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Genetic association and transcriptome integration identify contributing genes and tissues at cystic fibrosis modifier loci

Author

Listed:
  • Jiafen Gong
  • Fan Wang
  • Bowei Xiao
  • Naim Panjwani
  • Fan Lin
  • Katherine Keenan
  • Julie Avolio
  • Mohsen Esmaeili
  • Lin Zhang
  • Gengming He
  • David Soave
  • Scott Mastromatteo
  • Zeynep Baskurt
  • Sangook Kim
  • Wanda K O’Neal
  • Deepika Polineni
  • Scott M Blackman
  • Harriet Corvol
  • Garry R Cutting
  • Mitchell Drumm
  • Michael R Knowles
  • Johanna M Rommens
  • Lei Sun
  • Lisa J Strug

Abstract

Cystic Fibrosis (CF) exhibits morbidity in several organs, including progressive lung disease in all patients and intestinal obstruction at birth (meconium ileus) in ~15%. Individuals with the same causal CFTR mutations show variable disease presentation which is partly attributed to modifier genes. With >6,500 participants from the International CF Gene Modifier Consortium, genome-wide association investigation identified a new modifier locus for meconium ileus encompassing ATP12A on chromosome 13 (min p = 3.83x10-10); replicated loci encompassing SLC6A14 on chromosome X and SLC26A9 on chromosome 1, (min p

Suggested Citation

  • Jiafen Gong & Fan Wang & Bowei Xiao & Naim Panjwani & Fan Lin & Katherine Keenan & Julie Avolio & Mohsen Esmaeili & Lin Zhang & Gengming He & David Soave & Scott Mastromatteo & Zeynep Baskurt & Sangoo, 2019. "Genetic association and transcriptome integration identify contributing genes and tissues at cystic fibrosis modifier loci," PLOS Genetics, Public Library of Science, vol. 15(2), pages 1-36, February.
    • Handle: RePEc:plo:pgen00:1008007
    DOI: 10.1371/journal.pgen.1008007
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    References listed on IDEAS

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    1. Oliver Stegle & Leopold Parts & Richard Durbin & John Winn, 2010. "A Bayesian Framework to Account for Complex Non-Genetic Factors in Gene Expression Levels Greatly Increases Power in eQTL Studies," PLOS Computational Biology, Public Library of Science, vol. 6(5), pages 1-11, May.
    2. John D. Storey, 2002. "A direct approach to false discovery rates," Journal of the Royal Statistical Society Series B, Royal Statistical Society, vol. 64(3), pages 479-498, August.
    3. Claudia Giambartolomei & Damjan Vukcevic & Eric E Schadt & Lude Franke & Aroon D Hingorani & Chris Wallace & Vincent Plagnol, 2014. "Bayesian Test for Colocalisation between Pairs of Genetic Association Studies Using Summary Statistics," PLOS Genetics, Public Library of Science, vol. 10(5), pages 1-15, May.
    4. Xiaoquan Wen & Roger Pique-Regi & Francesca Luca, 2017. "Integrating molecular QTL data into genome-wide genetic association analysis: Probabilistic assessment of enrichment and colocalization," PLOS Genetics, Public Library of Science, vol. 13(3), pages 1-25, March.
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