genotyping

Genotyping is the process of determining which genetic variants an individual or sample possesses at specific locations in the genome. It focuses on identifying known polymorphisms or discovering novel variants at predetermined loci or across the genome. Genotyping differs from full DNA sequencing in that it typically targets a subset of variants and is designed to be faster and cheaper.

Common methods include targeted assays such as PCR-based genotyping (for example TaqMan assays) and Sanger sequencing for individual loci; SNP arrays (microarrays) that assay thousands to millions of predefined single-nucleotide polymorphisms; and sequencing-based approaches, including whole-genome sequencing (WGS) and whole-exome sequencing (WES), which provide more comprehensive variant information and can enable de novo discovery. Genotyping-by-sequencing and reduced-representation methods offer intermediate throughput.

Data processing involves quality control, alignment to a reference genome, and variant calling to determine the genotype at each locus. Phasing and imputation can be used to infer haplotypes or missing genotypes, and results are typically reported as homozygous reference, heterozygous, or homozygous variant calls with associated quality metrics.

Applications span medical genetics, pharmacogenomics, and risk assessment; population and evolutionary genetics; forensic science; and agricultural and animal breeding. In clinical contexts, genotyping informs disease susceptibility, carrier status, and drug response, though interpretation depends on the strength of evidence and clinical guidelines. Limitations include assay design constraints, coverage gaps, and privacy concerns.