Table 2.

Benefits, Misconceptions, and Limitations of the Genomewide Association Study.

Benefits

Does not require an initial hypothesis

Uses digital and additive data that can be mined and augmented without data degradation

Encourages the formation of collaborative consortia, which tend to continue their collaboration for subsequent analyses

Rules out specific genetic associations (e.g., by showing that no common alleles, other than APOE, are associated with Alzheimer’s disease with a relative risk of more than 2)

Provides data on the ancestry of each subject, which assists in matching case subjects with control subjects

Provides data on both sequence and copy-number variations

Misconceptions

Thought to provide data on all genetic variability associated with disease, when in reality only common alleles with large effects are identified

Thought to screen out alleles with a small effect size, when in reality such findings may still be very useful in determining pathogenic biochemical pathways, even though low-risk alleles may be of little predictive value

Limitations

Requires samples from a large number of case subjects and control subjects and therefore can be challenging to organize

Finds loci, not genes, which can complicate the identification of pathogenic changes on an associated haplotype

Detects only alleles that are common (>5%) in a population

Requires replication in a similarly large number of samples