Power of data mining methods to detect genetic associations and interactions.
Hum Hered
; 72(2): 85-97, 2011.
Article
en En
| MEDLINE
| ID: mdl-21934324
ABSTRACT
BACKGROUND:
Genetic association studies, thus far, have focused on the analysis of individual main effects of SNP markers. Nonetheless, there is a clear need for modeling epistasis or gene-gene interactions to better understand the biologic basis of existing associations. Tree-based methods have been widely studied as tools for building prediction models based on complex variable interactions. An understanding of the power of such methods for the discovery of genetic associations in the presence of complex interactions is of great importance. Here, we systematically evaluate the power of three leading algorithms random forests (RF), Monte Carlo logic regression (MCLR), and multifactor dimensionality reduction (MDR).METHODS:
We use the algorithm-specific variable importance measures (VIMs) as statistics and employ permutation-based resampling to generate the null distribution and associated p values. The power of the three is assessed via simulation studies. Additionally, in a data analysis, we evaluate the associations between individual SNPs in pro-inflammatory and immunoregulatory genes and the risk of non-Hodgkin lymphoma.RESULTS:
The power of RF is highest in all simulation models, that of MCLR is similar to RF in half, and that of MDR is consistently the lowest.CONCLUSIONS:
Our study indicates that the power of RF VIMs is most reliable. However, in addition to tuning parameters, the power of RF is notably influenced by the type of variable (continuous vs. categorical) and the chosen VIM.
Texto completo:
1
Colección:
01-internacional
Banco de datos:
MEDLINE
Asunto principal:
Epistasis Genética
/
Estudios de Asociación Genética
/
Minería de Datos
Tipo de estudio:
Health_economic_evaluation
/
Prognostic_studies
/
Risk_factors_studies
Límite:
Humans
Idioma:
En
Revista:
Hum Hered
Año:
2011
Tipo del documento:
Article