DNA is the foundation of life and is found throughout the environment. Because of shedding, humans leave a continuous trail of DNA that can be measured and sequenced. Genetic scientists have now discovered how to easily sequence environmental DNA, called E-DNA. The implications to privacy and sanctuary are absolutely staggering and police/intelligence units are salivating to get their hands on it.⁃ TN Editor
David Duffy, a wildlife geneticist at the University of Florida, just wanted a better way to track disease in sea turtles. Then he started finding human DNA everywhere he looked.
Over the last decade, wildlife researchers have refined techniques for recovering environmental DNA, or eDNA — trace amounts of genetic material that all living things leave behind. A powerful and inexpensive tool for ecologists, eDNA is all over — floating in the air, or lingering in water, snow, honey and even your cup of tea. Researchers have used the method to detect invasive species before they take over, to track vulnerable or secretive wildlife populations and even to rediscover species thought to be extinct. The eDNA technology is also used in wastewater surveillance systems to monitor Covid and other pathogens.
But all along, scientists using eDNA were quietly recovering gobs and gobs of human DNA. To them, it’s pollution, a sort of human genomic bycatch muddying their data. But what if someone set out to collect human eDNA on purpose?
New DNA collecting techniques are “like catnip” for law enforcement officials, says Erin Murphy, a law professor at the New York University School of Law who specializes in the use of new technologies in the criminal legal system. The police have been quick to embrace unproven tools, like using DNA to create probability-based sketches of a suspect.
That could pose dilemmas for the preservation of privacy and civil liberties, especially as technological advancement allows more information to be gathered from ever smaller eDNA samples. Dr. Duffy and his colleagues used a readily available and affordable technology to see how much information they could glean from human DNA gathered from the environment in a variety of circumstances, such as from outdoor waterways and the air inside a building.
The results of their research, published Monday in the journal Nature Ecology & Evolution, demonstrate that scientists can recover medical and ancestry information from minute fragments of human DNA lingering in the environment.
Forensic ethicists and legal scholars say the Florida team’s findings increase the urgency for comprehensive genetic privacy regulations. For researchers, it also highlights an imbalance in rules around such techniques in the United States — that it’s easier for law enforcement officials to deploy a half-baked new technology than it is for scientific researchers to get approval for studies to confirm that the system even works.
Genetic trash to genetic treasure
It has been clear for decades that fragments of our DNA cover the planet like litter. It just didn’t seem to matter. Scientists believed DNA in the environment was too small and too degraded to be meaningfully recovered, much less used to identify an individual human being, unless it came from distinct samples like a bloodstain or an object someone had touched.
Wildlife researchers embraced environmental DNA anyway because they’re only looking for very small segments of DNA — scanning for what they call bar codes that will identify the creatures in a sample to a species level. But after finding “surprising” levels of human eDNA in their samples while monitoring disease in Florida sea turtles, Dr. Duffy and his team set out to get a more accurate picture of the condition of human DNA in the environment, and to see how much information it could reveal about people in an area.
As a proof of concept in one of their experiments, the researchers scooped up a soda-can-size sample of water from a creek in St. Augustine, Fla. They then fed the genetic material from the sample through a nanopore sequencer, which allows researchers to read longer stretches of DNA. The one they used cost about $1000, is the size of a cigarette lighter and plugs into a laptop like a flash drive.
From the samples, the team recovered much more legible human DNA than they had anticipated. And as knowledge expands about human genetics, analysis of even limited samples can reveal a wealth of information.
The researchers recovered enough mitochondrial DNA — passed directly from mother to child for thousands of generations — to generate a snapshot of the genetic ancestry of the population around the creek, which roughly aligns with the racial makeup reported in the latest census data for the area (although the researchers note that racial identity is a poor proxy for genetic ancestry). One mitochondrial sample was even complete enough to meet the requirements for the federal missing persons database.
They also found key mutations shown to carry a higher risk of diabetes, cardiac issues or several eye diseases. According to their data, someone whose genetic material turned up in the sample had a mutation that could lead to a rare disease that causes progressive neurological impairment and is often fatal. The illness is hereditary and may not emerge until a patient’s 40s. Dr. Duffy couldn’t help but wonder — does that person know? Does the person’s family? Does the person’s insurance company?
Surveillance and forensics
Anna Lewis, a Harvard researcher who studies the ethical, legal and social implications of genetics research, said that environmental DNA hadn’t been widely discussed by experts in bioethics. But after the findings from Dr. Duffy and his colleagues, it will be.
Technology focused on eDNA, she said, could be used for surveillance of certain kinds of people — for example, people with a specific ancestral background or with particular medical conditions or disabilities.
The implications of such uses, researchers agree, depend on who is using the technology and why. While pooled eDNA samples could help public health researchers determine the incidence of a mutation that causes a disease in a community, that same eDNA sample could equally be used to find and persecute ethnic minorities.