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High-Quality Human DNA Recovered From Multiple Environmental Samples Using Deep Sequencing

NEW YORK — Humans are shedding their DNA almost everywhere now as researchers have managed to recover high-quality human DNA from environmental samples such as air, water, and footprints, according to a newly published study.

These findings on how human DNA can be retrieved from practically anywhere could have beneficial applications in medicine, forensics, and environmental science, for instance, but also carry serious ethical and societal implications, the authors said.

The study, published in Nature Ecology and Evolution on Monday, was led by researchers at the University of Florida, who were able to collect human DNA from nearly everywhere they looked — a phenomenon they refer to as "human genetic bycatch."

The project had initially started with a hunt for DNA samples of green sea turtles in beach sand footprints. However, the researchers knew that human DNA would end up in their turtle samples.

Using shotgun deep sequencing on the samples, they detected human-aligning reads at levels almost as high as that of the green sea turtles.

When they studied the ocean and rivers surrounding their laboratory, they retrieved good quality human DNA. However, in samples from a remote island that likely had no prior human visitors, no human DNA was found.

"We've been consistently surprised throughout this project at how much human DNA we find and the quality of that DNA,” corresponding author David Duffy, professor of wildlife disease genomics at the University of Florida who led the project, said in a statement. "In most cases the quality is almost equivalent to if you took a sample from a person."

His team also recovered human DNA from rooms where people went about their regular working activities and from air samples from a veterinary hospital environment.

Traditionally, environmental DNA research had relied on techniques such as quantitative PCR and metabarcoding, which could not recover high quantities of quality human DNA from environmental samples. "However, improvements in deep sequencing technology and novel bioinformatics refinements mean that untargeted shotgun-sequencing-based approaches are becoming feasible, which more fully capture the true extent of genetic diversity within a sample," the authors noted.

With this shift toward shotgun-sequencing approaches, the researchers feel that in the future, large volumes of human environmental DNA could be retrieved. While there are benefits, the authors worry that it could open a Pandora's box.

"It's standard in science to make these sequences publicly available. But that also means if you don't screen out human information, anyone can come along and harvest this information," Duffy said. "That raises issues around consent. Do you need to get consent to take those samples? Or institute some controls to remove human information?"

Researchers also feel that it's a complex problem for the general public who are mostly unaware of the technology used and oblivious to the fact that their genetic information may inadvertently get captured.

The researchers were further able to identify the genetic ancestry within pooled human populations as well as variants associated with disease susceptibility. These findings raise concerns about how the technology could be used for surveillance of individuals, minority groups of specific genetic ancestry, or those with genetically driven disabilities, or even to obtain genomic information from local populations without their knowledge or consent, the authors wrote.

Despite the worrisome ethical concerns, they noted that sampling of human environmental DNA could have many societal benefits. For instance, the technology could be used in community health monitoring, finding population-based disease risk susceptibility, and in search-and-rescue missions and forensic investigations.

Given their findings, the authors argued, policymakers and scientific communities need to take issues around consent and privacy seriously, said the authors. "Such planning should be initiated immediately, preempting the technology becoming even more widespread, affordable, and entrenched, be it for beneficial or exploitative applications," they wrote.