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Mini-haplotypes as lineage informative SNPs (LISNPs) and ancestry inference SNPs (AISNPs)

NCJ Number
European Journal of Human Genetics Volume: 20 Issue: 11 Dated: 2012 Pages: 1148-1154
Date Published
7 pages

This article proposes that haplotyped loci with high heterozygosity can be useful in human identification, especially within families, if recombination is very low among the sites. 


Three or more SNPs extending over small molecular intervals (<10 KB) can be identified in the human genome to define miniature haplotypes with moderate levels of linkage disequilibrium. Properly selected, these mini-haplotypes (or minihaps) consist of multiple haplotype lineages (alleles) that have evolved from the ancestral human haplotype but show no evidence of recurring recombination, allowing each distinct haplotype to be equated with an allele, all copies of which are essentially identical by descent. Historic recombinants, representing rare events that have drifted to common frequencies over many generations, can be identified in some cases; they do not equate to frequently recurring recombination. The authors have identified examples in the data collected on various projects and present eight such mini-haplotypes comprised of informative SNPs. They also discuss the ideal characteristics and advantages of minihaps for human familial identification and ancestry inference; they compare them to other types of forensic markers in use and/or that have been proposed. The authors anticipate that it is possible to conduct a systematic search and identify a useful panel of mini-haplotypes, with even better properties than the examples presented here. (publisher abstract modified)

Date Published: January 1, 2012