NEW YORK (GenomeWeb) — Last week, law enforcement officials in Washington state announced a major development in a 30-year-old unsolved double homicide case: They had arrested a suspect whose DNA, they said, matched DNA from the crime scene thought to belong to the perpetrator.
“We’ve had over 300 suspects on the list for this case” prior to the arrest, said Shari Ireton, a spokesperson for the Snohomish County Sheriff's Office. “Detectives have gone through and ruled out each and every one of them.”
At a press conference, Snohomish Country Sheriff Ty Trenary said that the new suspect had been identified through genetic genealogy — the same method that had recently led to the arrest of a California man alleged to be the “Golden State Killer.” But this time, the process was performed by a private company that is hoping its forensic application of genetic genealogy will take off.
Parabon NanoLabs, based in Reston, Virginia, announced May 8 that it is commercially offering this service, called Snapshot Genetic Genealogy Service. But while the company is celebrating the first instance where its technology has helped investigators make arrests in murder cases, critics say that its approach violates the privacy of users of genetic genealogy websites and is conducted without sufficient oversight.
“There are two applications” of its service, Parabon CEO Steve Armentrout said. “Finding candidate suspects or identifying unknown persons.”
The Snohomish and Skagit County sheriff’s offices, which worked in tandem on the case, are the first of almost 100 Parabon clients to go public with their use of the service.
While traditional forensic DNA profiling uses short tandem repeats (STRs), analyzed by capillary electrophoresis, to identify individuals, genetic genealogy is pushing SNP microarray technology into forensics. Using SNP arrays comparable to those used by many consumer genotyping services, like Ancestry.com and 23andMe, Parabon creates profiles from the DNA of suspects or unidentified individuals that can be uploaded to third-party websites that have been billed as a place for people to find relatives using their genotyping results.
These sites determine the genetic distance between the subject's DNA and that of other users. From there, Parabon can surmise family relationships and apply more traditional genealogical techniques, such as obituaries and other public records, to generate information that can support an investigation, like a list of names.
In the Washington cold case, Parabon’s report came up with a single person. Law enforcement officers then tailed that person and picked up a cup he had discarded on the road. The DNA from the cup, which was analyzed using STRs, matched the original crime scene DNA sample, to the degree that the only other possible match was an identical twin, which the suspect does not have. Since his arrest, he has been charged with one homicide.
While the process appears to have delivered results to Parabon’s partners, some have raised concerns that the use of genetic genealogy databases by law enforcement encroaches on the privacy of those who have contributed their genetic information to these sites. Likewise, a suspect's DNA sequence could be made public without their consent.
Armentrout said some of the concerns were misunderstandings. At the press conference for the Washington case, he stressed that the suspect's DNA data was never made publicly available, for example. In an email, Parabon said the databases it uses “do not disclose or expose any raw genetic data; only the amount and chromosomal location of shared DNA segments can be seen. Thus, these searches are simply looking for connections among individuals to generate leads, in the same way investigators might use public Facebook photos to make connections.”
Jennifer King, a researcher at Stanford University Law School’s Center for Internet and Society, has studied the attitudes of people who have shared their genetic info after purchasing 23andMe’s genotyping kit. “The key question is, ‘How OK are people with the fact that they uploaded data for one purpose and law enforcement is using it for another?’” King said.
“It is our understanding that persons contacted thus far by investigators during the course of genetic genealogy research for our cases have been glad to volunteer their assistance," a spokesperson for Parabon said in an email. "That seems to be the overwhelming sentiment on social media as well. In fact, we have been contacted by a number of people asking how best to give a sample of their DNA to help these investigations.”
“A lot of people may be inclined to say, 'Hey, it’s ok, because how can I not be in favor of that?’ At the same time though, we have absolutely no regulation about how law enforcement accesses this data," said King. "They can pretty much use it without restraint.”
From phenotyping to genotyping
Prior to launching its genetic genealogy product, Parabon developed familiarity with SNP profiling through another product for law enforcement, Snapshot DNA Phenotyping, where it turns SNP microarray results into information about a subject’s physical appearance.
Specifically, Parabon uses Illumina’s SNP microarray platform. It doesn't disclose which particular array product it uses but said that the array contains more than 98 percent of the SNPs that are on the chip used by Ancestry.com.
“I don’t think we ever really considered another [type of array],” Armentrout said. “That’s what the databases we have are based on. The kits have the SNPs we need.” He added that the firm wanted to make sure the data generated for genetic genealogy would be concordant with its phenotyping service.
Parabon said it has not performed its own validation of Illumina’s microarrays for phenotyping applications but pointed to a validation study for forensic applications published in 2013 in the International Journal of Legal Medicine. In that study, researchers assessed an Illumina microarray's performance in determining "biogeographical ancestry, appearance, relatedness, and sex" using DNA samples of varying quality and quantity.
“We have tested different sample types, quantities, and qualities from the same individual to ensure that the genotyping results are concordant," the Parabon spokesperson said. "We have observed that the call rates can decrease with decreasing sample quantity and quality, but the genotypes that are called are concordant as long as a minimum call rate threshold is reached. Samples that perform below that threshold are not used for analysis.”
SNP arrays aren't the only genomic technology breaking into the forensics market. Cydne Holt, CSO at Verogen, an Illumina spinoff focusing on forensic applications of several Illumina technologies, said that the market opportunity for next-generation sequencing "eclipses" that of SNP microarrays because of several technical challenges. "SNP arrays require high-quality and high-quantity DNA that is only from a single source," she said. "They're not practical and it's not an efficient method for routine [crime lab] operations. Clearly, it can be super important, but for a very few cases; it's an important [tool] but a last resort."
In the Washington cold case, the two sheriff offices had contracted with Parabon for the phenotyping product, in an attempt to get a break in the case, Ireton said. But in April, Armentrout offered to provide the company’s new product at no cost, she said.
Armentrout said that Parabon currently offers its Snapshot Genetic Genealogy service on a case-by-case basis. What a customer receives “can range wildly, depending on the case,” he said. “Everything from some surnames that might appear to 'Here’s the name and address of someone you’re going to want to talk to.’”
The results are presented in a report, he said. Price varies: Lab work and initial screening costs $1,500, and “based on those results, the price of the subsequent work is negotiated," he said.
Armentrout said he’s aware of freelance genealogists who can perform genetic genealogy searches, but not of other outfits offering the additional services, like phenotyping and additional kinship testing, that Parabon offers. “We’re a one-stop shop for this type of advanced DNA analysis,” he said.
One component of the process that Parabon does not control is the database used to generate family relationships. For the Washington cold case, that database was GEDmatch, a not-for-profit genealogy site operating outside the networks created by major consumer DNA testing companies, where individuals can upload their genotyping profiles and find relatives. Law enforcement officials used GEDmatch in the case that led to the arrest of the suspected Golden State Killer.
“One of the interesting questions raised in the Golden State Killer case is, ‘How did law enforcement join the site?' They probably violated site's terms," said King. "What I understood was that you’re not supposed to upload data that doesn’t belong to you.”
Recently, GEDmatch updated its terms and conditions to include language that says genetic information submitted to the site may be used in a law enforcement investigation and that the data may be uploaded if “obtained and authorized by law enforcement” to identify perpetrators of violent crimes or remains of a dead person.
Curtis Rogers, of GEDmatch, said in an email that the changes were made in response to the upcoming deadline for sites to be in compliance with the European Union’s General Data Protection Regulation, which requires sites to inform users how their data will be used.
But even going forward, as GEDmatch’s terms explicitly allow for forensic genetic genealogy, King said, there’s reason for users to be concerned. “Law enforcement is able to get this data without any oversight,” she said. “That’s where the concern lies. There’s a difference between obtaining evidence through those means and getting a warrant or subpoena to go into their database.”
Meantime, Parabon is expecting its partners to announce more results about solved crimes. "Three homicides have been solved in the past few weeks" using the genotyping product, said Ellen Greytak, director of informatics at Parabon. "Those will be made known in time. It's a real game changer."