An SNP array is a technology designed to survey an individual’s DNA for a vast number of common genetic variations simultaneously. It allows scientists to efficiently examine hundreds of thousands to millions of specific sites across a person’s genetic blueprint. This cost-effective approach provides broad insights into an individual’s genetic makeup. The technology serves as a foundational tool for researchers and clinicians understanding human diversity and health.
Understanding Single Nucleotide Polymorphisms
Single Nucleotide Polymorphisms, or SNPs (pronounced “snips”), represent the most frequent type of genetic variation found among individuals. These variations occur when a single DNA building block, a nucleotide, is altered at a specific position in the genetic code.
While millions of SNPs have been identified across the human genome, most do not have an observable impact on health or development. However, some SNPs located within genes or their regulatory regions can influence gene function. Such variations can help predict an individual’s response to medications, their susceptibility to environmental factors, or their likelihood of developing particular diseases.
The SNP Array Laboratory Process
The process of analyzing DNA using an SNP array begins with obtaining a DNA sample, typically from saliva or blood. The DNA is extracted and often amplified using Polymerase Chain Reaction (PCR) to create many copies, ensuring enough genetic material for subsequent steps.
The prepared DNA is then cut into smaller fragments, and a fluorescent label is attached. The core of the technology is the microarray chip, a small glass slide containing hundreds of thousands to over a million microscopic spots. Each spot harbors a unique, short DNA probe designed to match a specific known SNP site in the human genome.
The labeled DNA fragments are washed over the chip. During hybridization, the patient’s DNA fragments bind to their complementary DNA probes. After hybridization, the chip is washed to remove unbound or non-specifically attached DNA fragments. Finally, a specialized scanner reads the chip, detecting fluorescent signals where the patient’s labeled DNA has successfully attached to a probe.
Interpreting SNP Array Data
After the SNP array chip is scanned, fluorescent signals at each probe location are converted into raw intensity values. Specialized software processes these values to determine the specific genetic makeup, or “genotype,” at each SNP site. For example, an individual might have two copies of the ‘A’ version (AA), two copies of the ‘G’ version (GG), or one of each (AG).
A single SNP genotype offers limited information. The power of SNP array technology comes from analyzing collective patterns across hundreds of thousands of individual SNP calls. Advanced bioinformatics tools and statistical methods compare these patterns from an individual’s DNA to large reference databases. This analysis helps researchers identify associations between specific SNP patterns and various genetic traits or conditions.
Applications in Science and Medicine
SNP arrays are an important tool across various fields of science and medicine, offering diverse applications. In medical research, they are used for genome-wide association studies (GWAS), which systematically scan the entire genome to identify SNPs linked to common diseases such as diabetes, heart disease, or Alzheimer’s. These studies help pinpoint regions of the genome that may harbor disease-contributing genes.
The technology also finds widespread use in pharmacogenomics, a field focused on understanding how an individual’s genetic makeup influences their response to medications. By analyzing a person’s SNP profile, clinicians can predict whether a specific drug will be effective or cause adverse reactions, allowing for personalized drug selection and dosage.
Beyond disease research and drug response, SNP arrays are foundational for consumer genetics services, which offer insights into ancestry. These services analyze thousands of an individual’s SNPs to estimate their ethnic background and identify potential distant relatives by comparing their genetic patterns to global populations. In agriculture, SNP arrays are applied to improve crop and livestock breeding. They enable the selection of plants and animals with desirable traits, such as increased yield, disease resistance, or improved nutritional content, by identifying associated SNP markers.