Scientists are enabling DNA analysis to function as a virtual sketch artist to figure out who people are and what they look like even in situations with no eyewitnesses. The developments have particular application to counterterrorism but could affect a wider array of fields as well. Even more importantly, the personnel are developing bioinformatic software solutions databases to manage quick interpretation of data for usability.
The work is taking place at Battelle Memorial Institute, Columbus, Ohio, in its identity management section in part because of the convergence of the importance of counterterrorism activities and the dramatic decrease in the cost of DNA sequencing. Brian Young, director of strategic initiatives for identity management at the institute, explains that expenses for the latter have fallen at a rate faster than Moore’s Law over the past decade, reducing by orders of magnitude. The result is that law enforcement and national security officials now better can afford to sequence DNA. Information from the samples reveals data about sex, race, height, hair color, eye color and more. “It is amazing,” Young states.
However, because all human DNA is much the same, analysts have to find the small percentage of genetics that actually identifies individuals. Battelle’s bioinformatic solutions aim to assist that process, quickly combing through gigabytes if not terabytes of data coming from the sequences. “Addressing how folks do this in the field is important,” Young says. The field might be a local police station or an overseas military environment. Both require reasonably affordable analytical equipment with easy-to-use laboratory technology. The institute’s work for 2013 focuses on next-generation sequencing (NGS). This technology sequences millions of DNA molecules simultaneously in massively parallel fashion. Prior to the advent of the NGS, DNA was sequenced one molecule or a few molecules at a time. The massively parallel technique has helped drive down sequencing costs, making DNA sequencing affordable for new application areas, including forensic DNA analysis. At present, the technology is only feasible in a laboratory and not in the field. Battelle is participating in the development of the practical-use version.
Mike Dickens, general manager of identity management at Battelle, explains that his program has three big priorities for the next three years. First and foremost, the team will finalize its algorithms and beta testing for the bioinformatic software. Second, it will launch that software. Third, the researchers aim to publish the results of their research, especially in the area of how to extract short tandem repeats (STRs) from the NGS. The STRs are repeating sequences of two to six nucleotides. All of the STRs used in forensic DNA analysis worldwide are either four-nucleotide repeats or five-nucleotide repeats.
Battelle already has published information in the past and has three more documents pending. “Our research is openly vetted in the forensics community prior to release,” Dickens states. He adds that putting information out for others to see is extremely important because it shows the conservative organizations that would use the technology that validated methods are coming out of an academic laboratory.
Technology alone will not enable widespread implementation of the capabilities. Young explains that others in government can support Battelle’s work by enacting public policy that allows the capabilities to develop while protecting individual privacy rights. He shares that it is typical to have a strain on many new developments because the policy does not keep up with the technical advancement.
Young says that overall his section considers itself as studying humans in a new frontier in signature detection. There are several fields under that, such as behavioral identification or intent identification, but Battelle focuses most on the DNA. Three significant projects are underway in that area.
One involves developing the NGS as a genotype for forensic DNA analysis, allowing much more extensive analysis than current technology. Another project develops methods to predict appearance and ancestral origin from evidence left behind at crime scenes and other places. The last one is the development of a data management strategy and analytic tools for genomic data for law enforcement and national security purposes.
Current technology used in those fields tends to look into only a small portion of the DNA in the genome instead of the entire set. The NGS allows interrogation of the entire genomic complement. “That is a tremendous amount of data,” Young states. Because not all of that data is of interest, examiners are challenged to find the informative bits. More and more evidence is available because the DNA can be obtained from trace samples that as recently as five years ago would have been too minimal to use. Today, technology has advanced to the point where almost any fluid or cell left behind can provide information.
Law enforcement officials use mainstream DNA analysis to match profiles to databases. The NGS takes the efforts much further, allowing users to make predictions about who committed crimes without anyone having seen the perpetrators. For the new technology to be valuable, it must present the novel capabilities while still meeting current database requirements. Young explains that Battelle is an innovator in developing methods that allow sequencing to analyze DNA for the legacy STR format. “That was a hard problem,” he says, because STRs are long stretches of DNA relative to what short-read NGS sequencers can achieve today. Also, the repeating structure of STR loci make them difficult to analyze.
Creating the solutions to the complex problems demands a multidisciplinary approach. Dickens explains that his core group of people, not including Battelle at large, incorporates molecular biologists, software developers, statisticians and more. The identity management group also works with many academics who make discoveries out of their disease research programs. Dickens explains that all the work underway is important as counterterrorism solutions continue to remain an extremely high priority for national security and defense. “Battelle really responded to that need by investing in and establishing this core group,” he explains.
Also critical is having additional ways of approaching the DNA problem. As technology evolves, it offers the ability to have more granularity in the data. The advancements enable researchers to identify someone within hours or days instead of weeks or months, Dickens says. The eyewitness-free sketch artist capability and the faster turnarounds are especially important when trying to track terrorists.
Unlike portrayals on popular crime television shows, DNA is not collected for all types of crimes. However, it is being collected more often, including after property crimes. Constraints on collection come down to budget more than technology, because law enforcement divisions have only so much money to process their case loads. Leadership must determine when to pay for analysis. Another consideration is legal limitation. State laws vary about when DNA can be collected and whether that information can be retained.
Battelle’s work also could have application to mass casualty and missing person situations. It even could help with microbial forensics, detecting invaders that perturb the environment.
As lab researchers revolutionize the now, they also are keeping tabs on trends of the future. In the next five years they expect a new generation of reagentless sequencers to make a big difference in the identity management field. Just as the most expensive part of printers is the ink, the most costly part of many sequencers is reagents. If the new reagentless versions are successful, they can alter usage, enabling more ruggedized and affordable technology. They also will be simpler to use. And, in overseas operations, they will require less gear to transport. The result would be more field and even clinical laboratory applications as opposed to central laboratory scenarios.
Industry can help aid development efforts in the various projects by continuing to innovate in areas such as sequencing and genomic technology. Young says companies have done a great job to reach the current point where costs have fallen so quickly. Academia can assist through basic research into the genetics of human beings and finding out which portions of genetic code reveal which traits. As all that works goes on, the lab will continue transitioning new discoveries from academia and industry into usable products for the public sector.