A multipurpose panel of microhaplotypes for use with STR markers in casework

Abstract

A small panel of highly informative loci that can be genotyped on the same equipment as the standard CODIS short tandem repeat (STR) markers has strong potential for application in forensic casework. Single nucleotide polymorphisms (SNPs) can be typed by a couple of methods on capillary electrophoresis (CE) machines and on sequencers, but the amount of information relative to the laboratory effort has hindered use of SNPs in actual casework. Insertion-deletion markers (InDels) suffer from similar problems. Microhaplotypes (MHs) are much more informative per locus but have similar technical difficulties unless they are typed by massively parallel sequencing (MPS). As forensic labs are acquiring sequencing machines, MHs become more likely to be used in casework, especially if multiplexed with STRs. Here we present the details of a multipurpose panel of 24 MHs with the highest effective number of alleles (A_e) from previous work. An augmented STR panel of 24 loci (20 CODIS markers plus four commonly typed STRs) is also considered. The A_e and ancestry informativeness (I_n) distributions of these two datasets are compared. The MH panel is shown to have better individualization and population distinction than the augmented CODIS STRs. We note that the 24 MHs should be better for mixture analyses than the STRs. Finally, we suggest that a commercial kit including both the standard CODIS markers and this set of 24 MH would greatly improve the discrimination power over that of current commercial assays.

Keywords: Ancestry; CODIS; Microhaplotype; Population genetics; SNP; STR.

Fig. 1.

Scatterplot of the 24 microhaplotypes by their A_e and I_n values for 79 populations. The values are in Supplemental Table S1. The values plotted are based on Pakstis et al. [7]; Table S1 also contains the values based on 30 populations [5].

Fig. 2.

Scatterplot of 24 augmented CODIS markers for A_e and I_n based on 32 populations. The same scale is used for both Figs. 1 and 2 to allow better visual comparison. Because SE33 has such a high A_e value, average A_e = 14.69 and I_n = 0.674, it is out of range and does not appear in this image.

Fig. 3.

A negative logarithm plot of the population specific Random Match Probabilities and most common genotype frequencies for the 24 MH. Populations are in the same order as in Pakstis et al. [7] and Fig. 4. For most of the world the RMP is around or less than 10⁻³⁰. See Table S4 for the population names corresponding to the 3-character abbreviations.

Fig. 4.

A negative logarithm plot of the population specific RMP values for the augmented CODIS panel of 24 loci. (Data from popSTR downloaded January, 2022.) The values for this global set of populations fall around 10⁻²⁸ except for the Pacific and Native American populations. Note that the Dominicans are Afro-Caribbean and are “American” by geography, not ancestry.

Fig. 5.

STRUCTURE results for highest likelihood runs at K = 8 and 9 for the 24-microhaplotype, 79-population dataset. Each fine vertical line represents one individual. Blowups are shown for regions of several small populations to make the clustering and population labels clearer.

Fig. 6.

PCA of 79 populations based on the 24 microhaplotypes.

Fig. 7.

PCA of 32 populations based on the augmented CODIS data from popSTR database.

Fig. 8.

Examples of mixture results. The mixture ratios are given for each example and the read numbers for the haplotypes seen are plotted. The four-person results for mh13KK-218 indicate at least four persons contributed to the mixture. The four-person results for mh21KK-320 indicate at least three persons contributed. The three-person results for mh13KK-218 indicate at least three persons contributed. The three-person results for mh02KK-134 indicate at least three persons contributed to the mixture.