Moving Implementation Mountains: Experiencing the Forensic Laboratory MPS Workflow through Simulation
At the International Symposium on Human Identification (ISHI) in Minneapolis, MN on September 26, 2016, the NIJ’s Forensic Technology Center of Excellence (FTCoE) presented at a workshop that provided attendees with a unique opportunity to learn best practices to implement massively parallel sequencing (MPS) into a typical forensic laboratory workflow. Supported by the FTCoE, University of North Texas Health Science Center, and North Carolina State University, an immersive and interactive virtual simulation tool was showcased that guides DNA practitioners through three commercially available forensic laboratory processes amenable to two MPS instruments. Attendees were given the opportunity to virtually employ laboratory protocols as well as analyze forensically relevant genetic loci through commercially available and third-party software applications.
► Despite various workshops and presentations, a substantial barrier to the adoption of MPS technology is bridging the knowledge gap between the laboratory bench workflow and the theoretical basis of the MPS chemistry. Through the developed interactive simulation tool, attendees were able to make the connection between the chemistry of MPS (MID design, bead manipulation, emulsion PCR, etc.) with respect to the molecular biological mechanisms of the technologies (bridge amplification, adaptor ligation, etc.). Additionally, attendees learned how these technologies are both similar and distinct from currently employed forensic protocols.
► Attendees navigated through the physical workflow of the Promega PowerSeq™ (STR) kit, the Illumina ForenSeq™ (STR, Y-STR, SNP) kit, and the Life Technologies AmpliSeq™ mtDNA kit. This exercise included immersive and interactive virtual demonstrations through the simulation tool of how to load onto the Illumina MiSeq™ (Powerseq™ and Forenseq™) and the Ion Torrent (AmpliSeq™) platforms. By demonstrating multiple technologies on two platforms, a more comprehensive experience was provided so that the attendees would have a better foundation on which to select the best platform to meet their agency’s needs and thereby further facilitate adoption.
► Attendees also learned how to analyze real data obtained from MPS technologies through vendor and third-party software applications. The instructors lead informative and engaging discussion on the bioinformatics processes of sequence data analysis (FASTA, FASTQ, PHRED quality scoring, etc.), and attendees were exposed to various software applications, including Illumina Universal Analysis Software package, STRait RAZOR, and HIrisPlex. Participants learned how MPS may provide additional mitochondrial DNA information on a sample of interest beyond what Sanger Sequencing may provide. Additionally, the end-user learned how other forensic markers of interest (SNPs) can be exploited to provide additional information which is not possible with current forensic genetic markers.
Virtual Laboratory Simulation Tool
Virtual Laboratory Standard Operating Procedures (PLEASE READ BEFORE ENTERING THE VIRTUAL LABORATORY)
Quick-look guide to navigating the virtual laboratory (PLEASE READ BEFORE ENTERING THE VIRTUAL LABORATORY)
► Moving Implementation Mountains: Experiencing the Forensic Laboratory NGS and Bioinformatics Workflow through Simulation- Introduction and Data Analysis of the Illumina Analysis Software | Donia Slack, RTI International
► Overview of Moving Implementation Mountains: Forensics, NGS, Bioinformatics | Dr. Bruce Budowle, University of North Texas Health Science Center
► An Introduction to the Ion S5™ and Ion Chef Technologies | Dr. Jennifer Churchill, University of North Texas Health Science Center
► Analysis of Massively Parallel Sequencing Data Using the STR Allele Identification Tool- Razor (STRait Razor) | Frank Wendt, University of North Texas Health Science Center
► Bioinformatics for the Forensic Scientist | Dr. Seth Faith, North Carolina State University
► Implementing Mitochondrial DNA Massively Parallel Sequencing into Forensic Casework | Dr. Walther Parson, Institute of Legal Medicine, Innsbruck Medical University
Donia Slack, M.S.
Donia Slack is the Associate Director for the NIJ’s Forensic Technology Center of Excellence (FTCoE) where she assists the center with leading cutting-edge, technology-driven efforts in support of the Sponsor’s mission. Ms. Slack has over 12 years of experience in the forensic DNA community, directing and overseeing a number of internally and federally funded forensic projects pertaining to genomic analyses of human, plant, and microbial DNA. Ms. Slack has managed complex research and operational efforts serving the DOD, DOJ, and the Intelligence Community, and has provided programmatic oversight of contracts and subcontracts. Ms. Slack is a certified Project Management Professional (PMP), has a Bachelor of Science degree in Biology from the University of Miami, and a Master of Science degree in Cellular and Microbial Biology from the Catholic University of America.
Bruce Budowle, Ph.D.
University of North Texas Health Science Center
Dr. Bruce Budowle received a Ph.D. in Genetics in 1979 from Virginia Polytechnic Institute and State University. From 1979-1982, Dr. Budowle was a postdoctoral fellow at the University of Alabama at Birmingham. Working under a National Cancer Institute fellowship, he carried out research predominately on genetic risk factors for such diseases as insulin dependent diabetes mellitus, melanoma, and acute lymphocytic leukemia. From 1983-2009, Dr. Budowle was employed at the FBI Laboratory Division and carried out research, development, and validation of methods for forensic biological analyses. Dr. Budowle has worked on laying some of the foundations for the current statistical analyses in forensic biology and defining the parameters of relevant population groups. He has published more than 485 articles, made more than 550 presentations, and testified in well over 200 criminal cases in the areas of molecular biology, population genetics, statistics, quality assurance, and forensic biology. He has been a chair and member of the Scientific Working Group on DNA Methods, Chair of the DNA Commission of the ISFG, and a member of the DNA Advisory Board. He was one of the architects of the CODIS National DNA database, which maintains DNA profiles from convicted felons, from evidence in unsolved cases, and from missing persons. Some of Dr. Budowle’s efforts over the last decade are in counter terrorism, primarily in identification of victims from mass disasters and in efforts involving microbial forensics and bioterrorism. Dr. Budowle was an advisor to New York State in the effort to identify the victims from the WTC attack. In the area of microbial forensics, Dr. Budowle has been the chair of the Scientific Working Group on Microbial Genetics and Forensics, whose mission was to set QA guidelines, develop criteria for biologic and user databases, set criteria for a National Repository, and develop forensic genomic applications. In 2009 Dr. Budowle became Executive Director of the Institute of Applied Genetics and Professor in the Department of Forensic and Investigative Genetics at the University of North Texas Health Science Center at Fort Worth, Texas. His current efforts focus on the areas of human forensic identification, microbial forensics, and infectious disease.
Jennifer Churchill, Ph.D.
University of North Texas Health Science Center
Jennifer Churchill received her Bachelor of Science degree in Biochemistry from Texas A&M University. Her undergraduate research at Texas A&M involved the application of molecular genetic technologies to the study of population and conservation genetics of the North American bison. Jennifer earned her Ph.D. in Biomedical Sciences specializing in Human and Molecular Genetics at the University of Texas Graduate School of Biomedical Sciences. Her dissertation work focused predominantly on the use of linkage and next-generation sequencing technologies to identify novel autosomal dominant Retinitis Pigmentosa genes. As a postdoctoral research associate, Jennifer’s current research includes the forensic development and application of human identification genetic marker analyses with massively parallel sequencing technologies.
Seth Faith, Ph.D.
North Carolina State University
Dr. Seth A. Faith is currently an Asst. Professor at the Forensic Science Institute at North Carolina State University. Dr. Faith received his Bachelors of Science in Microbiology from The University of Akron and a PhD in Cell and Molecular Biology from Kent State University and Northeastern Ohio Universities College of Medicine. He completed postdoctoral training at the University of Pittsburgh Regional Biocontainment Laboratory. Dr. Faith’s current research focuses on developing state-of-the-art methods and bioanalytical tools for characterizing and analyzing human and microbial nucleic acid sequences derived from next generation sequencing platforms. Dr. Faith et al. was the first to publish a method demonstrating the ability of next-generation sequencing and bioinformatics to produce full CODIS STR genotypes. Dr. Faith’s continuing work is focused on developing and deploying DNA sequencing technology for the forensics community to perform human identification, kinship analysis, phenotype determination, and mixture deconvolution.
Walther Parson, Ph.D.
Institute of Legal Medicine, Innsbruck Medical University
Walther Parson received his doctorate in forensic molecular biology in 1999 and holds an associate professorship at the Institute of Legal Medicine, Innsbruck, Austria, and an adjunct associate professorship at Penn State Eberly College of Science, PA, USA. He set up the Austrian National DNA Database Laboratory and is an Austrian representative in the European Network of Forensic Sciences (ENFSI) DNA Working Group and the European DNA Profiling (EDNAP) Group. He serves as adviser on international boards and steering committees. Since 2009, Walther Parson is an elected member of the National Academy of Sciences Leopoldina. Walther Parson has authored more than 200 peer-reviewed original articles in the past ten years and received international scientific prizes. Walther Parson was repeatedly consigned to handle international requests on DNA fingerprinting such as the DNA identification of the Asian Tsunami victims, the remains of the Russian Tsar family or historical cases such as putative Mozart art skull. He is currently interested in the forensic application of novel DNA technologies.
Frank Wendt, Ph.D. Candidate
University of North Texas Health Science Center
Frank Wendt is a Molecular Genetics Ph.D. Candidate under the mentorship of Dr. Bruce Budowle at the University of North Texas Health Science Center (UNTHSC) in Fort Worth, Texas. He received his Bachelor of Science degree in Forensic Science, with a concentration in biology, from The Pennsylvania State University. His undergraduate research projects involved evaluation of rapid DNA technologies and use of massively parallel sequencing (MPS) to assess degrees of mitochondrial DNA heteroplasmy in maternal relatives. Frank’s doctoral work focuses primarily on use of MPS to characterize known and novel, pharmacogenetically relevant polymorphisms in opiate metabolism and analgesic response genes.
MPS Simulation Technical Lead
Sarah Norsworthy, M.S.
Sarah Norsworthy is a Forensic Scientist for the NIJ’s Forensic Technology Center of Excellence (FTCoE) where she supports outreach and dissemination initiatives, and provides technical assistance on human DNA analysis efforts and cross-disciplinary projects. Ms. Norsworthy previously worked as a Research Associate for NetBio, Inc. where she was involved in the development of protocols for processing human samples as part of the Disaster Victim Identification project, as well as low DNA content samples. Ms. Norsworthy received her Master of Science degree in Biomedical Forensic Sciences from Boston University School of Medicine. Aspects of her master’s thesis research include determining the most appropriate method for characterizing allelic dropout rates based on the analysis of single-source calibration data and assessing how dropout impacts estimating the number of contributors to a forensic DNA sample through the simulation of mixture profiles using GGETIt, a simulation tool for the generation and evaluation of genotypes. Ms. Norsworthy has two Bachelor of Arts degrees in Biology and Mathematics from Smith College.
MPS Simulation Tool – Technology Development Team
John Holloway is a Senior Multimedia Specialist at RTI International. In this role, Mr. Holloway serves as a member of the application development team responsible for developing concept and project content and managing content and code generation by subcontractors. Mr. Holloway generates two-dimensional (2-D) and three-dimensional (3-D) graphic content and associated interactive scripting and coding for virtual reality, as well as 2-D interactive applications. His work includes the creation of 2-D/3-D coding, animation, simulation, and still visualization, and he has also developed interactive courseware programming. Mr. Holloway received his Associate of Applied Science degree in Scientific Visualization and C++ 3D Graphics Programming from Wake Technical Community College. Additionally, Mr. Holloway has a Bachelor of Fine Arts degree in Oil Painting from the University of Cincinnati, School of Design Art and Architecture.
Edward (Chip) Hill
Edward (Chip) Hill is a Computer Graphics Software Consultant and Founder of Tarheel Technologies® in North Carolina. Mr. Hill has over 20 years of experience developing 3D computer graphics applications and simulations, business software solutions, and graphics rendering software. His current focus areas are graphical simulations built with commercial and open source 3D toolkits and business software development aimed at fulfilling enterprise computing needs. Previously, Mr. Hill was a Senior VR Software Engineer at RTI International in charge of the design and development of 3D virtual reality software used in desktop and web-based training applications for the U.S. military. While at RTI, Mr. Hill was also a Graphics Technology Mentor, Technical Manager for project software subsystems, and a Functional Manager responsible for the professional development of technical staff. Mr. Hill has completed several Masters level coursework in computer science and received his Bachelor of Science degree in Chemistry from the University of North Carolina at Chapel Hill.