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January 2016 - Issue 4
Welcome to our monthly eNewsletter focused on the powerful new diagnostic capabilities that Applied Genomics delivers and the people who make them happen.
Battelle works with the Applied Genomics Today Newsletter will keep you up-to-date on cutting edge technologies, services and processes.
Battelle and the Department of Justice’s National Institute of Justice are proud to be collaborating on a two-phase applied research program to evaluate Next-Generation Sequencing (NGS) technologies in the field. The Battelle-led study, which began in April 2015 and will span 19 months, will give the forensic community an objective understanding and assessment of NGS technology, with the goal of ultimately complementing capillary electrophoresis (CE)-based forensic DNA testing currently used by law enforcement agencies across the United States.
Battelle is engaging its subject matter experts to include Principal Investigator Dr. Mark Wilson, Program Manager Richard Guerrieri and Principal Researcher Christine Baker, as well as Research Scientists Elizabeth Montano, Jocelyn Bush, Dr. Rachel Spurbeck and Nick Fackler, and Bioinformaticists Dr. Esley Heizer and Angela Minard-Smith. Battelle is also joined by recognized experts from the forensic DNA community, with representatives covering the city, county, state and federal levels, in addition to distinguished scientists from academia and research. The list of respective participants includes:
From August 2014 through June 2015, Battelle worked to identify NGS commercial providers for platforms, amplification reagents and analysis software packages, gaining agreements from each to provide uniform lots of commercially manufactured materials necessary for the execution of this project. As an objective third party evaluator and thought leader in NGS technology and applications, Battelle will direct the participating institutions in this two-phased program.
In Phase I, which spanned late September into the beginning of November 2015, Battelle conducted an evaluation of the available NGS products in accordance with manufacturer-provided technical specifications. This phase also included an assessment of performance data generated by Battelle scientists. Specifically, Battelle conducted and coordinated the sequencing of DNA samples provided by NIST through a progressive series of internal performance testing processes and across each of the commercially available NGS workflows.
With standard operating procedures now optimized, Battelle invited technical representatives from participating laboratories to attend a 3½-day research planning session at Battelle’s NGS Laboratory in Columbus, Ohio. The session kicked off on November 30, and concluded on December 3. Battelle scientists provided demonstrations and hands-on exposure to participants for each of the three NGS workflows. Technical lectures and presentations to clarify operational methods, quality assurance steps as well as software applications augmented the analytical sessions. Procedural insight, which Battelle scientists have gleaned through experience with the NGS processes, has been assembled by Battelle in the form of a Research User Guide to supplement the instruction and potentially assist the partner laboratories in gaining familiarity and ultimately command of the workflows. The session was designed to support participants for success in completion of the corresponding external research studies upon return to their respective laboratories.
The primary goal of the Battelle study is the advancement of technical knowledge, understanding, exposure and experience of forensic DNA scientists regarding NGS technology. Through insight and experience within the Battelle network, coupled with the invaluable participation and contributions from our distinguished collaborators, it is hoped that this study will support forensic DNA scientists in the development of strategic pathways for NGS implementation—plans that will ultimately facilitate the use of this technology to serve the mission of the criminal justice system.
The groundbreaking study will culminate in the fall of 2016 with the generation of a formal report that will be delivered to the scientific community. This will be followed by scholarly manuscripts, instructional opportunities (webinars) and presentations at international science meetings, all of which will result in the dissemination of valuable information into the forensic science and criminal justice communities.
Battelle has proven and unique capabilities that have been successfully applied to microbial ecology, human forensics and wildlife population biology investigations. Equivalent DNA analysis methods have been used by others to discriminate between domestically produced and illegally hunted pork products based on species of origin[i]. Similarly, the types of DNA analysis capabilities at Battelle have been used to determine the species of origin of artifacts and mementos such as meat and medicinal animal parts, tusks, and horns[ii].
The Gray Whale Story: Gray whales feed in the summer off the northeastern coast of Sakhalin Island, Russia, in areas near oil and gas facilities and occupying a general range known to be within the historic distribution of the western stock of North Pacific gray whales. This population is of great interest to conservationists as it is considered to be the last surviving remnant of the western gray whale which was hunted along the coastal areas of Japan and Korea during the 19th and early 20th centuries. The western gray whale was previously reported to be extinct. Now, the western gray whale is considered as critically endangered by the International Union for Conservation of Nature (IUCN). The oil and gas industry expends considerable effort to monitor the population including its movements, feeding and population size.
Solving the problem: Battelle worked with an international oil company in 2014 to evaluate the use of environmental DNA (eDNA) methods to detect and type gray whales using sloughed DNA that is suspended in sea water. The study extended species detection abilities reported in recent eDNA studies[iii] by also providing evidence of maternal lineage (haplotypes) through analysis of variable regions of the recovered mitochondrial DNA (mtDNA).
Study Results: Water samples were collected offshore of Sakhalin Island in the vicinity of known gray whale habitat. Filtered water samples were shipped to and analyzed by Battelle’s Genomic Sequence Analysis Laboratory in Columbus, Ohio. Results confirmed the presence of gray whale DNA and the sequence was confirmed to be haplotype B, which is the second most common among the 22 gray whale haplotypes in the Sakhalin Island range.
Significance: This study demonstrated the recovery and analysis of DNA, specifically western gray whale mtDNA, of sufficient quality and quantity to enable haplotyping for determination of lineage. Similar methodologies could be applied to forensic analysis of animals or animal products and to survey areas for the presence of threatened, endangered or otherwise controlled species.
[i]Sanches et al., 2012. Illegal hunting cases detected with molecular forensics in Brazil. Investigative Genetics 3:17.
[ii] Linacre and Tobe, 2011. An overview to the investigative approach to species testing in wildlife forensic science. Investigative Genetics 2:2.
[iii] Kelly, et al., 2014. Using environmental DNA to census marine fishes in a large mesocosm. PloS one 9(1):e86175.
Want to know more about Next Generation Sequencing (NGS)? NicheVision, Inc., is rolling out a new education series for those interested in the most current and applicable information on use of NGS in forensic applications. The free bi-monthly series, debuting this month, will offer news, practical advice and educational programming for forensics labs at all stages of NGS implementation.
The ExactID® 411 Education Series will include research briefs, webinars, white papers and other educational materials designed to help laboratory personnel stay up-to-date on the latest advances in NGS and demystify the implementation process. NicheVision is offering the series free as part of their ongoing commitment to support the forensics community.
NicheVision develops and distributes innovative software and integrated solutions for forensic laboratories. Through an agreement with Battelle, they distribute ExactID®, a powerful NGS analytical tool, and provide NGS implementation support to law enforcement, government and commercial entities worldwide.
Battelle Research Leader Richard Guerrieri was a featured speaker at the recent TEDx Columbus. His session focused on disruptive innovations in criminal investigations. Next-Generation Sequencing (NGS) methods for DNA analysis are revolutionizing forensics and shedding new light on cases previously thought to be unsolvable. In his talk, Rich demonstrates innovative applications of these new technologies and explores their potential for disrupting cycles of crime.
His talk was part of the seventh annual TEDx Columbus, presented at the Capitol Theatre at the Riffe Center in Columbus, Ohio. TEDx is a program of local, self-organized events that build off the popular TED Talks. TEDx events feature short (15-18 minute) presentations on provocative topics designed to spark deep discussion and connection in a small-group forum. This year’s TEDxColumbus theme was Disruption.
Richard Guerrieri received a M.S. in Forensic Chemistry from the University ofPittsburgh in 1980, and presently serves as the Research Leader with Battelle Memorial Institute’s Applied Genomics Program, directing forensic and biometric initiatives for the development and implementation of next-generation sequencing technology in support of the forensic DNA community.
Mr. Guerrieri’s career as a Forensic Scientist began in 1981 with the Commonwealth of Virginia, and expanded into forensic DNA analysis through his involvement in establishing Virginia’s forensic DNA analysis program in 1988. In 1992, as Assistant Director of Roche Biomedical Laboratories' Forensic Identity Program, Mr. Guerrieri was responsible for establishing a forensic DNA testing laboratory in the RTP NC facility, to include the validation and implementation of PCR-based DNA assays.
In 1995, Mr. Guerrieri became a member of the FBI Laboratory, and for the next 20 years he served in progressive capacities as a Forensic DNA Examiner, Chief of the Nuclear Casework and Federal DNA Database Units, as well as the FBI Laboratory’s Quality Manager and Chief of the Quality Assurance and Safety Unit. Mr. Guerrieri is a former chair and member respectively of the FBI’s Scientific Working Group on DNA Analysis Methods (SWGDAM) and the National DNA Index System Board (NDIS). Mr. Guerrieri was also responsible for leading technology initiatives in the areas of process re-engineering and high through-put/robotic analysis to eliminate DNA backlogs, and was recognized through receipt of the FBI Director’s Award for Outstanding Scientific Achievement in 2011.
Across the past 34 years Mr. Guerrieri had the privilege to work on some of the most challenging investigations of national importance, reporting the analysis of several hundred cases, and providing expert witness testimony in over 250 criminal trials spanning 31 states and three U.S. Territories.