Genotyping Arrays Explained: Measuring Selected Genetic Variation

This article is part of the Foundations of Genomic Data series.

What do genotyping arrays measure?

Genotyping arrays measure variation at a predefined set of genetic locations across the genome. Each location corresponds to a known genetic variant, most commonly a single-nucleotide polymorphism.

Unlike DNA sequencing, genotyping arrays do not read continuous stretches of DNA. Instead, they query whether specific variants are present or absent in a sample.

The resulting data represent a sparse but structured snapshot of genetic variation.

Designed measurement rather than discovery

The variants included on a genotyping array are selected in advance. Their choice reflects prior knowledge about population genetics, disease associations, and linkage disequilibrium structure.

As a result, genotyping arrays are designed to measure known variation efficiently rather than to discover novel mutations.

Types of genotyping platforms

Most modern genotyping arrays are based on SNP microarray technology and are produced by platforms such as Illumina and Affymetrix.

Some arrays are designed for specific populations or traits, while others aim to provide broad genome-wide coverage.

Multi-ethnic arrays attempt to capture variation across diverse ancestral backgrounds by including variants informative in multiple populations.

From sparse measurement to genome-wide coverage

Although genotyping arrays directly measure only a subset of variants, their coverage can be expanded through imputation.

Imputation uses reference panels, such as the 1000 Genomes Project, HRC, or TOPMed, to infer unmeasured variants based on patterns of linkage disequilibrium.

This process leverages the structured correlation between nearby variants to infer a denser representation of genetic variation.

What genotyping arrays are well suited for

Genotyping arrays are widely used in large-scale population studies where cost, consistency, and sample size are critical considerations.

Common applications include genome-wide association studies, polygenic risk score construction, ancestry inference, and epidemiological research.

Their standardized design enables direct comparison across cohorts and studies.

What genotyping arrays do not measure

Genotyping arrays do not capture rare or novel variants outside their predefined set. Structural variants and non-SNP variation are also poorly represented.

Like DNA sequencing, arrays do not provide information about gene expression or regulatory activity.

Genotyping arrays as one layer of genomic data

Genotyping arrays occupy a middle ground between comprehensive sequencing and functional assays. They provide scalable access to genetic variation while relying on population structure for inference.

In combination with sequencing, RNA measurements, and other data types, genotyping arrays contribute to a layered understanding of genotype–phenotype relationships.

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