Supplementary Materials

Supplementary Material for:

Functional variants in the LRRK2 gene confer shared effects on risk for Crohn's disease and Parkinson's disease

Ken Y. Hui, Heriberto Fernandez-Hernandez, Jianzhong Hu, Adam Schaffner, Nathan Pankratz, Nai-Yun Hsu, Ling-Shiang Chuang, Shai Carmi, Nicole Villaverde, Xianting Li, Manual Rivas, Adam P. Levine, Xiuliang Bao, Philippe R. Labrias, Talin Haritunians, Darren Ruane, Kyle Gettler, Ernie Chen, Dalin Li, Elena R. Schiff, Nikolas Pontikos, Nir Barzilai, Steven R. Brant, Susan Bressman, Adam S. Cheifetz, Lorraine N. Clark, Mark J. Daly, Robert J. Desnick, Richard H. Duerr, Seymour Katz, Todd Lencz, Richard H. Myers, Harry Ostrer, Laurie Ozelius, Haydeh Payami, Yakov Peter, John D. Rioux, Anthony W. Segal, William K. Scott, Mark S. Silverberg, Jeffery M. Vance, Iban Ubarretxena-Belandia, Tatiana Foroud, Gil Atzmon, Itsik Pe'er, Yiannis Ioannou, Dermot P. B. McGovern, Zhenyu Yue, Eric E. Schadt, Judy H. Cho, Inga Peter*

*Corresponding author. Email: inga.peter{at}

Published 10 January 2018, Sci. Transl. Med. 10, eaai7795 (2018)
DOI: 10.1126/scitranslmed.aai7795

This PDF file includes:

  • Materials and Methods
  • Fig. S1. Schematic workflow of genetic analysis by analytic stages.
  • Fig. S2. Variants identified through exome sequencing by MAF and imputation quality.
  • Fig. S3. Principal components analysis.
  • Fig. S4. Q-Q plot of CD association results shows enrichment of true-positive signals below 10−3.
  • Fig. S5. Single-point association with CD and PD in the Ashkenazi Jewish cohort using imputed genotypes within the LRRK2 locus, conditioned and unconditioned on the CD-associated coding variant N2081D.
  • Fig. S6. Log odds ratio–weighted additive risk allele burden scores.
  • Table S1. Power calculations.
  • Table S2. Ashkenazi Jewish enriched exome variants genotyped as custom content.
  • Table S3. Sample cohort description.
  • Table S5. LRRK2-phased haplotype association.
  • Legends for tables S4 and S6

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Other Supplementary Material for this manuscript includes the following:

  • Table S4. All variants with Ashkenazi Jewish CD discovery P < 2 × 10−5 (Excel file).
  • Table S6. All imputed variants with nominal CD or PD association (P < 0.05) within the LRRK2 locus (Excel file).

[Download Tables S4 and S6]