Getting more from DNA

Getting more from DNA

“Indigo is a bugger,” says Derrill Prevett, a Nanaimo, B.C.-based prosecutor, talking about the problems with extracting and analyzing DNA samples from evidence sources such as indigo-dyed fabrics like blue jeans.


Such contamination is a problem that’s plagued police and prosecutors since DNA made its debut in criminal casework in the United Kingdom in 1987 following the work of British genetics researcher Sir Alec Jeffreys.

And Prevett knows what he’s talking about. With Cecilia Hageman and Wayne Murray, he’s the author of the DNA Handbook for the legal profession. It was Prevett who stickhandled DNA evidence through the Robert Pickton serial-killing case that resulted in six convictions for second-degree murder in 2007. That case backlogged Canada’s labs for months with more than 200,000 DNA samples flowing from the killer’s Port Coquitlam, B.C. property.

Now, however, there’s a breakthrough from a University of British Columbia department of physics and astronomy research team that may remove that indigo problem as well as other contamination roadblocks to extracting usable evidentiary DNA. Those include humic acid from soil, melanin from hair samples, and hematin from blood. All of those can co-extract with DNA. As such, in cases where there is insufficient DNA or co-extraction, it’s estimated 10 per cent of crime scene samples may fail.

The new method, say investigators and prosecutors, could provide better evidentiary samples for both police and court processes. “It’s a great advancement for cleaning up and getting samples that in the past would be problematic,” says Ron Fourney, RCMP director of forensic science and identification services.

There are things that render a sample useless by degrading the DNA. “Bleach will do it, so will ultraviolet light. Things growing on it will do it,” says Prevett. Further, Fourney is the first to admit the complexities of DNA forensic science are frequently a bit of a “twilight zone.”

DNA, or deoxyribonucleic acid, is a nucleic acid in a double-helix chain containing the genetic instructions used in the development and functioning of all known living organisms and some viruses. Each human cell contains 23 base pairs of chromosomes, each containing close to 100,000 genes and DNA chains made up of 100 million base pairs of nucleotides. In short, the complete human genetic code is based on three billion base pairs dictating everything from height to hair colour. In order to build a genetic fingerprint from a sample taken from a crime scene, forensic scientists need a clean sample which is then cut to produce samples of differing lengths. It’s here that Prevett suggests the new process is interesting as a contaminant such as indigo can inhibit the chemical scissoring process for cutting the DNA strands.

The segments are then sorted in a process called gel electrophoresis. Short segments move faster than long ones in the electrified process which allows for sorting. The resulting sequences are then transferred to a nylon membrane and identified according to the code they contain using radioactive markers. The result is a series of bars known as short tandem repeats. And, just as a barcode identifies a specific product, so does a DNA sequence identify a specific person (except in cases of identical births).

Basically, says Prevett, the process involves extraction, quantification, amplification, and interpretation.

According to the DNA Handbook, forensic work now uses polymerase chain reaction (PCR) processes as the standard DNA typing system. Prevett says it allows scientists to quickly locate particular areas of DNA, “the molecular equivalent of finding a needle in a haystack.” When that needle is found, it can be used to pinpoint the person from whom it came. But, experts caution, DNA can be used not only for helping prove a case against someone, but also for ruling out suspects.

As the technology has progressed since its usage began in British courts almost 25 years ago, it has been used to exonerate the wrongly convicted. Everything must be seen in the context of the case. “Semen left upon the body of an assault victim connotes not only timing but that its owner was the perpetrator of the sexual assault,” Prevett says. “My semen is found in a woman who is dead,” he illustrates. “‘Aha!’ Then it turns out she’s my girlfriend. If it turns up in a woman I don’t know, then it has meaning.”

Which brings us back to the indigo. What if the mystery semen is on a pair of blue jeans? Well, explains UBC engineering physicist Andre Marziali, the indigo inhibits the PCR process. That’s where the new SCODA (synchronous coefficient of drag alteration) concentration method comes in.  It’s the brainchild of Marziali and his team. He says the SCODA process can reject contaminants such as indigo, acids from environmental sources, soil, and blood. The clean DNA then moves into the PCR process for typing. “We can reject between a hundred to a thousand times more [contaminants] than other processes,” he says.

Marziali has been working in DNA research at both UBC and California’s Stanford University for years, but says he did not set out to find the process. Rather, it’s an idea that came up over coffee with colleague Lorne Whitehead, who posited the initial mathematical formula for the concept. But, Marziali chuckles, there was no eureka moment. “It was a discovery,” he says.

The team’s method employs a DC electric current to drive negatively charged molecules, including both DNA and contaminants, into a gel in a lab vessel. Rotating electric fields are applied to the gel to concentrate the DNA at the gel’s centre. That is extracted for analysis.

“By exploiting the physical traits of DNA — electric charge, length, and flexibility — we’ve been able to extract DNA from samples that would otherwise not produce enough clean DNA for analysis,” says Marziali. That clean DNA, says Prevett, can then be subjected to standard DNA analysis techniques.

Marziali says extracting DNA by conventional methods — which rely on the molecules’ chemical properties — is challenging when there are only trace amounts of DNA or when the source sample has contaminants with similar chemical traits. “We’ve found that DNA and RNA respond to electric fields in a way that is very different from other molecules,” says Marziali. “By exploiting this unique property, we were able to extract high-quality DNA from a highly contaminated sample from the Athabasca oilsands.”

And, the team successfully tested the technique on samples provided by the RCMP, confirms Fourney. He says the RCMP had advance warning that “a new and exciting technology was around the corner,” calling it a promising step forward in intelligence-led policing. The process, he says, is “potentially useful for more challenging samples.”

But, Fourney cautions, there are steps police need to take before SCODA can be definitively added to the police toolbox and used in the charge-approval process, and prosecutions. “We would vigorously validate this, many more samples . . . how it would operate in the real world,” he stresses. “This is very exciting. The silence of the grave is a poetic anachronism. Volumes can be spoken to those who will listen, and this is one of those situations.”

And, Fourney says, with a climate such as Canada’s, that real-world validation means seeing how SCODA will be useful on DNA sources that have been frozen and thawed, which can break down the nucleic acid. The problem right now, he notes, is the SCODA system is slow, each sample taking half an hour to run. It’s a shortcoming Marziali and his team are working on. He wants to move that rate to 48 samples an hour.

Fourney says the current magnetic bead-extraction process, which is less efficient at producing clean samples, can process 96 samples at once. What’s more, the process must leave the extracted DNA open to the possibility of replication so other labs can also examine it.

The leading bead-extraction processes are marketed by Promega Corp.and Qiagen. Marziali hopes to eventually replace those methods with SCODA. But, adds Prevett, that whole validation process needs to be verified as acceptable in the chain-of-evidence process before a court. “You have to be careful that the end result will do what you want it to.” 

Fourney agrees. “It would have to be peer-reviewed and validated by the scientific community and presented to the court,” he says. That’s an eventuality Marziali anticipated. “Eventually, I’ll have to show up in court and explain how this works,” he laughs. “I don’t view it as being that hard of a sell and having it validated to a view of it being used for casework.”

The SCODA technique is being commercialized through Boreal Genomics Inc., a UBC spinoff company, and is expected to have broad applications from basic life-science research to forensic sample analysis, bio-defence, and pathogen detection for food safety and clinical diagnostics. The technology is also drawing international interest from health authorities, criminal investigators, as well as military and intelligence organizations.

Fourney adds one last caution: the whole process is useless without initial investigators who know what they’re doing at a crime scene. “One of the things we’re very concerned about is that anyone collecting samples at a crime scene is very well trained to do so.” 

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