Genetic Databases Bump Up Against Privacy Concerns

Jared Kaltwasser
JUNE 19, 2018

bradley malin,jim ostell,bio privacy,bioethics,genetic database

Digging Up Data

If someone wants to access a cache of genetic data, or genomic data for a single person, there are at least 3 key categories of databases. One category is government, academic, and nonprofit agencies that collect, store, and release data for research purposes. Another category are the for-profit companies that collect and analyze data as a consumer service. The last category is law enforcement.

Data collected by the federal government or used in research funded by the federal government are subject to strict privacy guidelines.

Jim Ostell, PhD, director of the National Center for Biotechnology Information at the NIH’s National Library of Medicine, said the information his center stores is generally stripped of private information that could be used to identify donors.

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“The NCBI database of Genotypes and Phenotypes (dbGaP), for example, contains measurements, lab test results, and genetic data that were contributed by individuals who voluntarily enrolled in biomedical research studies, but the database does not include any direct identifiers to patient information,” he said. “Terms of use of the database and the code of conduct for researchers who are granted access to the database specifically prohibit any attempts to re-identify individual participants, e.g., by merging dbGaP data with other data sources.”

Although many of the government’s database resources, such as ClinicalTrials.gov, make aggregate-level data freely available to the public, individual-level study data is only made available to senior researchers who agree to follow restrictions on how the data are used.

Malin, who co-chairs the data privacy and security working group for the NIH’s All of Us health data initiative, said the federal government has a good track record of data protection.

“Even though the federal government is a little bit hamstrung in terms of the requirements that they have to adhere to in terms of how to get new technology certified and into place, I do think they’re still doing best practice in terms of the technologies that they can use,” said Malin, who wasn’t speaking on behalf of the All of Us initiative.

Meanwhile, the private sector is quickly compiling its own databases of genetic data in support of the burgeoning direct-to-consumer genetics industry. Malin said oversight over these companies is somewhat lagging.

“It’s a rapidly growing environment with a relatively limited oversight, because it’s treated as if it’s just a general consumer product,” he said. “So, mainly, the Federal Trade Commission has oversight with respect to what’s taking place.”

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Malin said the Food and Drug Administration has also taken on a role, though its focus is primarily in ensuring the companies provide accurately interpreted products.

Among the biggest players in the direct-to-consumer space is 23andMe.

Asked about its privacy protections, 23andMe provided a statement saying the company does not sell individual customer information and requires a patient’s voluntary and informed consent before their data are included in data sets made available to researchers.

“23andMe customers are in control of their data—customers can choose to consent, or not to, at any time,” the company said. “Our consent document and privacy statement are published online for everyone to read, and our research is overseen by an independent third party (IRB) to ensure research meets all legal and ethical standards.”

The company said more than 100 peer-reviewed publications have been written using the company’s data.

In general, well-established companies have strong privacy records because they see it as integral to their business models, Malin said.

“Some of the more reputable companies that see a strong relationship with their consumers as being the driving force behind their business are very strongly motivated to have these types of protections in place,” he said.

However, Malin warned that there are an increasing number of smaller firms may not have the same capabilities to protect consumers.

One such company, GEDmatch, was recently in the news when law enforcement officials in California arrested a man they believe to be the “Golden State Killer” based on a match between DNA found at a crime scene and DNA found using the free genealogical analysis tool.

Malin said law enforcement agencies’ use of data opens up a number of privacy and confidentiality issues, which are still evolving. But law enforcement does a good job of locking down its data, he added.


Patient Advice

All of this begs the question: What should a patient do in such a fraught landscape? After all, science is dependent upon voluntary participation in scientific research, and the more data collected, the easier it will be for researchers to make breakthroughs.

“My advice would be to be wary of institutions or entities you don’t know,” Rothstein said. “If you donate your samples and information to a well-known institution, you can have a reasonable degree of confidence that your information will not be wrongfully disclosed.”

For other entities, Rothstein said, users should not simply click “I agree” without reading the full agreement, lest they find out too late that they unwittingly gave the company permission to sell their data or even to match it with other personal data, such as contacts or GPS information.

Clayton said she wouldn’t be worried about donating to a medical or academic institution, since she has confidence in the guidelines—both legal and ethical—that they follow. However, if the potential donor is unsure, it’s key to ask questions.

“I would want to know that data about me are going to be shared in a de-identified fashion with entities that are going to take seriously the need to protect the privacy and security of the data,” she said. “That’s what I would want to know.”

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