Better Forensic Markers: Microhaplotypes and Ancestry SNPs

Kidd lab has studied single nucleotide polymorphisms (SNPs) since the early 1980’s, and began advocating use of SNPs in forensics about 15 years ago. SNPs (as a panel of individual SNPs or assembled into Microhaplotypes) are now generally recognized as important in the future of forensic practice because they can provide more information than the conventional short tandem repeat (STR) polymorphisms (STRPs) (e.g. CODIS markers). With the revolution in forensic methodology from capillary electrophoresis (CE) to massively parallel sequencing (MPS), SNPs and STRPs can be multiplexed using a single technology. In 2007, we defined four types of SNP panels for use in forensics: IISNPs for individual identification, AISNPs for ancestry inference, PISNPs for phenotype (visible trait) inference, and LISNPs for lineage/family/clan inference. Using our unique resources of population samples and accumulated data on them—nearly 3,000 individuals typed for several hundred up to 5,000 SNPs—we propose to continue looking for better AISNPs for improved ability to assign an individual’s ancestry to ever more refined regions. We will use TaqMan to genotype our samples for SNPs that appear to be good candidates for these objectives. We will also focus on improving the available microhaplotypes, by identifying additional SNPs within the region of some of our existing 182 microhaplotypes as well as by searching the public databases for candidates that may be significant better than the existing loci we have characterized on up to 96 populations. TaqMan will also be used to obtain some initial sense of what microhaps are most promising.

We propose a major emphasis on improving the available set of microhaplotype loci to provide (1) better individualization measured as random match probability (RMP); (2) better resolution of mixtures; and (3) better inference of ancestry and LISNPs. Then we will turn to MPS of the 100 best candidates to provide complete documentation of the variation in each of the 100 microhap segments. With MPS we are able to identify currently known SNPs within existing microhaplotypes including those we cannot type by TaqMan as well as rare and uncommon, even previously unknown, SNPs. We will multiplex 100 microhaps for paired-end sequencing on a MiSeq sequencer. The MPS technology will allow identification of otherwise cryptic variants that may exist in one or few populations. It is these rare variants/polymorphisms that may be most useful for what follows.

With this improved knowledge, we are in a better position to increase the utility of SNP and microhaplotype panels. We have demonstrated the feasibility of microhaplotypes (200-300pb in length) to detect DNA mixtures in case samples; the same criteria apply to familial studies. Thus, it is clear that better microhaplotypes will be of great importance in resolving the common problem of mixtures of DNA at crime scenes and provide great power at identification of familial relationships in mass disaster and missing person situations. This project will provide important new and improved tools for forensics made possible by our unique collection of population samples and data resources.

This project contains a research and/or development component, as defined in applicable law, and complies with Part 200 Uniform Requirements - 2 CFR 200.210(a)(14).

CA/NCF