Software verifies someone’s identity by their DNA in minutes

Tests show the method can validate an individual’s identity after cross-checking between 60 and 300 variants, the researchers report. Within minutes, it verified the identity of the study’s lead author, Sophie Zaaijer, a former member of NYGC and now a postdoctoral researcher at Cornell Tech.

To do this, the MinION matched the readout of Zaaijer’s genome, gleaned from a sample of cheek cells, with a reference profile stored among 31,000 other genomes on the public database, Erlich’s identity was verified the same way, with initial sequencing done by Columbia students in the Ubiquitous Genomics class he and Zaaijer taught in 2015.

They call their re-identification technique “MinION sketching” which Zaaijer compares to the brain’s ability to make out a bird from a few telling features in an abstract Picasso line-drawing.  The MinION’s genetic “sketch” of a cell-sample is compared to a growing database of sketches —similarly incomplete genetic profiles produced by at-home DNA-test kits like 23andMe, and donated to science by consumers.

“Using our method, one needs only a few DNA reads to infer a match to an individual in the database,” says Zaaijer. 

The most promising use for MinION sketching may be as a cheap cell-authentication tool in experimental research, say scientists familiar with its capabilities. In the study, researchers quickly matched a strain of leukemic cells sequenced by the MinION against a reference file in the Cancer Cell Line Encyclopedia database, they report. When they tried contaminating the cells with other cultures, it correctly rejected a match if contamination levels climbed above 25 percent.

The use of misidentified or contaminated cell lines in medical research is blamed for as much as a third of the estimated $28 billion spent each year on studies that can’t be replicated, according to one recent study. In a 2014 essay in Science, the director of the National Institute of General Medical Sciences, Jon Lorsch, called for new policies and technologies to address the problem.

Lacking the expensive machinery needed to validate cell lines on their own, most researchers either skip validation or ship their cultures to specialized labs which can delay important findings and treatments. If an easier alternative were available, most researchers would use it, says Neville Sanjana, a core faculty member at NYGC and assistant professor at NYU’s Department of Biology who works on skin and lung cancer cell lines and was not involved in the study.

“No one wants to waste time and reagents working on the wrong cells,” he says. “At the right price, every lab will adopt this.”

Coauthors of the study are Assaf Gordon at NYGC; Daniel Speyer at Columbia Engineering and NYGC; Robert Piccone at Columbia’s Data Science Institute and Simon Cornelis Groen, at NYU’s Center for Genomics and Systems Biology.

— Read more in Sophie Zaaijer, “Rapid re-identification of human samples using portable DNA sequencing,” eLife 6 (28 November 2017) (DOI: 10.7554/eLife.27798); and watch a video showing researchers use the MinION and a laptop to validate a sample of cells from a NYC rooftop.