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​Battelle NIJ Grant Update - Evaluating NGS Technologies in the Field

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: 

  • Armed Forces DNA Identification Laboratory (AFDIL);
  • Bureau of Alcohol, Tobacco and Firearms (ATF);
  • California Department of Justice (CAL-DOJ);
  • Federal Bureau of Investigation (FBI);
  • Harris County Institute of Forensic Sciences (HCIFS);
  • National Institute of Standards and Technology (NIST);
  • New York Office of the Chief Medical Examiner (NY-OCME);
  • North Carolina State University (NCSU).

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.

Phase I: Performance Testing

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.

  • Illumina’s ForenSeq™ DNA Signature Prep Kit; MiSeq® FGx Forensic Genomics System; ForenSeq™ Universal Analysis Software
  • Thermofisher’s HID-Ion AmpliSeq™ Identity and Ancestral Panels; HID-Ion AmpliSeq™ library kit;  Ion Chef™ and PGM™ Systems; Variant Caller 4.0 software followed by the HID SNP Genotyper plug-in
  • Promega’s PowerSeq™ Auto/Y System; Illumina’s TruSeq® DNA PCR-Free Sample Prep Kit; Illumina® MiSeq® Desktop Sequencer; Battelle’s ExactID® Analysis Software.

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.

Phase II: Inter-laboratory Testing

Phase II, which will commence in early 2016, will consist of a series of sample exchanges between Battelle and each of the participating laboratories. Battelle has designed a testing matrix to assess the performance of each NGS workflow. The assessment will address key validation elements of the DNA Quality Assurance Standards for NGS applications to include concordance, reproducibility, sensitivity, mixtures and accuracy. Additionally, participating laboratories may include a fourth study, non-probative (adjudicated or simulated) forensic samples, to gain a greater perspective on the overall capabilities of the NGS technology. For standardization and uniformity, NIST is graciously assisting Battelle through the generation of pre-quantitated genomic DNA samples for the Phase II studies, with DNA samples of established genotypes (via short tandem repeat analysis across capillary electrophoresis).

Goal

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.