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September 2016 - Issue 7
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) is now a mainstream technology in many academic areas, and has led to revolutionary discoveries in medicine, biology and environmental science. But most forensic laboratories are not yet ready to implement the technology. What can be done to accelerate adoption and bring the advantages of MPS to the forensic community?
For the past year, Battelle and the Ohio Bureau of Criminal Investigation (Ohio BCI) have been working together to implement MPS in an Ohio BCI lab. The project builds on five years of work by Battelle for the Department of Defense (DoD) and National Institute of Justice (NIJ). The lessons learned have now been translated into an implementation roadmap for forensic labs wishing to get up and running with MPS.
MPS (sometimes known as Next Generation Sequencing, or NGS) uses massively parallel processing to increase the speed and processing power of DNA sequencing. In essence, this means that MPS devices can process millions of reads (sequences of nucleotides) per run. This gives MPS vastly more resolution than CE sequencing technologies.
That resolution is of critical importance when it comes to some of the most difficult cases in forensic science, including identification of human remains. With MPS, a single sequencing run may generate data that encompasses a wide range of genetic markers, such as short tandem repeats (STRs), single nucleotide polymorphisms (SNPs) and even mitochondrial DNA (mtDNA). This can provide a significant advantage when dealing with samples of limited quality, including highly degraded samples and complex mixed samples.
MPS provides another crucial advantage over CE sequencing: it allows forensic labs to extract meaningful information from samples even when database searches do not confirm a match. This can include statistical predictions for ancestry and geographic origin, potential familial relationships and even certain physical characteristics (phenotypes) such as hair and eye color, skin tone and some facial characteristics. This ability may prove to be of critical significance in providing clues for identification of unknown human remains.
These advantages were key considerations in Ohio BCI’s decision to begin the incorporation of MPS capabilities within their forensic DNA Laboratory for the initial support of missing person investigations. The highly degraded condition of unidentified human remains, which often limits typing success through traditional CE analyses, and the lengthy turn-around-times frequently associated the outsourcing of such samples, may both be addressed through the MPS technology. The consolidation of a battery of informative genetic markers into a single assay, serving to reduce sample quantity and quality requirements, while significantly increasing the output of information generated across an overall reduced time-frame, are capabilities which distinguish the MPS applications for support of missing person investigations.
However, getting there requires changes in instrumentation, workflow, quality control, validation and training. For the past year, Battelle and OBCI have worked together to implement MPS in an OBCI lab and conduct a joint validation study on the technology and workflows. Together, Battelle and OBCI have developed an implementation roadmap to guide implementation for other forensic laboratories, which includes:
The OBCI project builds on Battelle’s prior work with DoD and NIJ. The Battelle Applied Genomics team led a five-year project to implement MPS technology in the field for the DoD. In 2015, Battelle was chosen to lead an NIJ project evaluating NGS methods in forensic labs around the country. The 19-month study evaluated commercially available MPS technologies and workflows, involving seven labs across the country. Battelle also designed a testing matrix to assess the performance of each MPS workflow and address key validation elements of the DNA Quality Assurance Standards including concordance, reproducibility, sensitivity, mixtures and accuracy.
Moving MPS into the mainstream for forensic application will require dedicated effort from forensic laboratories. In the meantime, outsourcing remains an option. Battelle provides outsourcing service options for forensic DNA analysis using massively parallel DNA sequencing.
For labs that are ready to move forward with MPS implementation, Battelle offers turnkey technology transfer and implementation services, including education and training, method development and validation, and analytic software.
As polar bears move into closer proximity with humans, oil and gas developers working in the arctic may soon find themselves working near protected polar bear populations. Battelle has developed new environmental DNA (eDNA) collection methods to allow scientists to monitor polar bear populations using DNA left behind in their paw prints. A new study for the North Slope Borough of Alaska will validate eDNA methods for monitoring polar bear activity.
eDNA is DNA collected from cells or excretions left behind in water or sediments rather than collected from live animals. As animals move through the environment, they shed hair and skin cells and leave behind traces of DNA in urine, saliva and feces. Researchers can extract and sequence the DNA in environmental samples to determine what species are present or have passed through the area, from microbes to large animals. It allows for faster, easier and more cost-effective data collection for required biodiversity studies and environmental monitoring.
Battelle has already used genomics, including eDNA sampling methods, to monitor marine mammals including bowhead whales and gray whales. Genomic studies of bowhead whales, conducted on behalf of the North Slope Borough, were used to inform hunting quotas for indigenous villagers as well as oil & gas development activities. Similar studies are currently underway to provide new insights into gray whale population diversity and migration. Oil & gas companies can use data from eDNA studies to plan development activities and monitor environmental impact on protected species.
Current eDNA methods extract DNA from marine or freshwater environmental samples. This limits their utility for monitoring the movement of animals on land. Battelle has pioneered new methods that would allow DNA to be extracted from polar bear paw prints in snow. Snow samples from the paw prints are melted before extracting and amplifying DNA for analysis. This approach also promises to be transferrable to studies of non-aquatic species such as terrestrial bears.
DNA fingerprinting methods for polar bears are being developed using polar bear blood samples and environmental samples provided by the Columbus Zoo. The samples will be used to develop primers that can detect the presence of polar bears and to identify genetic loci (SNPs) that can be used to fingerprint individual bears. This will allow researchers to answer questions about population size, range and genetic variability to inform conservation efforts.
The North Slope Borough study begins this fall. In phase one, researchers will validate the eDNA collection methods. Phase two includes demonstration and validation of the DNA fingerprinting methods to track individual bears. Ultimately, data will be collected in order to estimate population size and set appropriate hunting quota limits for hunts conducted by the Eskimos in the North Slope. Indigenous populations in Alaska, Canada and parts of Russia depend on the bears for subsistence and ceremonial hunts in their traditional way of life.
Studies of polar bear genomics could help researchers monitor the success of conservation efforts and international treaties aimed at protecting polar bears. Polar bears are considered to be especially vulnerable to the effects of climate change. However, many polar bear populations have not been thoroughly studied, making it difficult to monitor changes in population size or genetic variability over time. eDNA studies could help to fill in some of these knowledge gaps by making it faster, safer and cheaper to gather genomic data.
Battelle scientists are continuing to study and validate new eDNA methods. Eventually, researchers hope to use similar methods to extract DNA from soil samples, further expanding the range over which land animals could be monitored and the species that could be studied.
Battelle and the Ohio Bureau of Criminal Investigation (Ohio BCI) have made significant progress in optimizing and validating methods, equipment and workflows for Massively Parallel Sequencing (MPS) in an Ohio BCI lab. Three new studies, to be presented at the International Symposium for Human Identification (ISHI) this month, highlight some of the latest results.
Battelle is working with the Ohio BCI to implement MPS (sometimes referred to as Next-Generation Sequencing, or NGS) in their forensic laboratories in London, Ohio. MPS, while widely used in academic labs, is still a relatively new technology for forensic laboratories. DNA typing using MPS requires additional laboratory steps compared to more familiar CE-based technologies. Implementing MPS for forensics requires optimization and validation of technologies, workflows and methods specific to forensic applications. The joint Battelle/Ohio BCI project is breaking new ground for the industry and defining methods that will soon be able to be applied by other forensic labs across the country.
The three Battelle studies examine specific aspects of the project.
Results of all three studies will be presented by Battelle researchers and Ohio BCI personnel during poster presentations at ISHI. Battelle and Ohio BCI will build on this work as they complete the MPS technology transfer project over the next several months. Lessons learned will be used to develop guidelines for other forensic laboratories planning to implement MPS.