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The Use of Genome-Wide eQTL Associations in Lymphoblastoid Cell Lines to Identify Novel Genetic Pathways Involved in Complex Traits

Author

Listed:
  • Josine L Min
  • Jennifer M Taylor
  • J Brent Richards
  • Tim Watts
  • Fredrik H Pettersson
  • John Broxholme
  • Kourosh R Ahmadi
  • Gabriela L Surdulescu
  • Ernesto Lowy
  • Christian Gieger
  • Chris Newton-Cheh
  • Markus Perola
  • Nicole Soranzo
  • Ida Surakka
  • Cecilia M Lindgren
  • Jiannis Ragoussis
  • Andrew P Morris
  • Lon R Cardon
  • Tim D Spector
  • Krina T Zondervan

Abstract

The integrated analysis of genotypic and expression data for association with complex traits could identify novel genetic pathways involved in complex traits. We profiled 19,573 expression probes in Epstein-Barr virus-transformed lymphoblastoid cell lines (LCLs) from 299 twins and correlated these with 44 quantitative traits (QTs). For 939 expressed probes correlating with more than one QT, we investigated the presence of eQTL associations in three datasets of 57 CEU HapMap founders and 86 unrelated twins. Genome-wide association analysis of these probes with 2.2 m SNPs revealed 131 potential eQTLs (1,989 eQTL SNPs) overlapping between the HapMap datasets, five of which were in cis (58 eQTL SNPs). We then tested 535 SNPs tagging the eQTL SNPs, for association with the relevant QT in 2,905 twins. We identified nine potential SNP-QT associations (P

Suggested Citation

  • Josine L Min & Jennifer M Taylor & J Brent Richards & Tim Watts & Fredrik H Pettersson & John Broxholme & Kourosh R Ahmadi & Gabriela L Surdulescu & Ernesto Lowy & Christian Gieger & Chris Newton-Cheh, 2011. "The Use of Genome-Wide eQTL Associations in Lymphoblastoid Cell Lines to Identify Novel Genetic Pathways Involved in Complex Traits," PLOS ONE, Public Library of Science, vol. 6(7), pages 1-14, July.
    • Handle: RePEc:plo:pone00:0022070
    DOI: 10.1371/journal.pone.0022070
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    1. Yirong Shi & Yiwei Niu & Peng Zhang & Huaxia Luo & Shuai Liu & Sijia Zhang & Jiajia Wang & Yanyan Li & Xinyue Liu & Tingrui Song & Tao Xu & Shunmin He, 2023. "Characterization of genome-wide STR variation in 6487 human genomes," Nature Communications, Nature, vol. 14(1), pages 1-18, December.

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