Modeling gene-by-environment interaction in comorbid depression with alcohol use disorders via an integrated bioinformatics approach

Table 1 Comparison of Whole Genome Association (WGA) to text based, Entrez Gene, search for candidate genes.

	Identifying Candidate Genes
	WGA	Text Based Search
Data Source	Genotyping and Phenotyping	Entrez Gene
Current Availability of Data	Limited	Available
Expense	High	Free (Taxpayer Subsidized)
Sensitivity	Low; limited number of markers tested	Low; much remains unknown about most genes
Positive Predictive Value	Low; many false positives	High; curated information is backed by experimental data and peer review
Population Specific	Yes	Generally no, although population specific information may be included in some records
Specific Variants Identified	Yes, although SNPs that tag haplotypes may not be disease causing variants	Generally no, although specific variants may be annotated. Separate genotyping is usually required for validated candidates
Multi-Gene Effects on Phenotype	Limited	Yes
Complex Phenotypes	Limited	Yes

Text based searches, using data at NCBI as the first source for candidate gene data, provide advantages in data availability, price, and positive predictive value.

ISSN: 1756-0381