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                            Library & Multimedia
 Mixture Deconvolution by Massively Parallel Sequencing of Microhaplotypes
NCJ Number
              254165
Journal

*International Journal of Legal Medicine* Volume: 133 Issue: 3 Dated: 2019 Pages: 719-729
Author(s)
          Lindsay Bennett;
                        Fabio Oldoni;
                        Kelly Long;
                        Selena Cisana;
                        Katrina Madella;
                        Sharon Wootton;
                        Joseph Chang;
                        Byo Hasegawa;
                        Robert Lagace;
                        Kenneth K. Kidd;
                        Daniele Podini
Date Published

2019
Length
              11 pages
Annotation
              The purpose of this project was to demonstrate that the increasing number of loci described in the literature, along with initial mixture investigations, supports the potential for microhaps to aid in mixture interpretation.
Abstract
              Short tandem repeat polymorphisms (STRs) are the standard markers for forensic human identification. STRs are highly polymorphic loci analyzed using a direct PCR-to-CE (capillary electrophoresis) approach; however, STRs have limitations particularly when dealing with complex mixtures. These include slippage of the polymerase during amplification causing stutter fragments that can be indistinguishable from minor contributor alleles, preferential amplification of shorter alleles, and limited number of loci that can be effectively co-amplified with CE. Massively parallel sequencing (MPS), by enabling a higher level of multiplexing and actual sequencing of the DNA, provides forensic practitioners an increased power of discrimination offered by the sequence of STR alleles and access to new sequence-based markers. Microhaplotypes (i.e., microhaps or MHs) are emerging multi-allelic loci of two or more SNPs within <300 bp that are highly polymorphic, have alleles all of the same length, and do not generate stutter fragments. In the current study, a panel of 36 microhaplotypes, selected from a set of over 130 loci, was tested with the Ion S5 MPS platform (Thermo Fisher Scientific) on single-source samples, synthetic two-to-six person mixtures at different concentrations/contributor ratios, and on crime scene-like samples. The panel was tested both in multiplex with STRs and SNPs and individually. The analysis of single-source samples showed that the allele coverage ratio across all loci was 0.88 +/-  0.08, which is in line with the peak height ratio of STR alleles in CE. In mixture studies, results showed that the input DNA can be much higher than with conventional CE, without the risk of oversaturating the detection system, enabling an increased sensitivity for the minor contributor in imbalanced mixtures with abundant amounts of DNA. Furthermore, the absence of stutter fragments simplifies the interpretation. On casework-like samples, MPS of MHs enabled the detection of a higher number of alleles from minor donors than MPS and CE of STRs. These results demonstrated that MPS of microhaplotypes can complement STRs and enhance human identification practices when dealing with complex imbalanced mixtures. (publisher abstract modified)
      
  
          Additional Details
Grant Number(s)
        2017-DN-BX-0164
                                2015-DN-BX-K023


  
  
        
  Agencies
        NIJ-Sponsored


  
  
        
  Publication Type
        Research (Applied/Empirical)
                                Report (Study/Research)
                                Report (Grant Sponsored)
                                Program/Project Description


  
  
        
  Award
        Powerful Forensic Markers Optimized for Massively Parallel Sequencing
                                Massively parallel sequencing of 89 microhaplotypes for the selection of an operational and effective subset for forensic applications.
    
  
  
Date Published: January 1, 2019
    
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