Response to Comment On: Perry et al. (2009) Interrogating Type 2 Diabetes Genome-Wide Association Data Using a Biological Pathway-Based Approach. Diabetes;58:1463–1467
- From the Genetics of Complex Traits, Peninsula Medical School, Exeter, U.K.
- Corresponding author: John R.B. Perry, john.perry{at}pms.ac.uk.
We agree with Elbers et al. (1) that there are a number of limitations to genome-wide association (GWA) study pathway-based approaches as currently implemented. Not least of which are the incomplete knowledge and characterization of human genes and pathways and the statistical difficulties in assessing the significance of a pathway. We would, however, like to address some of their specific criticisms.
First, we would like to respond to the concern that few of the type 2 diabetes loci genes are represented in the pathways tested. Our study used three different pathway datasets: Kyoto Encyclopedia of Genes and Genomes (KEGG), BioCarta, and Gene Ontology (GO; level 4 annotations in Biological Process …
