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. 2022 Jul 24;13(8):1322.
doi: 10.3390/genes13081322.

State of the Art for Microhaplotypes

Kenneth K Kidd  1 , Andrew J Pakstis  1
Affiliations

State of the Art for Microhaplotypes

Kenneth K Kidd et al. Genes (Basel). .

Abstract

In recent years, the number of publications on microhaplotypes has averaged more than a dozen papers annually. Many have contributed to a significant increase in the number of highly polymorphic microhaplotype loci. This increase allows microhaplotypes to be very informative in four main areas of forensic uses of DNA: individualization, ancestry inference, kinship analysis, and mixture deconvolution. The random match Probability (RMP) can be as small as 10−100 for a large panel of microhaplotypes. It is possible to measure the heterozygosity of an MH as the effective number of alleles (Ae). Ae > 7.5 exists for African populations and >4.5 exists for Native American populations for a smaller panel of two dozen selected microhaplotypes. Using STRUCTURE, at least 10 different ancestral clusters can be defined by microhaplotypes. The Ae for a locus is also identical to the Paternity Index (PI), the measure of how informative a locus will be in parentage testing. High Ae loci can also be useful in missing persons cases. Finally, high Ae microhaplotypes allow the near certainty of seeing multiple additional alleles in a mixture of two or more individuals in a DNA sample. In summary, a panel of higher Ae microhaplotypes can outperform the standard CODIS markers.

Keywords: SNP; ancestry; forensic genetics; individualization; kinship; microhaplotype; mixture deconvolution; paternity index; random match probability.

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Conflict of interest statement

The authors declare no conflict of interest.

Figures

Figure 1
Figure 1
Yearly distribution of forensic papers about human microhaplotypes since the first in 2013 through 25 June 2022. Note that 2022 is outpacing 2021 so far. All fields were searched for “microhaplotype” or “micro-haplotype” in PubMed and in the journal Forensic Science International Genetics Supplemental Series, which is not included in PubMed.
Figure 2
Figure 2
The distribution by the average Ae values of the 90 MHs [11,14] with the 24 MH [13] matched to the common STRs in [13].
Figure 3
Figure 3
Average RMP in major world regions for a dataset of 90 MHs and 79 populations (from [14]) and for the best subset of 24 MHs [13].
Figure 4
Figure 4
Average Ae and average In in 6 major world regions for 90 microhaplotypes.
Figure 5
Figure 5
Average Ae of the 24 best MHs in 6 world geographical regions.
Figure 6
Figure 6
Individual bar plots of 13 East Asian population samples from STRUCTURE runs of the 90 MH dataset. This reanalysis with STRUCTURE was conducted by omitting other populations studied in [14]. The results of the highest likelihood runs at K = 3, 4, and 5 are shown.
See this image and copyright information in PMC

References

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