ArticlePloS one2012
Using prior information from the medical literature in GWAS of oral cancer identifies novel susceptibility variant on chromosome 4--the AdAPT method.
Article in PloS one, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 papers, 2 of them syntheses that pooled it.
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Who cites it
9 citing papers in PubMed, 2 syntheses or guidelines pooled it, 24 citations in OpenAlex.
- Identification of lung cancer histology-specific variants applying Bayesian framework variant prioritization approaches within the TRICL and ILCCO consortia.Carcinogenesis · 2015Pooled it
- Bayesian test for colocalisation between pairs of genetic association studies using summary statistics.PLoS genetics · 2014Pooled it
- Variants in FAT1 and COL9A1 genes in male population with or without substance use to assess the risk factors for oral malignancy.PloS one · 2019Article
- Single nucleotide polymorphisms as markers of genetic susceptibility for oral potentially malignant disorders risk: Review of evidence to date.Oral oncology · 2016Review
- The role of regulatory variation in complex traits and disease.Nature reviews. Genetics · 2015Review
- Big data in medicine is driving big changes.Yearbook of medical informatics · 2014Review
- Detecting signals in pharmacogenomic genome-wide association studies.The pharmacogenomics journal · 2014Article
- Associating disease-related genetic variants in intergenic regions to the genes they impact.PeerJ · 2014Article
- Getting more out of biomedical documents with GATE's full lifecycle open source text analytics.PLoS computational biology · 2013Article
Corrections and comments
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Authors and funding
51 authors at 20 institutions in 15 countries.
Funding
Abstract
backgroundGenome-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.
methodsWe 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 previous lung cancer GWAS, and subsequently applied it in a two-phase GWAS of oral cancer.
resultsKnown lung cancer susceptibility SNPs were consistently ranked higher by AdAPT BFDPs than by p-values. In the oral cancer GWAS, we sought to replicate the top five SNPs as ranked by AdAPT BFDPs, of which rs991316, located in the ADH gene region of 4q23, displayed a statistically significant association with oral cancer risk in the replication phase (per-rare-allele log additive p-value [p(trend)] = 2.5×10(-3)). The combined OR for having one additional rare allele was 0.83 (95% CI: 0.76-0.90), and this association was independent of previously identified susceptibility SNPs that are associated with overall UADT cancer in this gene region. We also investigated if rs991316 was associated with other cancers of the upper aerodigestive tract (UADT), but no additional association signal was found.
conclusionThis study highlights the potential utility of systematically incorporating prior knowledge from the medical literature in genome-wide analyses using the AdAPT methodology. AdAPT is available online (url: http://services.gate.ac.uk/lld/gwas/service/config).
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