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

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

  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
  1. 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.