New System to Speed Up DNA Analysis

Special labs and trained personnel will no longer be required

4 February 2013

DNA is considered the gold standard for identifying people, according to the National Academy of Sciences. It’s used to determine a suspect’s association with a crime, exonerate the wrongly accused, identify deceased victims of disasters, and establish ancestry and familial relationships, to name just a few applications.         

But DNA analysis performed in traditional forensic labs is expensive and slow. That’s because each analysis requires skilled workers in a certified forensic laboratory using special equipment in a controlled environment. It can take anywhere from 12 to 20 hours to generate results—that is, if the lab has no backlog. And the backlog can be huge. Reports say that hundreds of samples are waiting to be processed in crime labs across the United States; it could take months or even years to clear the logjam.

The processing of DNA samples could soon be speeded up, however. A new, rapid DNA analysis system developed by NetBio, a small company in Waltham, Mass., can generate high-quality DNA profiles in less than 90 minutes. And this can be done by nontechnical personnel outside a laboratory setting. NetBio described its work in November at the 2012 IEEE International Conference on Technologies for Homeland Security.

Taking this process out of the lab and putting it in the field will be a game changer for law enforcement, the military, and homeland security agencies, according to Melissa May, who coauthored the paper, “Field-Deployable Rapid DNA Analysis: Fully Integrated, Fully Automated Generation of Short Tandem Repeat Profiles of Buccal Swabs.” She is senior director of strategic planning at NetBio.

“To create a device that rapidly generates DNA profiles outside a controlled laboratory environment, required some really significant changes,” May says. “First, all sample processing and data analysis steps currently performed by highly trained forensic scientists had to be automated and integrated into a single, easy-to-use device so that operators with no DNA analysis training, like a police officer or soldier, could reliably generate forensic-quality DNA profiles. Second, traditional processes and equipment had to be significantly optimized or redesigned to achieve the rapid results.” The system also had to be made rugged, so it could be moved around in police stations or combat zones and wouldn’t need to be recalibrated after each bump or bang.

According to May, NetBio’s Rapid DNA Analysis System produces high-quality DNA profiles in 84 minutes.

SYSTEM SPECS
The NetBio system’s possibilities were first recognized outside the company in 2009, when it received a competitive award from the U.S. government to develop a fully integrated rapid DNA analysis device. Its use was postulated for law enforcement, homeland defense, and military applications. The project, named Accelerated Nuclear DNA Equipment, is sponsored today by the FBI and the U.S. departments of defense and homeland security.

The company’s rapid DNA analysis machine includes three components: its BioChipSet Cassette, the DNA scan instrument, and a DNA analysis system. The cassette consists of swabs for taking a DNA sample and a fully automated instrument with a built-in microfluidic biochip. The instrument analyzes repeated DNA sequences widely found throughout the human genome that are known as short tandem repeats (STR). Because an STR profile of an individual is unique and unalterable, it is more reliable than any other biometric technology. With the exception of identical twins, the odds of two unrelated people having the same STR profile are 1 in 575 trillion, according to May.

DNA samples can be obtained in several ways, but the NetBio system relies on cotton swabs to collect cheek cells (called buccal cells) from inside a person’s mouth. To ensure that the sample is tracked and the chain of custody is maintained throughout the process, each swab has a barcode and RFID tag, and each sample taken is tied to its operator by means of a secure login.

The operator inserts the swab with its sample into the BioChipSet Cassette, a single-use, plastic, disposable lab-on-a-chip that can simultaneously process five samples. It contains all reagents and performs all the process steps required for DNA typing. The onboard reagents remain stable at room temperature for six months, eliminating the need for the refrigerators or freezers required by conventional labs.

The BioChipSet and its samples are then loaded into the instrument, and the operator simply closes the access door to initiate a “run.” A touch screen monitor on the instrument provides easy-to-follow instructions to guide the operator through the sample-loading process.

The BioChipSet measures about 11.5 inches long by 6.5 inches wide by 3.5 inches high. The instrument, about the size of a large microwave oven, is 26.5 inches by 16.5 inches by 23 inches. Installation requires only that it be plugged into a wall outlet.

“It had to be portable and easily lifted and installed in an operational setting,” notes May.

ANALYSIS PROCESS
Once a run is complete, onboard software processes the raw data and generates several data files. To maintain privacy, the ID fields include only a unique identifier or bar code number, RFID information, and a time stamp; no personally identifiable information is stored on the instrument.

The system generates an STR profile, which provides the individual’s unique genotype based on 16 STR regions on the chromosome, called loci. These loci were selected because they have a high degree of variability from person to person and are made up of noncoding regions of DNA; therefore, they do not provide any phenotypic data about an individual, such as information about appearance or medical conditions. Moreover, this type of DNA data is widely accepted in the criminal justice systems in Japan, the United States, and Western Europe.

An automated system generates several files. One is in a CODIS-compatible common message format that can be uploaded to a DNA database and used to search for DNA matches; another is in a raw data file compatible with commercially available genotype analysis software programs used by forensic analysts. The profiles generated by the system meet STR typing interpretation guidelines and do not require an expert analyst’s review, says May.

CODIS is the acronym for the FBI’s Combined DNA Index System. This compatibility is important because CODIS—which uses 13 STR loci—is a national database that stores DNA profiles submitted by federal, state, and local crime laboratories in the United States.

“In order to upload a sample in the CODIS database or to search for one, you have to go through a very stringent exercise, so the NetBio system must still undergo developmental validation and accreditation by the FBI along with the Scientific Working Group on DNA Analysis Methods, which writes the quality assurance standards and definitions for DNA profiles entered into CODIS,” May says. The forensic community is reviewing its current policies and practices, however, to determine how best to apply these profiles to rapid DNA analysis to keep the implementation of this technology moving forward, according to May.

The system is currently undergoing testing and evaluation by its government sponsors. In addition, NetBio recently partnered with GE Healthcare, which will market, sell, service, and distribute the system to law enforcement agencies globally.

May reports her company is already working on making the machine even more compact and lightweight and expanding the system’s capability so it can analyze 27 loci per sample. This would enable enhanced kinship analysis and the processing of touch samples, which are samples such as fingerprints recovered from handled objects that contain small amounts of DNA.  The current system can already process blood samples and purified DNA.

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