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Table 10 Pros and cons of arrays versus whole genome sequencing [49]

From: Establishing analytical validity of BeadChip array genotype data by comparison to whole-genome sequence and standard benchmark datasets

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