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DNA Detective

Phil Danielson (pictured) and his team recently helped solve a hit-and-run case by analyzing a tiny fragment of hair that investigators recovered from the windshield. Photo: Wayne Armstrong

When you walk into Phil Danielson’s research lab in DU’s Seeley Mudd Building, you find yourself in an exact replica of the Colorado Bureau of Investigation’s forensic DNA facility. State-of-the-art genetic analysis instruments fill the benches in between spotless vented hoods under which Danielson and his team can work with recovered crime scene evidence without running the risk of contaminating it.

Here, behind heavily secured doors, Danielson (PhD biology ‘96) and his colleagues have developed a novel forensic analysis technique that may soon become a ubiquitous tool in solving crimes. Over the past seven years the team has invented, fine-tuned, and successfully tested DHPLC profiling—a completely new method for identifying DNA.

Danielson’s technique is much faster and cheaper than anything forensic investigators have been using so far. And, DHPLC profiling can help investigators solve crimes they weren’t able to crack before because it can pick apart the individual components of DNA mixtures, such as those from an attacker and a victim. Before, mingled samples were useless.

The project started when Danielson, graduate student Robby Shelton (BS ’02) and Greggory LaBerge, director of the Denver Police Department’s DNA lab, had the idea to employ an instrument usually used to sniff out cancer mutations for DNA analysis. Armed with blood and saliva samples from 96 DU students and faculty members and real-life forensic samples supplied by various police departments, Danielson’s team got to work.

Danielson funded the initial research with a few thousand dollars out of his own pocket but within a few months, the U.S. Department of Justice and the National Center for Missing and Exploited Children saw the procedure’s potential and began to fund the work.

The team’s new technique is a drastic departure from traditional DNA analysis methods. Instead of sequencing — reading every single one of the millions of letters that make up DNA — DHPLC profiling takes one quick snapshot of the entire molecule.

Just think of a bag of pretzels. “Instead of counting them all individually, you can just weigh the entire bag,” Danielson explains.

The new procedure cuts analysis time from days to minutes and shaves off 95 percent of the cost. “It’s an instant thumbs up or thumbs down test that tells us whether or not two samples match,” says Danielson, who has published research papers, coauthored with students, in numerous peer-reviewed scientific journals.

Criminals always leave their signatures at the crime scene; semen, blood, a drop of saliva on the rim of a glass or a bottle — any of these traces provide investigators with the perpetrator’s unique genetic fingerprint. DNA evidence can seal a court case against an attacker.

But ever since genetic testing arrived on the forensic scene, scientists have faced a big dilemma: While the DNA that is coiled up inside a cell’s inner core, or nucleus, provides a perfect tool for identifying people, it’s extremely fragile. This nuclear DNA decays quickly when taken out of its protective home inside a cell, Danielson explains. And, some places simply don’t contain enough nuclear DNA to begin with, making an analysis impossible. “Hair shafts are one example. You can’t do nuclear DNA testing on that,” Danielson says.

But cells also house a second, much sturdier, type of DNA called mitochondrial DNA, or mtDNA, that easily persists for decades. And, while cells carry only two copies of nuclear DNA, they contain thousands of mtDNA molecules, boosting the chances of finding a usable sample. “That makes mtDNA evidence incredibly powerful,” Danielson says.

Traditional mtDNA analysis methods are very expensive and time-consuming, however, and therefore rarely used. “Only in the most extreme cases, such as really egregious murders or sexual assaults, can you justify spending tens of thousands of dollars to do this kind of testing.”

Thanks to Danielson’s new technique, that is about to change. DHPLC profiling is a high-speed, low-cost technology that can serve as a screening tool with which forensic scientists can compare different mtDNA samples — for example, one taken from a suspect and one recovered from a crime scene. “We can tell whether or not two samples are identical in a few minutes and for no more than about 100 dollars,” Danielson says.

The strength of this screening process is the ability to weed out irrelevant evidence, such as a victim’s own hair or blood. “Imagine you find 12 hairs on the crime scene of a child molestation that happened in the child’s bedroom,” Danielson says. “Chances are that most of those hairs belong to the child or perhaps the parents and probably only one or two hairs come from the perpetrator.”

Before DHPLC profiling, a police lab would have to analyze all 12 hairs and get the child and parents tested — 15 samples at $2,000 to $3,000 apiece. “With our technology we can quickly and cheaply rule out those hairs that are not the criminal’s,” Danielson explains. “So now, instead of spending more than $30,000 on testing, we only spend $2,000.”

But DHPLC profiling has another unique advantage: It is the first technology that can unscramble mixtures that contain the mtDNA of more than one individual. That’s important because often, the tiny samples of body fluids that crime scene units bring back to the lab are mixtures of victim and attacker. Traditional methods can’t separate those samples, rendering what could be proof that a suspect is guilty completely useless. “All you can do in such a case is throw your hands in the air and say ‘Okay, we simply can’t use that,'” Danielson says. In fact, if the FBI has any reason to believe that a sample is a mixture, they won’t even analyze it, he says.

Danielson’s technology can separate mixtures without a problem; he and his team have successfully sorted out the individual components of 27,000 mtDNA mixtures so far.

That feat opens up unique opportunities, says Terry Melton, president and CEO of Pennsylvania-based Mitotyping Technologies LLC. “The last and biggest problem encountered in forensic mtDNA testing is the large number of mixed samples that can’t be resolved using current technologies,” she says. “That’s why Danielson’s DHPLC system has the potential to be extremely useful.”

DHPLC profiling could also help solve missing person cases or assist with the identification after mass disasters such as the Sept. 11 attacks.

Unlike nuclear DNA, which comes from both parents, mtDNA is passed down from mother to child. That’s why samples from maternally related relatives are usually an exact match, which means that any such relative of a missing person can supply reference samples, Danielson explains.

Danielson and his team — which also includes PhD candidate Richard Kristinsson (BS ’01, MS ’03) — have successfully completed a validation study for their new technology required by the National Institute of Justice. Police and security agencies within the United States and in several European nations have expressed an interest in implementing DHPLC technology, and China is already using it to solve crimes, Danielson says.

Closer to home, the Danielson team has already begun to use DHPLC in actual criminal casework. Recently, the team helped solve a hit-and-run case by analyzing a tiny fragment of hair that investigators recovered from the windshield.

Developing the new technology has been an ideal opportunity for interdisciplinary research, Danielson says. Biology students worked on the actual testing and analysis, and Morgridge College of Education researchers helped with the statistics. Computer science and bioinformatics majors wrote the complex software required to handle the massive amounts of data, and Sturm College of Law faculty gave advice about some of the legal issues.

“It’s been a long process,” Danielson says, “but now we have achieved something that can be put into the hands of forensic scientists and practitioners and will actually be used. That is immensely rewarding.”

Recently, the team helped solve a hit-and-run case by analyzing a tiny fragment of hair that investigators recovered from the windshield.

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