Additional file 1 of A multilayered post-GWAS assessment on genetic susceptibility to pancreatic cancer
Creators: name: López de Maturana, Evangelina
name: Rodríguez, Juan Antonio
name: Alonso, Lola
name: Lao, Oscar
name: Molina-Montes, Esther
name: Martín-Antoniano, Isabel Adoración
name: Gómez-Rubio, Paulina
name: Lawlor, Rita
name: Carrato, Alfredo
name: Hidalgo, Manuel
name: Iglesias, Mar
name: Molero, Xavier
name: Löhr, Matthias
name: Michalski, Christopher
name: Perea, José
name: O’Rorke, Michael
name: Barberà, Victor Manuel
name: Tardón, Adonina
name: Farré, Antoni
name: Muñoz-Bellvís, Luís
name: Crnogorac-Jurcevic, Tanja
name: Domínguez-Muñoz, Enrique
name: Gress, Thomas
name: Greenhalf, William
name: Sharp, Linda
name: Arnes, Luís
name: Cecchini, Lluís
name: Balsells, Joaquim
name: Costello, Eithne
name: Ilzarbe, Lucas
name: Kleeff, Jörg
name: Kong, Bo
name: Márquez, Mirari
name: Mora, Josefina
name: O’Driscoll, Damian
name: Scarpa, Aldo
name: Ye, Weimin
name: Yu, Jingru
name: García-Closas, Montserrat
name: Kogevinas, Manolis
name: Rothman, Nathaniel
name: Silverman, Debra T
name: Albanes, Demetrius
name: Arslan, Alan A
name: Beane-Freeman, Laura
name: Bracci, Paige M
name: Brennan, Paul
name: Bueno-de-Mesquita, Bas
name: Buring, Julie
name: Canzian, Federico
name: Du, Margaret
name: Gallinger, Steve
name: Gaziano, J Michael
name: Goodman, Phyllis J
name: Gunter, Marc
name: LeMarchand, Loic
name: Li, Donghui
name: Neale, Rachael E
name: Peters, Ulrika
name: Petersen, Gloria M
name: Risch, Harvey A
name: Sánchez, Maria José
name: Shu, Xiao-Ou
name: Thornquist, Mark D
name: Visvanathan, Kala
name: Zheng, Wei
name: Chanock, Stephen J
name: Easton, Douglas
name: Wolpin, Brian M
name: Stolzenberg-Solomon, Rachael Z
name: Klein, Alison P
name: Amundadottir, Laufey T
name: Marti-Renom, Marc A
name: Real, Francisco X
name: Malats, Núria
Publisher: name: figshare
Year: 2021
Subjects: subject: Medicine
subject: Genetics
subject: FOS: Biological sciences
subject: Pharmacology
subject: Biotechnology
subject: Environmental Sciences not elsewhere classified
subject: Biological Sciences not elsewhere classified
subject: Cancer

description: Additional 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&amp;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.