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NCJRS Abstract

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NCJ Number: 246954 Find in a Library
Title: Progress Towards Developing The 'Pathogen Toolkit'
Author(s): Priyanka Kshatriya; Vinson Doyle; Bradley J. Nelson; Xiang Qin; John Anderson; Jeremy M. Brown; Michael L. Metzker
Date Published: May 2014
Page Count: 34
Sponsoring Agency: National Institute of Justice (NIJ)
Washington, DC 20531
NCJRS Photocopy Services
Rockville, MD 20849-6000
Grant Number: 2011-DN-BX-K534
Sale Source: NCJRS Photocopy Services
Box 6000
Rockville, MD 20849-6000
United States of America
Document: PDF
Type: Report (Grant Sponsored); Report (Study/Research); Research (Applied/Empirical)
Format: Document (Online)
Language: English
Country: United States of America
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
Main Term(s): Criminology
Index Term(s): AIDS/HIV transmission; Biological influences; Forensic pathology; Investigative techniques; Suspect identification
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