A method for detecting epistasis in genome-wide studies using case-control multi-locus association analysis

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2008
Author
Gayán, Javier
González-Pérez, Antonio
Bermudo, Fernando
Eugenia Sáez, María
Royo Sánchez-Palencia, José Luis
Quintas, Antonio
Galan, José J.
Morón, Francisco J.
Ramirez Lorca, Reposo
Real, Luis M
Ruiz González, Agustín
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Abstract
Background: The difficulty in elucidating the genetic basis of complex diseases roots in the many factors that can affect the development of a disease. Some of these genetic effects may interact in complex ways, proving undetectable by current single-locus methodology. Results: We have developed
an analysis tool called Hypothesis Free Clinical Cloning (HFCC) to search for genome-wide epistasis in a case-control design. HFCC combines a relatively fast computing algorithm for genome-wide epistasis detection, with the flexibility to test a variety of different epistatic models in multi-locus combinations. HFCC has good power to detect multi-locus interactions simulated under a variety of genetic models and noise conditions. Most importantly, HFCC can accomplish exhaustive genome-wide epistasis search with large datasets as demonstrated with a 400,000 SNP set typed on a cohort of Parkinson's disease patients and controls. Conclusion: With the current availability of genetic studies with large numbers of individuals and genetic markers, HFCC can have a great impact in the identification of epistatic effects that escape the standard single-locus association analyses.
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http://hdl.handle.net/10459.1/60016
DOI
https://doi.org/10.1186/1471-2164-9-360
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BioMed Central Genomics, 2008, vol. 9, núm. 360, p. 1-14
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Except where otherwise noted, this item's license is described as cc-by (c) Gayán et al., 2008