13073_2020_816_MOESM1_ESM.docx (1.51 MB)
Additional file 1 of A multilayered post-GWAS assessment on genetic susceptibility to pancreatic cancer
journal contribution
posted on 2021-02-01, 04:17 authored by Evangelina López de Maturana, Juan Antonio Rodríguez, Lola Alonso, Oscar Lao, Esther Molina-Montes, Isabel Adoración Martín-Antoniano, Paulina Gómez-Rubio, Rita Lawlor, Alfredo Carrato, Manuel Hidalgo, Mar Iglesias, Xavier Molero, Matthias Löhr, Christopher Michalski, José Perea, Michael O’Rorke, Victor Manuel Barberà, Adonina Tardón, Antoni Farré, Luís Muñoz-Bellvís, Tanja Crnogorac-Jurcevic, Enrique Domínguez-Muñoz, Thomas Gress, William Greenhalf, Linda Sharp, Luís Arnes, Lluís Cecchini, Joaquim Balsells, Eithne Costello, Lucas Ilzarbe, Jörg Kleeff, Bo Kong, Mirari Márquez, Josefina Mora, Damian O’Driscoll, Aldo Scarpa, Weimin Ye, Jingru Yu, Montserrat García-Closas, Manolis Kogevinas, Nathaniel Rothman, Debra T Silverman, Demetrius Albanes, Alan A Arslan, Laura Beane-Freeman, Paige M Bracci, Paul Brennan, Bas Bueno-de-Mesquita, Julie Buring, Federico Canzian, Margaret Du, Steve Gallinger, J Michael Gaziano, Phyllis J Goodman, Marc Gunter, Loic LeMarchand, Donghui Li, Rachael E Neale, Ulrika Peters, Gloria M Petersen, Harvey A Risch, Maria José Sánchez, Xiao-Ou Shu, Mark D Thornquist, Kala Visvanathan, Wei Zheng, Stephen J Chanock, Douglas Easton, Brian M Wolpin, Rachael Z Stolzenberg-Solomon, Alison P Klein, Laufey T Amundadottir, Marc A Marti-Renom, Francisco X Real, Núria MalatsAdditional file 1: Table S1. Characteristics of the study populations. Table S2. Replication of the SNPs reported as associated with pancreatic cancer risk in European population and published in GWAS Catalog. Table S3. Validated variants (at the nominal p-value), in PanScan and PanC4 populations, among the top 20 SNPs identified in the PanGenEU GWAS study. Figure S1. Functional in-silico analysis strategy followed to identify novel genomic regions previously prioritized using the 1D, 2D and 3D approaches. Figure S2. GWAS Manhattan plot for the PanGenEU study. The x-axis is the genomic position of each variant and the y-axis is the −log10 p-value obtained in the 1D analysis. Figure S3. Q-Q plots for pancreatic cancer risk of the association results using the PanGenEU case-control study (S2a) and PanGenEU&EPICURO study populations (S2b). Figure S4. Scatterplot of the local Moran’s index (LMI) obtained in the 2D approach and the –log10 p-value obtained in the GWAS analysis (1D approach). Figure S5. Results of the benchmarking test showing that the median rank position of the LMI values for the 22 pancreatic cancer signals from the GWAS Catalog is significantly higher than 10,000 randomly selected sets of the same size. Figure S6. Minor allele frequency (MAF) distributions for the top 97 SNPs identified by LMI (in pink) and by GWAS (in blue). Figure S7. LMI Manhattan plot for the PanGenEU study. The x-axis is the genomic position of each variant and the y-axis is the LMI value obtained in the 2D analysis. Figure S8. Q-Q plots show significant enrichment of SNPs with low p-values in the variants prioritized in the 2D-approach (S8a), and in the credible sets derived from them (S8b). Figure S9. Complementary NETWORK (in blue our input KEGG pathways; in green, the complementary pathways interconnected with them) obtained with Pathway-connector webtool.
