- A Single Nucleotide Polymorphism (SNP) array is a high-throughput genotyping technology used to detect genetic variation across the genome, focusing primarily on single nucleotide polymorphisms—the most common type of genetic variation in humans and many other organisms.
- SNPs represent changes at a single base pair in the DNA sequence and can influence traits, susceptibility to diseases, drug responses, and evolutionary adaptations. SNP arrays provide a cost-effective, efficient, and scalable way to analyze hundreds of thousands to millions of these variants in a single experiment, making them a cornerstone of modern genomics and precision medicine.
- The principle of SNP arrays relies on hybridization between DNA fragments and allele-specific oligonucleotide probes fixed onto a solid surface, usually a glass slide or silicon chip. Each probe corresponds to a specific SNP site in the genome. A DNA sample is fragmented, labeled with fluorescent markers, and allowed to hybridize to the array. The hybridization pattern, detected through fluorescence scanning, indicates the genotype at each SNP locus. Different array platforms, such as those developed by Affymetrix (now Thermo Fisher Scientific) and Illumina, use slightly different chemistries, but all are designed to provide highly reproducible and parallelized genotyping results.
- SNP arrays have numerous applications in research and clinical practice. In genome-wide association studies (GWAS), they are used to identify SNPs associated with complex diseases, traits, and phenotypes across large populations. Clinically, SNP arrays play a role in diagnostics and personalized medicine, where they are used to detect genetic predispositions, pharmacogenomic markers, and inherited disease mutations. They are also widely applied in oncology to identify chromosomal aberrations, copy number variations (CNVs), and loss of heterozygosity, aiding in cancer classification and prognosis. In agriculture and animal breeding, SNP arrays are used for genomic selection, trait mapping, and improving genetic diversity.
- One of the strengths of SNP arrays is their high accuracy and cost-effectiveness for large-scale genotyping. They are particularly useful in studies requiring genotyping across thousands of samples where whole-genome sequencing would be prohibitively expensive. However, they do have limitations: they are constrained to known variants that are pre-selected and represented on the chip, meaning novel mutations or rare variants cannot be easily detected. In contrast, sequencing technologies can provide comprehensive discovery of both known and novel variants. Despite this, SNP arrays remain a preferred tool for population-scale genetic studies due to their efficiency and reliability.
