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                            Library & Multimedia
 Progress Towards Developing The  'Pathogen Toolkit'
NCJ Number
              246954

Author(s)
          Priyanka Kshatriya;
                        Vinson Doyle;
                        Bradley J. Nelson;
                        Xiang Qin;
                        John Anderson;
                        Jeremy M. Brown;
                        Michael L. Metzker
Date Published

May 2014
Length
              34 pages
Annotation
              This study demonstrated the feasibility of full-length genome sequence production from individuals infected with HIV, using next-generation sequencing (NGS) technologies and phylogenomic analysis.
Abstract
              Using samples from the Texas HIV transmission case (CC samples), for a subset of full-length HIV genomes, the study yielded initial phylogenetic estimates from six non-overlapping genic regions that showed the monophyly of clones sampled from the same recipient individuals; variation in relationships among groups of clones from different individuals; and variation in rates of evolution across different genomic regions. These results are significant in demonstrating the integrity of the phylogenetic signal in these CC molecular clone sequences, since the extrinsic evidence, which was presented in criminal proceedings, strongly suggested that each individual included in the initial analyses acted only as a recipient within the Texas transmission cluster. Distinct relationships among clones from different individuals inferred from numerous genic regions constituted strong evidence of independent evolutionary histories. This provided greater confidence in forensic conclusions. Several technical challenges are currently being addressed. These include optimizing de novo assemblies that will produce larger numbers of successful full-length genome sequences with low SNP counts and also understanding the high estimates of human sequences in the subset of HIV molecular clone reads. Addressing these challenges will facilitate the development of a robust "pathogen toolkit" that can provide a detailed pathway for future forensics studies. 6 figures, 2 tables, and 56 references
      
  
          Additional Details
Grant Number(s)
        2011-DN-BX-K534


  
  
        
  Agencies
        NIJ-Sponsored


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


  
  
        
  Award
        Extending the Microbial Forensic Toolkit Through Whole Genome Sequencing and Statistical Phylogenomics
    
  
  
Date Published: May 1, 2014
    
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