Using prior information from the medical literature in GWAS of oral cancer identifies novel susceptibility variant on chromosome 4―the AdAPT method

Johansson, Mattias Roberts, Angus Chen, Dan Li, Yaoyong Delahaye-Sourdeix, Manon Aswani, Niraj Greenwood, Mark A Benhamou, Simone Lagiou, Pagona Holcatova, Ivana Richiardi, Lorenzo Kjaerheim, Kristina Agudo, Antonio Castellsague, Xavier Macfarlane, Tatiana V Barzan, Luigi Canova, Cristina Thakker, Nalin S Conway, David I Znaor, Ariana Healy, Claire M Ahrens, Wolfgang Zaridze, David Szeszenia-Dabrowska, Neonilia Lissowska, Jolanta Fabianova, Eleonora Mates, Ioan Nicolae Bencko, Vladimir Foretova, Lenka Janout, Vladimir Curado, Maria Paula Koifman, Sergio Menezes, Ana Wunsch-Filho, Victor Eluf-Neto, Jose Boffetta, Paolo Franceschi, Silvia Herrero, Rolando Fernandez Garrote, Leticia Talamini, Renato Boccia, Stefania Galan, Pilar Vatten, Lars Thomson, Peter Zelenika, Diana Lathrop, Mark Byrnes, Graham Cunningham, Hamish Brennan, Paul Wakefield, Jon McKay, James D eng 1R03DE020116/DE/NIDCR NIH HHS/ R01 CA092039 05/CA/NCI NIH HHS/ Research Support, N.I.H., Extramural Research Support, Non-U.S. Gov't 2012/06/05 06:00 PLoS One. 2012;7(5):e36888. doi:10.1371/journal.pone.0036888. Epub 2012 May 25. ; International audience ; BACKGROUND: Genome-wide association studies (GWAS) require large sample sizes to obtain adequate statistical power, but it may be possible to increase the power by incorporating complementary data. In this study we investigated the feasibility of automatically retrieving information from the medical literature and leveraging this information in GWAS. METHODS: We developed a method that searches through PubMed abstracts for pre-assigned keywords and key concepts, and uses this information to assign prior probabilities of association for each single nucleotide polymorphism (SNP) with the phenotype of interest―the Adjusting Association Priors with Text (AdAPT) method. Association results from a GWAS can subsequently be ranked in the context of these priors using the Bayes False Discovery Probability (BFDP) framework. We initially tested AdAPT by comparing rankings of known susceptibility alleles in a ...