A comparison of genotyping arrays

Area of Science:

• Genetics and Genomics
• Bioinformatics
• Molecular Biology

Background:

• Genotyping arrays are essential tools for genetic research, including genome-wide association studies (GWAS), clinical diagnostics, and linkage studies.
• The rapid expansion of array content necessitates a comprehensive comparison to guide researchers in selecting the most appropriate platform.

Purpose of the Study:

• To compare 28 commercially available genotyping arrays based on key performance metrics and content.
• To evaluate arrays for genome-wide coverage, imputation quality, inclusion of known GWAS loci, mtDNA variants, and clinically relevant genes (ACMG actionable, pharmacogenetic, HLA).

Main Methods:

• A systematic comparison of 28 genotyping arrays was conducted.
• Evaluated arrays for SNV count, genome-wide coverage, imputation quality across populations, and presence of specific gene sets (GWAS loci, mtDNA, ACMG, pharmacogenetics, HLA).

Main Results:

• Genome-wide coverage strongly correlates with the number of single-nucleotide variants (SNVs) on an array.
• Imputation quality, critical for GWAS, does not correlate with SNV count and was similar for European and African populations across tested arrays.
• Array content beyond SNV count, such as pharmacogenetic or HLA variants, should be the primary consideration for selection.

Conclusions:

• No single genotyping array is optimal for all research questions; selection depends on specific study needs.
• Imputation quality is a key factor for GWAS usability, but coverage and specific content (e.g., pharmacogenetics, HLA) are more differentiating criteria for array selection.
• This comparative analysis serves as a guideline to assist researchers in choosing the best genotyping array for their specific research requirements.