www.nature.com/ reprints/index.html.
  14. Fu, J. et al. Unraveling the regulatory mechanisms underlying tissue-dependent genetic variation of gene expression. PLoS Genet. 8, e1002431 (2012).
  15. Andiappan, A.K. et al. Genome-wide analysis of the genetic regulation of gene expression in human neutrophils. Nat. Commun. 6, 7971 (2015).
  16. Deelen, P. et al. Genotype harmonizer: automatic strand alignment and format conversion for genotype data integration. BMC Res. Notes 7, 901 (2014).
  17. Robinson, M.D. & Oshlack, A. A scaling normalization method for differential expression analysis of RNA-seq data. Genome Biol. 11, R25 (2010).

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Authors
Zhernakova, D. V., Deelen, P., Vermaat, M., van Iterson, M., van Galen, M., Arindrarto, W., van 't Hof, P., Mei, H., van Dijk, F., Westra, H.-J., Bonder, M. J., van Rooij, J., Verkerk, M., Jhamai, P. M., Moed, M., Kielbasa, S. M., Bot, J., Nooren, I., Pool, R., van Dongen, J., Hottenga, J. J., Stehouwer, C. D. A., van der Kallen, C. J. H., Schalkwijk, C. G., Zhernakova, A., Li, Y., Tigchelaar, E. F., de Klein, N., Beekman, M., Deelen, J., van Heemst, D., van den Berg, L. H., Hofman, A., Uitterlinden, A. G., van Greevenbroek, M. M. J., Veldink, J. H., Boomsma, D. I., van Duijn, C. M., Wijmenga, C., Slagboom, P. E., Swertz, M. A., Isaacs, A., van Meurs, J. B. J., Jansen, R., Heijmans, B. T., 't Hoen, P. A. C., & Franke, L.
ORCID
Deelen, Patrick
Venue
Nature Genetics
Publisher
Springer Science and Business Media LLC
Published
2016-12-05
Volume
49
Issue
1
Pages
139-145
ISSN
  • 1061-4036
  • 1546-1718
DOI
10.1038/ng.3737
Cited by
441
References
11
Language
en
Licence
www.springer.com/tdm (tdm)

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