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                            Library & Multimedia
 Resolution of mitochondrial DNA mixtures using a probe capture next generation sequencing system and phylogenetic-based software
NCJ Number
              305064
Journal

*Forensic Science International-Genetics* Volume: 53 Dated: July 2021
Author(s)
          Mary Wisner;
                        Henry Erlich;
                        Shelly Shih;
                        Cassandra Calloway
Date Published

July 2021
Annotation
              A mitochondrial genome probe capture Next-Generation Sequencing (NGS) system was used to sequence complex mtDNA mixtures and two different software programs to analyze the sequence data.
Abstract
              Interpreting mixtures with nuclear genetic markers remains one of the persisting challenges in forensic DNA analysis, particularly when the DNA is degraded or present in trace amounts. In these scenarios, analyzing mitochondrial (mt) DNA can be useful due to the higher copy number per cell compared to nuclear DNA. However, until the emergence of Next-Generation Sequencing (NGS) with its clonal sequencing capability, analysis of mtDNA mixtures was very challenging. In the current project, analysis of contrived mixtures of two contributors in 50:50 and 95:5 ratios as well as three-person mixtures ranging from near equal proportions (~33:33:33 ratio) to low amounts of the minor contributors (e.g., a 90:5:5 ratio) is reported, and this system was also applied to the analysis of mtDNA mixtures from forensically relevant samples. For data analysis, both the variant frequency-based software program GeneMarker®HTS and the phylogenetic-based software program Mixemt was used to de-convolute the mixtures. Using the massively parallel, clonal features of NGS, one can bioinformatically separate and count the individual sequence reads to calculate the proportions of individual contributors using phylogenetically informative polymorphisms. GeneMarker®HTS allows us to detect all mutations, including “private” mutations (non-phylogenetically informative polymorphisms) and assign them to individual contributors based on the frequency of the sequence reads, provided that the proportions of the various contributors are sufficiently different. Using a probe capture NGS system and both GeneMarker®HTS and Mixemt software programs, the interpretation of complex mixtures of equal proportion contributors, trace amount contributors, and more than two contributors in contrived mixtures, as well as interpretation of challenging forensic specimens is demonstrated. (Publisher abstract provided)
      
  
          Additional Details
Grant Number(s)
        2018-DU-BX-0183
                                2015-MU-MU-K044


  
  
        
  Agencies
        NIJ-Sponsored


  
  
        
  Publication Type
        Research Paper


  
  
        
  Award
        Development of a Probe Capture Next-Generation Sequencing Assay for Analysis of the Mitochondrial Genome and Nuclear STR and SNP Markers
    
  
  
Date Published: July 1, 2021
    
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      PatentsRelated Topics
        
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        Evidence analysis and processing
        Forensic biology
        Ancestral DNA
        Mitochondrial DNA



  
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