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Sunday, May 19, 2024

Cops Are Getting a New Tool For Family-Tree Sleuthing

You won’t find it on the commodities market, but the value of one substance has quietly skyrocketed over the past two years: DNA. Growing genetic databases have proven to be rich resources for discovering new drugs and other medical advances. Law enforcement agencies have perhaps been the biggest benefactors of this biometric boom.

It used to be that DNA could solve a case only if it matched the genetic profile of someone in a criminal database or an existing suspect. But the recent rise of genetic genealogy—a technique that makes it possible to identify people through relatives who have added their genetic information to genealogy databases—changed the odds. A skilled genetic genealogist can now turn an unknown DNA profile that strikes out in traditional forensic searches into a suspect’s name nearly half of the time.

But so far, those types of DNA profiles have been somewhat difficult to come by. They require a lot of high-quality genetic material to work with, and some bioinformatic massaging to make the file compatible with those generated by consumer DNA spit kits. That’s about to change.

Verogen, the foremost provider of next-generation DNA testing services for law enforcement, has spent the better part of this year developing a new test kit aimed at making genetic genealogy investigations both more convenient and more feasible to use for a wider range of crime scene samples. The fit-for-purpose genetic genealogy panel promises to push this still unregulated method toward becoming a mainstay of modern-day police work. “We think it’s going to be a real door-opener for public crime labs to get into next-generation sequencing,” Verogen CEO Brett Williams told WIRED in an interview.

Genetic privacy advocates are not exactly surprised by the move, but they are disheartened. “From the beginning, we were told that investigative genetic genealogy was too cumbersome, too expensive, too difficult to do routinely,” says Natalie Ram, a law professor at the University of Maryland. Such limitations were expected to restrict the technology, as a practical matter, to only the most serious crimes. But she expects that Verogen’s moves to make genetic genealogy more accessible will erode those logistical firewalls.

It was the same story with the first kind of forensic DNA testing, introduced in the early 1990s, says Ram. Unlike the profiles generated by consumer kits—which read out the actual letters of your genetic code and tell you things like what region of the world your ancestors hailed from or what your risk for certain cancers might be—forensic DNA fingerprints contain far less information. They’re basically tallies of junk sections of DNA, called STRs (for short-tandem repeats). In 1998 the FBI established the Combined DNA Index system, or Codis, to house these types of profiles. Codis entries consist of a set of numbers that represents the summed-up STR repeats found at each of 20 locations in the genome.

At first, law enforcement agencies were limited to using Codis to collect DNA from—and to search for—only felony sex offenders. Starting in 2004, states began extending its use to people convicted of any violent felony. Then it was people arrested for any violent felony. As of this year, eight states, including Louisiana, Arizona, and Minnesota, also force people who’ve been arrested for certain misdemeanors to surrender a cheek swab.

Ram sees in this evolution a cautionary tale for genetic genealogy. “This is the way that technology expands,” she says. “It starts with a use case that virtually no one will say is a bad thing. No one wants to see the Golden State Killer go free. And yet it’s quite foreseeable that this will expand into many broader uses. The development of this technology by Verogen and its growth into in-house public crime labs just makes that much more likely.”

In fact, if you already know about genetic genealogy, it’s most likely in connection to the Golden State Killer case. In 2018, investigators in California revealed that they had used a public DNA database called GEDmatch to crack the 40-year-old cold case. For nearly a decade before that, GEDmatch had existed in semi-obscurity, known only to a million or so hobbyist genealogists who used its homespun DNA analysis tools to fill in missing branches of their family trees. But afterward, the site emerged as a revolutionary crime-fighting tool. Law enforcement agencies all over the country reopened cold cases, and dozens of arrests ensued.

The sudden co-opting of the database by police opened a rift in the previously tight-knit genealogy community. For months, the site was roiled by one drama after another—from privacy-violating police searches to the discovery of serious security flaws. GEDmatch also made the process for consenting to police searches of your information opt-in, rather than the default, briefly zeroing out its usefulness for investigators. At the end of last year, GEDmatch’s aging owners agreed to let their embattled site, database and all, be acquired by Verogen.

In the following months, Verogen’s scientists began mining the GEDmatch database to better understand which genetic markers are the best predictors of kinship. Using that information, the company’s engineers designed a DNA test kit optimized for conducting relative searches in GEDmatch. Williams confirmed to WIRED that several public crime labs in the US and EU are currently beta testing Verogen’s kit, and that the company will be rolling out early release versions to a limited number of clients in the next few weeks. A full launch of the product is expected sometime next spring.

The company, which spun out of sequencing giant Illumina in 2017, is mostly a hardware supplier. It makes an instrument called the MiSeq FGX, which cracks open human cells and reads out the genetic code inside. And the company manufactures ready-made reagent kits for turning crime scene samples into digital DNA profiles. Though Verogen has made headway into big private labs, uptake of the technology in the nation’s 200 or so public crime labs, which process the majority of crime scene DNA in the US, has been much slower, says Williams. He estimates that Verogen machines have made it into fewer than half.

Moving from a DNA fingerprinting technique drilled into lab techs over decades to a new method with a new machine with its own quirks is not a trivial hurdle, says Danny Hellwig, who operates a not-for-profit crime lab in Utah dedicated to using next-generation sequencing to solve cold cases. Before starting Intermountain Forensics earlier this year, he worked as a DNA analyst in both public and private crime labs. “It’s a massive change in process, and it’s going to take a while for labs to get on board,” he says.

Intermountain Forensics is one of the labs expecting to receive early access to Verogen’s new tech. Hellwig has evidence from about 50 cold cases he’s hoping to analyze with the kits. Many of them are samples that were too small or too degraded to survive the typical genetic genealogy process. Companies like Parabon, which made a name for itself early on by being the first to offer bespoke genetic genealogy services to police forces, and its chief rival, FamilyTreeDNA, can sometimes require upwards of 20 nanograms of DNA to create a genetic profile that can be plugged into a genealogy database. “In forensic-speak, that’s a joke,” says Hellwig. “Especially with cold cases, you’re just never going to get that much DNA. We deal with the really crappy stuff.” But because it’s optimized for very small amounts of very low-quality DNA, he’s hopeful Verogen’s kit can help solve the estimated 250,000 murders of Americans whose killers have never been caught. Parabon vice president Paula Armentrout told WIRED via email that over the last several years the firm has successfully processed crime scene DNA samples as low as 1 nanogram for use in genetic genealogy investigations.

The other benefit he sees is the ability to create and store genetic data in-house. The way companies like Parabon and FamilyTreeDNA work is they do the DNA processing, database-searching, and family-tree building, then return a list of names of possible suspects to their law enforcement clients. That kind of work can get expensive quickly, which is why law enforcement agencies with limited budgets have tended to use such services only for very high-profile unsolved crimes.

Hellwig started Intermountain Labs to work on the other cases—the murders that didn’t make headlines, the unresolved missing persons cases, and the nation’s shameful backlog of more than 100,000 untested rape kits. “We’re a nonprofit, so we don’t care who solves the case, we just want to get it solved,” says Hellwig. By generating a genetic profile in-house, he’s free to share that data with volunteer genealogists at the Utah Cold Case Coalition, or with other groups of benevolent genetic sleuths. “No one has a monopoly on the data this way,” says Hellwig.

The steady stream of headlines hailing genetic genealogy as the cracker of cold cases over the past two years has created a new sense of urgency for law enforcement agencies to get in the game. Though there is no centralized count of cases solved with the method across different databases, Williams told WIRED that GEDmatch has so far been used to identify suspects in more than 200 cases. (There’s no tally available yet of how many of those people have been convicted, but it is not zero.) “There is no better motivator than that public pressure,” says Hellwig.

Verogen’s new genetic genealogy product is intended to provide the final push. But it also has features clearly intended to mollify privacy skeptics. The new kits generate a genetic profile that’s much skimpier than what you’d get out of an Ancestry or 23andMe test—about 15,000 data points versus 600,000. Because there’s so much less information, Verogen had to develop a different type of algorithm for turning up potential family members and estimating their degree of relatedness. Rather than comparing the amount of DNA overlap between two people, it now looks for patterns of similarities at single locations proven to be highly predictive of kinship. That means it’s not compatible with the existing profiles GEDmatch has on file for its users, only about 325,000 of whom have consented to law enforcement searches of the database.

So the company has converted those consented profiles into a format suitable for searching with the new DNA kit, while leaving out the profiles of legacy GEDmatch customers who hadn’t opted in. Their team is in the process of creating a separate portal just for law enforcement agencies to upload their crime scene sample data. The idea is to make it technologically impossible for unauthorized searches of non-consented users. (That’s a thing that has happened in the past, not just at GEDmatch, but at several private consumer databases, as The LA Times revealed last week.) Williams says the infrastructure changes should more completely wall off those who do not wish to involve their DNA with crime-solving intrusions from law enforcement.

Further, the DNA test kits don’t scan any portions of the genome known to be medically important, says Williams. “The way it’s been done before is really an appropriation of technology not intended for forensic use,” he says. That created understandable privacy concerns. In addition to family ties, the kinds of genetic data created from consumer spit kits can contain information about people’s looks, ethnic heritage, and medical risks. Though the US has laws preventing employers from discriminating against individuals based on their genes, police have much freer reign with such information. “So what we’re trying to do is step back and say, ‘How do we build something suitable for law enforcement investigators that minimizes privacy violations as much as possible?’” says Williams. “Because the genie is definitely out of the bottle at this point.”

Ram doesn’t find the argument convincing. For one thing, genomics is a rapidly evolving science. A genetic sequence that today has unknown function might turn out to be involved in cancer or autism. And for another, imputation algorithms are getting better at guessing unknown bits of genetic code from the surrounding snippets. So while a panel like Verogen’s might leave out the chapters in a person’s genetic manual that describe how well their heart pumps or their synapses fire, software can look at the letters it does read out and fill in some of the surrounding words and sentences. “I just don’t think you can draw a line between genealogically relevant data and medically relevant data with any amount of precision,” says Ram.

It’s a potentially legally important question. In 2013, when the Supreme Court upheld the constitutionality of government-held DNA databases, the decision hinged on the fact that the STR profiles don’t contain any information about a person’s appearance or health. They’re just a unique string of figures, like a Social Security number. But Ram says it’s one that likely won’t get tested in court for many years. That’s because the people who might have standing for a constitutional challenge (those who’ve had their DNA searched without their consent) aren’t the same people who can demonstrate they’ve been harmed by that search (the distant relative who wound up getting arrested as a result).

Because genetic genealogy hinges on the biological laws of inheritance, which results in relatives sharing genetic data in predictable patterns, Ram thinks there’s a legal argument to be made that people should have an expectation of privacy not only for the DNA that comes out of their own cells, but also for the sections that reside in the chromosomes of family members. “There are some hoops to make that legal argument work,” says Ram, who admits she’s somewhat radical in this viewpoint. “But the consequences of not making the argument is winding up in this constitutional black hole.”

Without the courts, it will likely be up to individual states to start regulating the use of forensic genetic genealogy. Last fall, the Department of Justice released interim guidelines for using the technology, which include exhausting a Codis search first and only using it for investigations of violent crimes. But only federal agencies like the FBI, and local law enforcement organizations that have received DOJ grant funding, are required to adhere to them. Currently, no states restrict police use of genetic genealogy. Last year, Maryland attempted to pass a law reigning in the technology’s application to crime-fighting, and Utah introduced a similar bill in January, but neither has so far succeeded. That leaves most police forces to decide on their own.

Williams admits that the technology has yet to be fully reckoned with by the American public. “At the end of the day, you have an absolute right to privacy, that’s one of the central tenets of our society,” he says. “But there is a competing priority, which is that you also have the right not to get raped or murdered. The question is, what’s the proportionality? How do you balance it? We’ve yet to have that conversation in this country.” In the absence of clear answers to those questions, Williams says, Verogen is trying to chart a responsible course. In its terms of service, the company has made it clear that police are only to use GEDmatch for investigating violent crimes. The company has no plans of changing that, “at least not while I’m CEO,” he says.

But one change he is interested in is creating another, separate tier for searches for missing persons. Right now, hunts for the identities of human remains are lumped in with investigations for criminal suspects. But Williams sees them as very different use cases. And he worries that ethical anxieties over one will hamper the other. “In my mind, adoptees searching for their birth parents is no different, so I see a real benefit toward using the whole database for missing persons,” he says. It remains to be seen if the majority of GEDmatch users agree. But if there’s one thing they’ve come to expect by now, it’s change.

Updated 12-16-20, 9:15 pm EST: This story has been updated to add comment from Parabon and to correct the size of DNA samples the company requires for its genetic genealogy investigations.

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