Abstract
Collapsing methods are used in association studies to exploit the effect of genetic rare variants in diseases. In this work we model an enriched collapsing approach by including genes, protein domains, pathways and protein-protein interactions data. We applied the collapsing technique to a data set of epileptic (85 cases) and healthy (61 controls) subjects. The method retrieved 4 genes, 5 domains, 33 gene interactions and 14 pathways showing a significant association with the disease. Collapsed data have been also used as features for prediction models. We found that the use of protein-protein interactions as model features increases the area under ROC curve (+1.5%) if compared to the solely gene-based approach.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
Preview
Unable to display preview. Download preview PDF.
References
Luo, L., Boerwinkle, E., Xiong, M.: Association studies for next-generation sequencing. Genome Research 21(7), 1099–1108 (2011)
Bansal, V., Libiger, O., Torkamani, A., Schork, N.J.: Statistical analysis strategies for association studies involving rare variants. Nat. Rev. Genet. 11(11), 773–785 (2010)
Li, Y., Byrnes, A.E., Li, M.: To Identify Associations with Rare Variants, Just WHaIT: Weighted Haplotype and Imputation-Based Tests. American Journal of Human Genetics 87(5), 728–773 (2010)
Dering, C., Hemmelmann, C., Pugh, E., Ziegler, A.: Statistical analysis of rare sequence variants: an overview of collapsing methods. Genetic Epidemiology 35(S1), S12–S17 (2011)
Price, A.L., et al.: Pooled association tests for rare variants in exon-resequencing studies. Am. J. Hum. Genet. 86(6), 832–838 (2010)
Tatonetti, N.P., Dudley, J.T., Sagreiya, H., Butte, A.J., Altman, R.B.: An integrative method for scoring candidate genes from association studies: application to warfarin dosing. BMC Bioinformatics 28(11), S9 (2010)
Della Mina, E., et al.: Improving molecular diagnosis in epilepsy by a dedicated high-throughput sequencing platform. Eur. J. Hum. Genet. (2014) (Epub ahead of print)
Riant, F., et al.: Identification of CACNA1A large deletions in four patients with episodic ataxia. Neurogenetics 11, 101–106 (2010)
Chioza, B., et al.: Association between the alpha-1A calcium channel gene CACNA1A and idiopathic generalized epilepsy. Neurology 56, 1245–1246 (2001)
Klassen, T., et al.: Exome sequencing of ion channel genes reveals complex profiles confounding personal risk assessment in epilepsy. Cell 145(7), 1036–1048 (2011)
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2015 Springer International Publishing Switzerland
About this paper
Cite this paper
Marini, S., Limongelli, I., Rizzo, E., Da, T., Bellazzi, R. (2015). A Genomic Data Fusion Framework to Exploit Rare and Common Variants for Association Discovery. In: Holmes, J., Bellazzi, R., Sacchi, L., Peek, N. (eds) Artificial Intelligence in Medicine. AIME 2015. Lecture Notes in Computer Science(), vol 9105. Springer, Cham. https://doi.org/10.1007/978-3-319-19551-3_12
Download citation
DOI: https://doi.org/10.1007/978-3-319-19551-3_12
Publisher Name: Springer, Cham
Print ISBN: 978-3-319-19550-6
Online ISBN: 978-3-319-19551-3
eBook Packages: Computer ScienceComputer Science (R0)