Table 10 Pros and cons of arrays versus whole genome sequencing [49]
Feature | SNP arrays (GSA) | WGS |
|---|---|---|
Cost | Lower cost | Higher cost |
Genomic coverage | Best for variants for which DNAs of all genotype combinations are available, i.e., not robust for rare variants | Appropriate for detection of nearly all genetic variation in the genome depending on the depth of sequencing, i.e., not robust for difficult to sequence regions |
Requires prior knowledge of the variant, i.e., unable to detect private variants not previously reported | Reduced accuracy in genomic regions of low complexity | |
Reduced accuracy in genomic regions of low complexity | ||
Analyses | Well established analytical protocols and tools for data analyses | High computational costs and greater analytical complexity |
Larger multiple testing burden when conducting single-variant tests | ||
Greater costs to store, process, analyze and interpret the resulting data | ||
Suitability | Screening | Diagnostic testing |
Analyzing known or candidate associations in large cohorts | Detecting and fine-mapping rare variants | |
Detecting low-frequency, common variant associations in large sample sizes | Detecting ultra-rare risk variants when it becomes economically viable to perform WGS at a very large scale |