Real-time DNA sequencing allows a person to be identified in minutes
Image credit: dt
Real-time DNA-authentication has been achieved thanks to new software developed by researchers at Columbia University and the New York Genome Center.
The software is designed to run on the MinION, an instrument the size of a credit card that pulls in strands of DNA through its microscopic pores and reads out sequences of nucleotides, or the DNA letters A, T, C, G.
The device has made it possible for researchers to study bacteria and viruses in the field, but its high error rate and large sequencing gaps have, until now, limited its use on human cells with their billions of nucleotides.
The new method could allow scientists or law enforcement to quickly and accurately identify people and cell lines from their DNA.
The technology has multiple possible applications, from identifying victims in a mass disaster to analysing crime scenes. But its most immediate use could be to flag mislabelled or contaminated cell lines in cancer experiments, a major reason that studies are later invalidated.
“Our method opens up new ways to use off-the-shelf technology to benefit society,” said the study’s senior author Yaniv Erlich, a computer science professor at Columbia Engineering. “We’re especially excited about the potential to improve cell-authentication in cancer research and potentially speed up the discovery of new treatments.”
In an innovative two-step process, the researchers outline a new way to use the $1,000 MinION and the abundance of human genetic data now online to validate the identity of people and cells by their DNA with near-perfect accuracy.
First, they use the MinION to sequence random strings of DNA, from which they select individual variants, which are nucleotides that vary from person to person and make them unique. Then, they use a Bayesian algorithm to randomly compare this mix of variants with corresponding variants in other genetic profiles on file. With each cross-check, the algorithm updates the likelihood of finding a match, rapidly narrowing the search.
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, 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, DNA.land.
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,” Zaaijer said.
The most promising use for ‘MinION sketching’ may be as a cheap cell-authentication tool in experimental research, said scientists familiar with its capabilities.