microhaplotypes

Microhaplotypes are short genomic regions, typically less than 200 base pairs in length, that contain two or more closely linked single nucleotide polymorphisms (SNPs). The alleles across these SNPs can be considered as a single multi-allelic haplotype, which is determined by high-resolution sequencing or other phasing methods. Because the SNPs lie in a compact interval, microhaplotypes can be typed with very short DNA fragments, enabling robust analysis of degraded or trace samples.

Compared with single SNP markers, microhaplotypes gain discriminatory power from the combination of multiple SNPs within the same locus. The resulting haplotype diversity often exceeds that of many STR loci while using shorter amplicons and typically avoiding STR-specific artifacts such as stutter. The mutation rate of microhaplotypes is generally low, akin to SNPs, and their composition across populations can inform ancestry patterns.

In forensic genetics, microhaplotypes are used for individual identification, mixture deconvolution, and kinship analyses when DNA is degraded or when assaying multiple low-template contributors. In population genetics, they serve as multi-allelic markers for assessing population structure, admixture, and demographic history. They are interrogated using next-generation sequencing platforms, targeted capture assays, or high-throughput amplicon sequencing, with computational phasing to infer haplotypes.

Limitations and considerations include the need for specialized reference data and analysis tools to define and compare microhaplotypes across laboratories, and the potential for recombination within the short locus to complicate interpretation in very diverse populations. Nevertheless, microhaplotypes have become a valuable addition to the genotyping toolkit, complementing SNP and STR analyses in both forensic and population contexts.