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                            Library & Multimedia
 A Phylogenetic Approach for Haplotype Analysis of Sequence Data From Complex Mitochondrial Mixtures
NCJ Number
              252430
Journal

*Forensic Science International-Genetics* Volume: 30 Dated: September 2017 Pages: 93-105
Author(s)
          Samuel H. Vohr;
                        Rachel Gordon;
                        Jordan M. Elzenga;
                        Henry A. Erlich;
                        Cassandra D. Galloway
Date Published

September 2017
Length
              13 pages
Annotation
              This article presents a powerful computational approach for determining the constituent haplotypes in massively parallel sequencing data from potentially mixed samples.
Abstract
              Massively parallel (next-generation) sequencing provides a powerful method to analyze DNA from many different sources, including degraded and trace samples. A common challenge, however, is that many forensic samples are often known or suspected mixtures of DNA from multiple individuals. Haploid lineage markers, such as mitochondrial (mt) DNA, are useful for analysis of mixtures because, unlike nuclear genetic markers, each individual contributes a single sequence to the mixture. Deconvolution of these mixtures into the constituent mitochondrial haplotypes is challenging as typical sequence read lengths are too short to reconstruct the distinct haplotypes completely. At the heart of the approach described in this article is an expectation maximization based algorithm that co-estimates the overall mixture proportions and the source haplogroup for each read individually. This approach, implemented in the software package mixemt, correctly identifies haplogroups from mixed samples across a range of mixture proportions. Furthermore, this method can separate fragments in a mixed sample by the most likely originating contributor and generate reconstructions of the constituent haplotypes based on known patterns of mtDNA diversity. (Publisher abstract modified)
      
  
          Additional Details
Grant Number(s)
        2013-MU-MU-K044


  
  
        
  Agencies
        NIJ-Sponsored


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


  
  
        
  Award
        Development of Probe Capture Next-Generation Sequencing Assays for Degraded DNA
    
  
  
Date Published: September 1, 2017
    
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