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July 2016 - Issue 6
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.
New technologies allow analysts to extract more information from DNA than ever before—but what can be done when nuclear DNA is not available or is too degraded to use? Researchers at Battelle are investigating new methods that use proteomics, or the analysis of proteins, to generate forensic data.
The proteome is the complete set of proteins that are produced or modified by an organism, system or cell. Studying the sequences of proteins in a sample can give us important clues about the DNA of the organism that produced them. Just as every individual has a unique genome that varies in small but important ways from others in their species, the proteome of each individual is unique. This means that it can potentially be used as an alternate method of identification in forensic investigations.
For example, hair is composed primarily of keratin, a fibrous protein that also comprises human fingernails and horns and hooves in animals. The cells contained in the hair shaft are dead and therefore do not contain nuclear DNA. That means that unless the sample contains the living cells at the root, hair samples do not provide nuclear genomic DNA for sequencing. However, proteomics may one day be able to provide an analysis of the protein sequences in the hair samples that could be used for human identification. It could also be useful in situations where DNA is too degraded to use, such as old blood or saliva stains. Proteins are often more stable than DNA molecules, so analysts may be able to recover usable information from proteins in samples of body fluids even if the DNA is not recoverable.
The science of forensic proteomics is still in its infancy, and much work remains to be done before proteomic data can be used for forensic purposes. In large part this is because proteomics is much more complicated than genomics. While each person has just one genome, each gene can produce multiple different protein variations from alternative splicing, post-translational modification and other events. However, forensic science can take advantage of these variations. Different cells in the body produce different proteins at different times as genes are switched on or off by body system activity or environmental factors. That means the proteins found in your saliva will look very different from the ones found in your blood, and the proteins found in a saliva sample after a heavy meal will be different from those found after a long fast. Thus, the proteome is rich with information regarding sample origin, exposure and other forensically valuable information.
In cases where proteins are to be used simply for human identification, researchers need to identify a set of biomarkers that are consistent over time for individuals and have enough variability between individuals to be useful for identification. Genetic polymorphisms (nearly identical genetic sequences) among individuals can be analyzed at the protein level as well, provided the genetic polymorphism encodes for a protein sequence change. However, unlike DNA, proteins cannot be copied and amplified for analysis; the proteins within the original sample are all that will be available for analysis. Also unlike DNA, proteins are not sequenced directly. Rather, they are analyzed using mass spectrometry in order to extrapolate their sequences. This makes analyzing and sequencing proteins more complicated and prone to interpretation errors than genomic sequencing.
Researchers at Battelle are investigating methodologies to make protein analysis easier, faster and more accurate. In order to make proteomic data useful for forensic purposes, the industry will need to develop standards and protocols for protein forensics, including extraction techniques, sample preparation protocols and analytical methods. Battelle’s proteomics work builds on similar work conducted over the last decade to advance the science of DNA forensics as well as proteomics for non-forensic applications. For the last few years, Battelle researchers have been heavily involved in developing, validating and evaluating new methods and technologies to bring Next Generation Sequencing (NGS) into forensic laboratories. Their proteomics research seeks to develop similar standards and methodologies for protein analysis. Specifically, they seek to define:
If researchers can identify the useful variations in the polypeptide sequences between individuals, those variations could be used to develop a reference panel for forensic identification.
Massively Parallel Sequencing (MPS), also known as Next Generation Sequencing (NGS), technologies have greatly enhanced the sensitivity, speed and informational power of DNA forensics. To turn massive amounts of sequencing data into usable forensic information, analysts rely on bioinformatics software. A new study of ExactID 2.0, a forensic NGS software tool from Battelle, demonstrates that it provides accurate genotypes using data generated by common commercially available forensic kits.
Battelle ExactID® 2.0 is the first commercially-available forensic NGS software tool that can be used to analyze data generated on a variety of NGS sequencing platforms. Unlike other commercial software programs, which are specific for the instrument they come with, ExactID can analyze data from many different types of NGS sequencers. That means that labs that have more than one type of sequencer can now analyze all of their data using a single software program and make apples-to-apples comparisons of data from multiple platforms.
ExactID allows users to access and evaluate the raw sequence data more thoroughly than platform-specific software tools. ExactID displays the sequence data so that stutter and noise patterns can be easily identified. Analytical threshold values can be set by the user and can be lowered to zero to allow for full evaluation and characterization of all sequence reads.
In order to ensure that ExactID provided accurate analysis for all types of sequencers, Battelle conducted a study using high-quality sequence data from three commercially available forensic kits generated on three different NGS platforms. The goal was to determine whether ExactID could generate accurate genotypes using data generated by each platform. Results from this study indicate that ExactID can be used to accurately evaluate forensic markers generated by any of the NGS platforms that currently support forensics applications.
For this experiment, eight samples were processed on the Thermo Fisher Personal Genome Machine (PGM), the Illumina MiSeq FGx and the MiSeq Desktop Sequencer. The HID AmpliSeq Ancestry and Identity single nucleotide polymorphism (SNP) panels were used on the PGM, the Illumina ForenSeq DNA signature prep kit was used for sequencing of SNPs and short tandem repeats on the MiSeq FGx, and the Promega PowerSeq kit was used to amplify autosomal and Y-chromosome short tandem repeat (STR) markers for sequencing on the MiSeq Desktop Sequencer instrument. All samples from all platforms were analyzed using the ExactID version 2.0 software.
Game-changing genomic technology offers new investigative options for missing person cases.
The Ohio Bureau of Criminal Investigation (Ohio BCI) and Battelle announced today that we are working together to validate and implement massively parallel sequencing (MPS), also called next-generation sequencing (NGS) technology in Ohio BCI’s forensic laboratory. Implementing MPS technology will further position Ohio BCI as a national leader in DNA forensics and expand their future DNA testing capabilities to include investigations surrounding missing persons and unidentified human remains.
MPS represents the most significant advance in forensic DNA analysis over the past 20 years, capable of providing increased powers of discrimination and enhanced sensitivity while maintaining compatibility with existing DNA databases. It also introduces the potential to predict bio-geographic ancestral and appearance characteristics (eye color, hair color, etc.)—a valuable asset for generating investigative leads. Ohio BCI is using Battelle ExactID® software, a groundbreaking genomic analysis system that rapidly processes voluminous levels of sequencing data, producing accurate results of the highest quality.
The new MPS laboratory is being established within the Ohio BCI’s Laboratory Division facility in London, Ohio. Battelle scientists initiated the first phase of MPS training for BCI laboratory staff in November and early December of 2015. Installation of specialized MPS instrumentation, equipment and materials was completed in December, and was followed by a comprehensive on-site training program across the first half of 2016. Through this unique teaming arrangement, Ohio BCI will be able to respond to the increasing demand for DNA testing from law enforcement agencies throughout the state.
The project includes Battelle’s strategically designed systems integration program for MPS technologies, processes and workflows, which may be a resource for forensic laboratories advancing forward into this technology area.
“This will position BCI to be a national leader in DNA forensics,” said Ohio Attorney General Mike DeWine. “I am proud to work with Battelle on the future applications of this cutting-edge technology because it’s a clear benefit to Ohio families of missing loved ones. With NGS at BCI, we hope to generate faster DNA results and obtain an expanded range of DNA information to help investigators make identifications.”
Ohio BCI began using DNA analysis for forensics in 1998. The technology enables law enforcement to use DNA profiles to link a suspect to a crime scene or eliminate potential suspects quickly by using trace amounts of evidence. Further, Ohio BCI participates in the Combined DNA Index System (CODIS), which links Ohio to a nationwide DNA database of millions of genetic profiles from crime scene evidence and convicted offenders. DNA profiles can be searched within the database in order to find an investigative lead. Ohio law requires DNA samples to be collected from adults arrested for a felony or anyone convicted of a felony. Massively parallel DNA sequencing technology promises to transform how future forensic DNA analysis will be performed.
“Ohio BCI has always been very forward looking in studying and embracing new and better ways to advance investigations and bring conclusion to cases,” said Michael Dickens of Battelle’s CBRNE Defense/Applied Genomics business line. “We are thrilled at this opportunity to work with and for Ohio BCI’s scientists and investigators to provide improved tools for their work.”
Advances in massively parallel sequencing stem from the completion of the Human Genome Project in 2003, which uncovered thousands of biomarkers that can be applied to DNA-based forensics. DNA has long been considered as objective evidence for forensic investigations. Traditionally, when DNA samples collected from a crime scene did not match the DNA of a potential suspect or samples from law enforcement databases, this would mean a setback for the investigation and potentially a dead-end for the DNA evidence. New MPS methods could allow law enforcement to draw important conclusions from the analysis of a single “unmatched” DNA sample, because this technology allows for the simultaneous typing of many more genetic markers.
Battelle is providing instrumentation, software, training and subject matter expertise to help Ohio BCI deploy, evaluate and validate MPS in their forensic laboratories. Employees from Battelle are being embedded in their London, Ohio facilities to support ongoing systems integration and validation activities. During the course of the project, Battelle will provide:
This will be the first time many of these technologies have been fully implemented in a working forensic laboratory. The Ohio BCI project will help to establish best practices and validate methods that can be applied in other forensic laboratories across the country.
The Ohio Bureau of Criminal Investigation has a staff of more than 400 employees within its four main divisions: laboratory, investigations, administration and identification. Ohio BCI operates three crime labs in Ohio, located in London, Bowling Green and Richfield, and processes more than 7,000 DNA cases each year. Over 19,000 offender investigative leads have been made by the Ohio database.
Are there novel genetic markers that can be used for more precise subject identification in forensic investigations? How can we know if a particular microbe carries the genes for resistance to an antibiotic? These are just a few of the questions Dr. Sara Nitcher has tackled for Battelle’s clients. Read More
Dr. Craig Bartling is unlocking the secrets contained in proteins to shed new light on problems ranging from pathogen identification to forensic analysis. He is working to find new applications for proteomics for medical diagnostics, intelligence, law enforcement and environmental management. Read More