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Massively parallel sequencing of 89 microhaplotypes for the selection of an operational and effective subset for forensic applications.

Award Information

Award #
Funding Category
Competitive Discretionary
Congressional District
Funding First Awarded
Total funding (to date)

Description of original award (Fiscal Year 2017, $492,892)

As submitted by the proposer:

The goal of this project is to massively parallel sequence 89 microhaplotypes (MHs) selected from previously-funded NIJ research, for the development of an effective subset for forensic applications. MHs are loci of two or more SNPs within a short distance from each other (<300 nucleotides) with three or more allelic combinations. MHs offer several advantages for forensic applications compared to conventional short tandem repeats (STRs) including no polymerase slippage during amplification resulting in absence of artifact stutter peaks, lower mutation rates, absence of preferential amplification of shorter alleles (MH alleles within a locus are all the same size), and can provide both individualization and ancestry prediction.

The selected MHs will be sequenced on at least 400 individuals from four different populations (European Americans, African Americans, Hispanic, East Asians) and 78 families, 63 of which have two or more children. The 89 MHs have been selected from a larger set of 130 identified based on effective number of alleles (Ae) and ancestry informativeness (In). Samples will be analyzed using the Ion S5 massively parallel sequencing platform to confirm PHASE inferred allele frequencies, possible linkage between loci, possible presence of recombination hot spots, and mutation rates. In addition, bioinformatics analyses of the sequences in between the SNPs defining the MHs will allow identifying less common SNPs that could greatly increase the power of discrimination of a profile.

Complex mixtures are currently one of the greatest challenges in forensic DNA analyses and stutter peaks complicate their interpretation, particularly when the minor contributor is in the stutter peak height range of the major. A stutter free MH-based assay will complement conventional STR markers and enhance mixture deconvolution capabilities. Furthermore, the lower mutation rate compared to STRs will improve family relationship testing, and the greater In will provide ancestry information. Results of this project will be disseminated through peer-reviewed publications and by presentations and workshops at national and international forensic DNA conferences.

Note: 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).


Date Created: September 29, 2017