Smartphone taught to genetically diagnose cancer

Taras Molotilin, N+1

An international team of scientists from Sweden and the USA has created a portable fluorescent microscope, which is a nozzle for a Nokia Lumia 1020 smartphone. Researchers have shown that using the new system, it is possible to analyze DNA samples and identify mutations associated with certain types of cancer in it with an accuracy almost equal to stationary laboratory equipment. The work was published in Nature Communications (Kuhnemund et al., Targeted DNA sequencing and in situ mutation analysis using mobile phone microscopy).

DNA fluorescence captured on a smartphone camera.
Here and below are drawings from an article in Nature Communications.

Molecular cancer diagnostics based on DNA analysis and detection of mutant sequences has reached great heights over the past 20 years and has become an accessible and almost routine task. However, these techniques still require expensive equipment, which is often not available even for large hospitals, and even more so for poor countries or field hospitals. Portable devices and ready-made diagnostic kits are being developed specifically for these purposes. At the same time, the authors of the works are increasingly turning to smartphones, since these devices have sufficient computing power and good optical sensors that can be adapted for microscopic tasks.

The device developed by the authors is an optical-mechanical nozzle that replaces the factory lens of a smartphone. In addition to a set of lenses, it also has two monochrome and one white diode, as well as a sample holder and a drive for moving it along three axes. The pixel size in the smartphone is about 1.1 microns, and taking into account the modified lens, the magnification of the entire system turned out to be about 2.6X.

The detection of mutant DNA was carried out in several stages. The authors examined both purified DNA isolated from colon cancer cells and tissue samples obtained by biopsy. Amplification of fragments of the KRAS gene, a well-known marker of colon cancer, was carried out by replication according to the rolling circle replication type: the KRAS gene, potentially containing mutations, was cut out of DNA and applied to a substrate to which short DNA "probes" were sewn. In the event that the gene did contain a mutation of interest to scientists, it was complementarily bound to the probe, as well as a fragment containing a fluorescent label, after which it was looped. The ring DNA was amplified, as a result of which a multiplied set of copies of the mutant KRAS gene containing a sufficient number of fluorescent groups was sewn to the substrate so that it could be seen on the screen of a smartphone equipped with a new microscope. In order for the application to distinguish the fluorescent DNA signal from extraneous noise, the authors used machine learning on pre-prepared and manually labeled samples.

A diagram of the device, as well as a description of the approach underlying the analysis of mutant DNA.

Scientists have shown that their method allows to determine mutant DNA in concentrations from one femtomol per liter, while the accuracy of calculating the proportion of mutant fragments in the sample was only a few percent inferior to a similar analysis on laboratory equipment. In addition, the authors also examined samples from which no preliminary DNA isolation was carried out: cancer cells and tissue samples obtained during colon biopsy. In both cases, the smartphone-based microscope successfully coped with the task.

According to the authors, the main goal of the new study was to create a mobile device with which it is possible to carry out fast and accurate molecular diagnostics in places where there is no access to clinical equipment. Scientists are confident that they succeeded, but emphasize that the problem has not been solved definitively, since many steps from their analysis still require certain qualifications and the presence of specific reagents. And the analysis and conclusion in any case can only be carried out by a specialist.

Previously, numerous attempts have already been made to create portable analogues of complex laboratory equipment based on conventional smartphones. In one of the works, the method of DNA amplification was also used (although the other was loop isothermal amplification) to identify the pathogens of herpes. Another group of scientists created a microscope attachment to study the diffraction pattern that occurs when marker particles interact with a cancer cell. 

Portal "Eternal youth" http://vechnayamolodost.ru  18.01.2017