Beyond CODIS

The changing face of forensic DNA analysis

A medical examiner in Texas confirms a homicide victim also has been raped. The DNA evidence is entered into the FBI Laboratory's Combined DNA Index System (CODIS) and gets a "hit" in another state. Unfortunately, there is no suspect. The matched DNA is from a crime scene in California where a victim also was murdered and raped, and there are no witnesses. The DNA is then subjected to ancestry analysis. The result is a "fuzzy photograph" (constructed by comparing the DNA of the suspect to those in a "control" database) very similar to a police artist's sketch, including eye color.

This isn't the fall premiere of "CSI 2010." It's cutting-edge DNA analysis being used today to assist investigators when the only substantial evidence may be DNA.

DNA revolution

In 1990, DNA developed into an indispensable tool. Today, a DNA match is virtually undisputable in court. DNA can identify a criminal with near absolute certainty or exonerate innocent suspects.

Since CODIS' creation in 1990, more than 4.2 million forensic and convicted offender profiles have been entered. Through January 2007, according to the FBI's CODIS Web site, there were 44,567 cases in 49 states and two federal laboratories where CODIS added value to the investigative process.

DNA does not come without problems, however. According to the Department of Justice Web site, there are more than 350,000 cases where DNA has been collected but not yet entered into CODIS for comparison. There also are an estimated 200,000 rape kits waiting to be processed — the issues being funding and laboratory resources.

John Morgan, deputy director of National Institute of Justice's (NIJ's) Office of Science and Technology, states, "In 2007, NIJ will be continuing its fourth year of funding through the President's DNA Initiative. The funding will support additional cold case work and address laboratory backlogs, laboratory improvement, and continued forensic science research in both DNA and non-DNA analysis. We'll also be providing much more training in cold case investigation and forensic analysis."

Although the backlog is being addressed, more samples are entering labs because of new legislation. "While states typically collect DNA from felons for inclusion in the DNA databases, we're seeing more states advocate for collecting DNA from misdemeanor offenders for sex-related crimes and, in some cases, stalking or harassment," Morgan continues. "As a result, we can expect this trend to generate a substantial surge of DNA samples entering labs for analysis."

He explains DNA is being applied to solve other crimes. "In addition to sexual assault or murder, DNA is actively being used to solve property crimes," he says. "For example, the NIJ is funding a burglary reduction program in several cities, including Denver, where as many burglaries are now solved with DNA as with all other methods combined."

"DNA testing has become critical in exonerating the innocent," Morgan says. "There have been nearly 200 post-conviction exonerations using DNA. The true power of DNA, like that of fingerprints, is its ability to positively identify an individual. That provides real confidence."

But CODIS and the United Kingdom's National DNA Database (NDNAD) have their limitations, notes Matthew Thomas, Ph.D., senior scientist for DNAPrint Genomics of Sarasota, Florida.

"The national and local databases require a match to a DNA sample that already exists," he says. "If no match is made, investigators have no information from their suspect's DNA. You are left waiting for the perpetrator to commit another crime to get into the system. Reducing the backlogs will help with this, but not help with the need for an investigation to develop information that leads to an arrest. Also, the only physical information from CODIS is a person's sex."

New techniques in DNA

New techniques employed by DNAPrint Genomics, such as DNAWitness, have served to increase DNA's utility in criminal investigations.

Scientists are continually increasing the number of markers available for analysis. DNA is made up of a string of four letters that spells out the blueprint for an organism. A short tandem repeat marker (STR) is a block of these letters repeating a number of times at a given location. A single nucleotide polymorphism (SNP), in contrast, is a change at a single letter of the code at a given location where one letter is swapped for another.

"Originally DNAWitness (the lab's ancestry process) utilized only 71 SNP markers; currently we use 176," notes Thomas. "By adding other powerful ancestry informative SNP markers, our analysis is more refined and robust. We have observed trends in groups of people from around the world, and we can supply that information to an investigation."

What is ancestry DNA?

Ancestry DNA analysis determines the bio-geographical ancestry (BGA) of a sample. It paints a picture of the relative incidence of the four major population groups — European, East Asian, Native American and Sub-Saharan African — in a given DNA sample. A person with 95-percent European ancestry is expected to be Caucasian and not Sub-Saharan African or Asian.

There are three specific areas where having ancestry information from DNA can assist investigators. It can:

  1. identify the physical characteristics of an unknown suspect,
  2. identify an unknown victim, and
  3. narrow the pool of "persons of interest."

Ancestry DNA analysis has already been successfully demonstrated. Consider the following cases:

In 2002 and 2003, the Lafayette Parish (Louisiana) Sheriff's Office investigated the murders of six victims linked to a single assailant near Baton Rouge and other locations in southern Louisiana. The DNA left behind at all the crime scenes matched, but there were conflicting eyewitness reports. As a result of combining standard and ancestry DNA analysis, Derrick Todd Lee was convicted in 2004.

In the small community of Mammoth Lakes, California, a hiker and his dog found a human skull near a campground in 2003. Forensic anthropologists first thought the victim might be Asian because of her size. Using ancestry DNA technology, she was found to be 100 percent Native American.

Meanwhile, investigators in London for 16 years have been investigating a series of rapes, which initially included more than 24,000 people of interest. Collecting DNA from such a large group was controversial and required significant resources. This time, using ancestry DNA technology, investigators pinpointed the probable origin of the rapist and narrowed the field of suspects considerably.

Identify physical characteristics

In the Louisiana case, the state's Multi-Agency Homicide Task Force initially had relied on eyewitness testimony to develop a "Caucasian" description for the person of interest. DNAPrint Genomics processed the DNA evidence and determined the suspect was 85-percent Sub-Saharan African and 15-percent Native American. Based upon those findings, the task force materially altered the focus of its investigation and included Lee as a person of interest.

Ray Wickenheiser, a forensic consultant in Irving, Texas, and former director of the Acadiana Criminalistics Laboratory in New Iberia, Louisiana, remembers the case's unique challenges.

"We used every technique at our disposal to help solve the case of the South Louisiana Serial Killer," he recalls. "The public was mobilized via the media. Every tip was evaluated and investigated. The killer left his DNA calling card at every crime scene, but no match was made. Thus, every friend and neighbor was a suspect."

He says common sense dictated that authorities develop a description from both the public's recollection and DNA evidence found at the crime scene. DNAPrint confirmed detectives' findings regarding opening the investigation to various suspect types, while eyewitness accounts had sent authorities in a different direction. "Developing more detailed discriminating power from evidence left by a perpetrator at a crime scene is the next wave in solving and preventing future crime," he says.

In December 2004, Lee was formally sentenced to death, and he is now sitting on death row while his attorneys churn out appeals.

Unknown victim

In the Mammoth Lakes case, skull shape and dental analysis originally indicated Southeast Asian or Native American, but the victim's small stature (4 feet 6 inches to 4 feet 9 inches, based on the bones) made it appear more likely she was Asian.

Forest service employees recall a Caucasian man, approximately 5 feet 9 inches tall, weighing about 180 pounds, and a very tiny "Asian-looking" woman talking with them in the fall of 2002.

Sgt. Paul Dostie with the Mammoth Lakes Police Department then began a forensic journey. He employed every type of technology available, including traditional and experimental techniques. DNAPrint's ancestry analysis determined the victim to be 100-percent Native American, not Asian. Subsequent mitochondrial testing by an independent laboratory confirmed that result. Further hair, teeth and bone testing determined the victim was probably a Zapotec Indian from Oaxaca, Mexico, and was likely in California about two years before she died. Skull reconstruction based on known measurements from Zapotec research remarkably matched the artist's drawings based upon descriptions provided by the forest service employees.

The combined technologies led to what investigators now believe are accurate representations of the physical appearance of a Native American woman. The case is ongoing. Because the couple is so unique, investigators feel media exposure will help lead to identification.

Dostie is hopeful about emerging technology. "We are just scratching the surface of what DNA can tell us," he says. "Ancestry DNA analysis gives us investigative clues, such as to which major population group a victim or suspect may belong and what they may look like. Unless we explore these new technologies and get input from investigators, the improvements will be slower."

Narrowing the field

In the United Kingdom, the Metropolitan Police Service in London is involved with Operation Minstead, an ongoing investigation seeking to identify a rapist who has been attacking elderly victims, predominantly women, across southeast London for the last 16 years.

The DNA samples taken from each crime scene did not match anything in the United Kingdom national database. It was believed the offender was black, between 25 to 45 years old, with a link to south London. These, and many other facts, including gaps in offending and a knowledge of the elderly, led to the identification of 24,000 people of interest.

What else could the suspect's DNA determine? Leading Operation Minstead, DSU Simon Morgan, senior investigating officer for the London Metropolitan Police, asked DNAPrint to assist in 2004.

Ancestry DNA analysis confirmed the offender was indeed black, but the mix of 12 percent Native American and 6 percent white European clearly indicated a Caribbean ancestry. From an investigative point of view, that group now can be prioritized ahead of the African, Asian and Dark European groups. The short list contains about 1,500 people of interest.

Morgan sees future success in ancestry DNA analysis. "If there is DNA and a question over the suspect's description or ethnicity, then this technique should be considered," he says. "As the type of information available expands, there should be even wider use. With time, I expect the processes will develop and become more refined, and the accuracy of the information also will improve. Other features such as skin, hair and eye color are promised.

"Databases like CODIS put names to crime stains," he says. "Ancestral DNA provides investigative leads when your offender is not in the database."

Privacy and profiling

Along with dynamic technology come questions about how it can be used. Investigators and prosecutors are quick to point out that this new application is just another tool used to solve crimes. It is the combination of new advances and standard police work that gets the job done.

In contrast to profiling, ancestry DNA analysis is factual and non-subjective.

"As with any new technology, this will be challenged in the courts, both from the admissibility in criminal trials to the civil liberty aspects," states George Schiro, DNA technical leader at the Acadiana Criminalistics Laboratory. "However, the testing should provide more objective information about a perpetrator than eyewitness testimony. The admissibility issue should be a minor one, since the test will be generating investigative information."

The actual source or potential source of the DNA sample would most likely be identified using traditional, court-accepted forensic DNA typing methods. Ancestry testing also has the potential of eliminating innocent people from suspicion who might otherwise have no means of clearing themselves. This would actually preserve their civil liberties and prevent them from being wrongfully accused or convicted of a crime.

Timothy Kupferschmid, the forensic laboratory director of Sorenson Forensics, a division of Sorenson Genomics in Salt Lake City, Utah, and member of the board of directors of the American Society of Crime Laboratory Directors, doesn't see DNA analysis as a threat to privacy.

"Taking a DNA swab from someone for the CODIS database is akin to taking their fingerprint because crime laboratories and police agencies do not have the resources, time or authority to determine sensitive information like someone's predisposition to disease," says Kupferschmid. "State and federal laws dictate the type of genetic information that can be extracted for law enforcement purposes and it is entirely for non-coding regions of the genome."

What's next?

The genetic basis for determining eye color has eluded scientists for decades. In the spring 2004 journal, "Genetics," DNAPrint first detailed a vital part of the eye color puzzle. The most recent (2007) blind validation test of samples of predominantly European ancestry exhibited 96 percent accuracy.

Thomas revealed testing and comparisons referring to face shapes, orbit distance and skin tone. "We've seen interesting trends comparing relatively crude photographs of people, not much more than a 'mugshot,' to their ancestry information. We often talk of our current technology providing a 'fuzzy photograph' of someone from his or her DNA. Now we want to bring that photo into focus. We've started to collect data using more sophisticated methods to better understand the link between genetics and physical features such as the space between the eyes, the shape of a jaw — all the things a sketch artist might want to know."

Dostie concludes, "As information about ancestry DNA gets out to cold case investigators, I think it will be embraced by them. Cold case investigators are a tenacious bunch always looking for the smallest piece of the puzzle. Ancestry DNA can provide a big piece of the puzzle."

Linda Spagnoli is a well-known law enforcement advocate in the areas of communication, child safety, officer safety and sex-offender tracking. Her focus is on interagency data sharing, emergency communications and media relations. She began her career assisting school resource officers in installing the D.A.R.E program in Long Island, New York, schools. Spagnoli maintains her position as director of communications for Code Amber, the largest Internet distribution for Amber Alerts.