SNPgenotyping

SNP genotyping is a molecular genetics technique used to determine which alleles individuals carry at predefined single-nucleotide polymorphism (SNP) loci. SNPs are single-base variations common in genomes and serve as markers for genetic variation across individuals and populations. Genotyping at many SNPs can reveal associations with traits, population structure, and ancestry.

Common approaches include PCR-based assays such as TaqMan and Kompetitive allele-specific PCR (KASP) for targeted SNP sets; high-throughput SNP arrays (microarrays) that genotype hundreds of thousands to millions of SNPs in parallel; and sequencing-based methods such as genotyping-by-sequencing (GBS) or whole-genome/exome sequencing followed by SNP calling. The choice depends on scale, cost, and study design.

Results are typically stored as genotypes for each SNP per sample, with quality metrics such as call rate, concordance, and potential biases evaluated. Data are often aligned to a reference genome and annotated with databases like dbSNP to identify known polymorphisms. Imputation can be used to infer missing genotypes based on reference panels, increasing genomic coverage for downstream analyses.

Applications span genome-wide association studies (GWAS), population genetics and ancestry research, pharmacogenomics and personalized medicine, plant and animal breeding, and forensics. Limitations include ascertainment bias in SNP panels, platform-specific error profiles, cost for very large studies, and the need for robust quality control and statistical methods to handle missing data and population structure.