Powerful Forensic Markers Optimized for Massively Parallel Sequencing

As submitted by the proposer: SNPs (as a panel of individual SNPs or assembled into Microhaplotypes) are increasingly important in forensics because they can provide more information than the conventional STR polymorphisms (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. The different panels require SNPs with different characteristics and all four panels require reference data (population-specific allele frequencies) on a global representation of populations. Our research has produced a finished IISNP panel composed of 45 up to 86 SNPs with random match probabilities, irrespective of population, of <10-15 to <10-30, respectively. We have also developed an AISNP panel that provides good resolution of up to 10 geographical regions. Our IISNP and AISNP panels are significant components of existing commercial panels for MPS in forensics. We now propose to develop a globally comprehensive set of panels of AISNPs with a “first tier” defining at least ten, ideally more, biogeographic regions and to develop different “second tier” panels for finer distinction within a region defined by the “first tier” AISNPs. These panels will provide a powerful tool for fine geographic resolution of ancestry that will be optimized for use with MPS. Identification of the family to which a DNA profile belongs is essential in mass disasters and missing person situations. We have been developing an LISNP panel of markers that is much more powerful for identifying relatives than is possible with the CODIS STRPs. We have demonstrated the feasibility of microhaplotypes (<~ 200pb in length) to detect DNA mixtures in case samples; the same criteria apply to familial studies. We are now proposing to develop a mature LISNP panel and the sequencing technology useful in minimizing the ambiguity of phase. Available resources (e.g., 1000 Genomes and other whole genome data on populations) will provide the candidates that we can then evaluate in the context of our broad population coverage to assure a powerful panel of LISNP loci. Note: This project contains a research and/or development component, as defined in applicable law. ca/ncf