tagSNPs

TagSNPs, or tagging single-nucleotide polymorphisms, are a subset of SNPs chosen to represent the genetic variation at other loci in linkage disequilibrium (LD). In genetic association studies, tagging SNPs are used to reduce genotyping burden by capturing information about nearby variants without directly typing every SNP.

LD-based tagging relies on LD patterns from reference panels such as HapMap or 1000 Genomes. The idea is that within regions of high LD, a small number of tagSNPs can predict other SNPs with high accuracy. Selection approaches include pairwise tagging, where each untagged SNP is correlated with at least one tagSNP (often using r^2 thresholds, e.g., r^2 ≥ 0.8), and multi-marker or aggressive tagging, where blocks are defined and a minimal set of SNPs is chosen to reconstruct common haplotypes.

Population dependence: LD structure varies across populations; tagSNPs chosen in one population may not tag well in another. Limitations: tagging tends to capture common variation but may miss rare variants; relies on LD patterns that may differ across populations; cannot detect functional variants directly and may require imputation or sequencing for fine-mapping.

Applications: used in GWAS and candidate-gene studies to increase efficiency, and in fine-mapping and pharmacogenomics. Software tools include Tagger (Haploview), LDselect, and others that implement pairwise or block-based tagging strategies.

See also: haplotype, linkage disequilibrium, imputation.