Open AccessBayesian and frequentist analysis of an Austrian genome-wide association study of colorectal cancer and advanced adenomas
Author(s) -
Philipp Hofer,
Michael Hagmann,
Stefanie Brezina,
Erich Dolejsi,
Karl Mach,
Gernot Leeb,
Andreas Baierl,
Stephan Buch,
Hedwig Sutterlüty,
Judith KarnerHanusch,
Michael Bergmann,
Thomas BachleitnerHofmann,
Anton Stift,
Armin Gerger,
Katharina Rötzer,
J. Karner,
Stefan Stättner,
Mélanie Waldenberger,
Thomas Meitinger,
Konstantin Strauch,
Jakob Linseisen,
Christian Gieger,
Florian Frommlet,
Andrea Gsur
Publication year - 2017
Publication title -
oncotarget
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.373
H-Index - 127
ISSN - 1949-2553
DOI - 10.18632/oncotarget.21697
Subject(s) - frequentist inference , colorectal cancer , medicine , bayesian probability , oncology , genome wide association study , cancer , bioinformatics , statistics , biology , bayesian inference , single nucleotide polymorphism , genetics , genotype , gene , mathematics
Most genome-wide association studies (GWAS) were analyzed using single marker tests in combination with stringent correction procedures for multiple testing. Thus, a substantial proportion of associated single nucleotide polymorphisms (SNPs) remained undetected and may account for missing heritability in complex traits. Model selection procedures present a powerful alternative to identify associated SNPs in high-dimensional settings. In this GWAS including 1060 colorectal cancer cases, 689 cases of advanced colorectal adenomas and 4367 controls we pursued a dual approach to investigate genome-wide associations with disease risk applying both, single marker analysis and model selection based on the modified Bayesian information criterion, mBIC2, implemented in the software package MOSGWA. For different case-control comparisons, we report models including between 1-14 candidate SNPs. A genome-wide significant association of rs17659990 (P=5.43×10 -9 , DOCK3 , chromosome 3p21.2) with colorectal cancer risk was observed. Furthermore, 56 SNPs known to influence susceptibility to colorectal cancer and advanced adenoma were tested in a hypothesis-driven approach and several of them were found to be relevant in our Austrian cohort. After correction for multiple testing (α=8.9×10 -4 ), the most significant associations were observed for SNPs rs10505477 (P=6.08×10 -4 ) and rs6983267 (P=7.35×10 -4 ) of CASC8 , rs3802842 (P=8.98×10 -5 , COLCA1,2 ), and rs12953717 (P=4.64×10 -4 , SMAD7 ). All previously unreported SNPs demand replication in additional samples. Reanalysis of existing GWAS datasets using model selection as tool to detect SNPs associated with a complex trait may present a promising resource to identify further genetic risk variants not only for colorectal cancer.