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June 2017 - Issue 8
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.
Massively Parallel Sequencing (MPS) technologies—also referred to as Next Generation Sequencing (NGS)—just got a lot closer to implementation in crime labs. A Battelle study for the National Institute of Justice (NIJ) demonstrates that the technology provides the accuracy, reproducibility and sensitivity needed to support forensic investigations.
DNA analysis has become a critical part of the forensic toolkit over the last few decades. However, traditional capillary electrophoresis (CE) used in most crime labs has significant limitations, especially when it comes to analyzing unknown, degraded or mixed samples.
MPS is a newer sequencing technology using massively parallel processing to vastly increase the speed, processing power and resolution of DNA sequencing compared to CE. It is already used for DNA sequencing in other types of scientific research, including zoology, microbiology and environmental studies. It could soon be used to complement traditional CE sequencing for criminal forensic work as well. However, before it can be used as evidence for forensic investigations, the technology must be validated for use in criminal forensic laboratories.
The Battelle-led NIJ study was initiated in 2015 to evaluate the use of MPS technologies in eight forensic laboratories across the country. In Phase I (Performance Testing), Battelle researchers evaluated commercially available MPS products and developed standard operating procedures and workflows to be used across all of the participating labs. In Phase II (Inter-Laboratory Testing), standardized samples provided by the National Institute of Standards and Technology (NIST) were sent to each of the participating laboratories for analysis. Battelle researchers used the results generated by the labs to determine whether the MPS technologies and workflows produced results that were accurate, concordant, reproducible and sensitive.
Each laboratory used the same equipment and followed the standardized workflows that Battelle evaluated in Phase I.
A comprehensive review of the Phase II results showed that MPS produces data that is “robust, reliable, reproducible and sensitive.” Laboratories performing the same workflows and using the same instruments and software produced results that were concordant with each other. In addition, the genotypes obtained through MPS were consistent with data obtained through CE typing (within allowances for the limitations of each technology type). The results indicate that the MPS technologies and workflows studied produce results that are accurate and reliable for criminal forensic investigations.
MPS could greatly expand the scope of applications for forensic genomic analysis. Forensic laboratories presently use CE-based typing of Short Tandem Repeats (STRs) for determining if associations (matches) can be made between DNA profiles from an evidentiary sample with a DNA database. MPS looks at a much broader range of genetic markers, including not only STRs but also single nucleotide polymorphisms (SNPs) and mitochondrial DNA (mtDNA). Using MPS, analysts can process millions of reads per run, providing a dataset with much higher resolution. This expanded resolution, along with advances in our ability to read and understand genomic information, allows MPS to provide meaningful information from unknown samples even when they do not produce a match in a forensic database. It also makes MPS more useful for analysis of highly degraded or mixed samples that often fail to produce results using CE.
MPS genomic analysis can provide important insights into forensically relevant information such as phenotype (e.g. hair color, eye color, sex, facial structure or height), kinship and ancestral origin. The first likely forensic laboratory application for MPS, already under evaluation at the Ohio Bureau of Criminal Investigation (OBCI), may be for human identification in missing person cases. Using these advanced genomic methods, investigators could provide closure for many of the thousands of families waiting for answers in missing person investigations. It also could be by forensic laboratories to generate investigative leads for evidence in which searches of DNA databases were unsuccessful.
The NIJ study adds to the knowledge base for forensic labs seeking to implement MPS. Battelle is continuing work to optimize MPS methods for forensic investigation and assist labs in rolling out the new technology.
For more information, attend our upcoming webinar.
In scenarios where DNA cannot be fully analyzed for forensic purposes (e.g., due to degradation, lack of nuclear DNA, etc.), human proteins could be a valuable source of forensic information.
The subset of single nucleotide polymorphisms (SNPs) that encode for amino acid changes (Non-synonymous SNPs or single amino acid polymorphisms, SAPs) would likely have forensic value if they can be routinely identified and SAP profile frequencies can be established. In fact, a few recent studies have shown that bottom-up (shotgun) proteomic techniques that use liquid chromatography tandem mass spectrometry (LC-MS/MS)-based protein sequencing can be used for human identification through the identification of genetically-variant peptides (GVPs) contained within SAPs.
To date, mainly hair samples have been analyzed, but skin and bone samples may also benefit from such analyses. Two main issues in the field are 1) developing a method that can analyze proteins from small amounts of sample, and 2) developing a robust peptide panel for routine measurement.
Researchers at Battelle have developed methods for hair that can identify GVPs from hair samples smaller than 2 cm. More specifically, they have successfully scaled the procedure down to 1.8 cm of hair, with partial success at 0.6 cm of hair.
Analysis of the dataset resulted in the successful identification of at least 30 GVPs from a single donor. Current research is focused on developing a GVP panel for hair and extending the protein-based identification methods to skin and bone samples.
Additionally, researchers are striving to make the methods compatible with mDNA analysis to increase discriminatory power. The goal is to identify a peptide panel in hair that can be used for routine identification purposes. Both the identity and quantity of the peptides in the panel could be used for human identification in a protein search engine-independent method that can be implemented in chemical forensics laboratories.
Join us at the Green Mountain DNA Conference July 24-26 to learn more. Battelle researcher Dr. Craig Bartling will share the full results of the study in a poster presentation.
In the increasingly interconnected and complex world, the ability to uniquely identify individuals, generate investigative leads, and attribute trace-level evidence are becoming essential for intelligence applications, national security, and criminal justice.
In 2015, the National Institute of Justice awarded Battelle, the world’s largest independent research and development organization, a 19-month applied research project to evaluate the feasibility of Massively Parallel Sequencing (MPS) technology, also known as Next Generation Sequencing (NGS), for forensic science applications. Battelle enlisted participation from prominent operational forensic laboratories spanning city, county, state and federal levels, and laboratories in research and academia.
Battelle anticipates that the data from this study, combined with the critical insight from participating thought leaders of the forensic DNA community, will facilitate the development of a strategic roadmap for eventual implementation of MPS to support law enforcement and the criminal justice community.
National Institute of Justice Study Report: Overview of the Testing Results for the Massively Parallel Sequencing (MPS) Feasibility and Guidance Study for Forensic DNA
Tuesday, Jun 27, 2017
2 p.m. EDT
Join us for this 60-minute webinar where we’ll reveal:
Lindsay Catlin is bringing new genomic technologies to criminal forensic laboratories. A Researcher on the Battelle Applied Genomics team, she provides support for implementation of Massively Parallel Sequencing (MPS) technologies for criminal investigation. Read More
Richard Chou, a Researcher on the Battelle Applied Genomics team, is working to find answers to the emerging questions in genomics. His past research spans molecular biology and genomics projects for agriculture, environmental science, forensics and biodefense. More recently, his work has been focused more exclusively on applied genomics. Read More