Pathogen Detection Tool Could Change Infectious Diseases Diagnoses.

Scientists at the University of Utah, ARUP Laboratories, and IDbyDNA, Inc., have developed ultra-fast, meta-genomics analysis software called Taxonomer that dramatically improves the accuracy and speed of pathogen detection. In a paper published today in Genome Biology, the collaborators demonstrated the ability of Taxonomer to analyze the sequences of all nucleic acids in a clinical specimen (DNA and RNA) and to detect pathogens, as well as profile the patient's gene expression, in a matter of minutes. Infectious diseases are one of the biggest killers in the world. Almost 5 million children under age 5 die each year from infectious diseases worldwide, yet many infections are treatable if the pathogen culprit can be quickly and accurately identified. "In the realm of infectious diseases, this type of technology could be as significant as sequencing the human genome," says co-author Mark Yandell, PhD, professor of human genetics at the University of Utah (U of U), H.A. & Edna Benning Presidential Endowed Chair holder, co-director of the USTAR Center for Genetic Discovery, and co-founder of IDbyDNA. "Very few people have inherited genetic disease. But at some point, everyone gets sick from infections." It is difficult for infectious pathogens to hide when their genetic material is laid bare. Taxonomer opens up an entirely new approach for infectious disease diagnosis, driven by sophisticated genomic analysis and computational technologies. After a patient's sample is sequenced, the data are uploaded via the internet to Taxonomer. In less than one minute, the tool displays a thumbnail inventory of all pathogens in the sample, including viruses, bacteria, and fungi. The interactive, real-time user interface of Taxonomer is powered by the IOBIO system developed by the laboratory of Gabor Marth, DSc, professor of human genetics at the U of U and co-Director of the USTAR Center for Genetic Discovery. Schlaberg explains that Taxonomer can identify an infection without the physician having to decide what to test for, something a PCR-based test cannot do. In other words, a doctor doesn't have to suspect the cause of a patient's infection, but can instead simply ask, "What does my patient have?" and Taxonomer will identify the pathogens. In the new study, Taxonomer was put to the test with real-world cases using data published by others and samples provided by ARUP Laboratories and the Centers for Disease Control and Prevention (CDC). Taxonomer determined that some patients who exhibited Ebola-like symptoms in the recent African outbreak did not have Ebola but severe bacterial infections that likely caused their symptoms. "This technology can be applied whenever we don't know the cause of the disease, including the detection of sudden outbreaks of disease. It is very clear we urgently need more accurate diagnostics to greatly enhance the ability of public health response and clinical care," says Seema Jain, MD, medical epidemiologist at the CDC. Another unique feature of Taxonomer is its ability to delve into human gene expression profiling, which provides information on how or if the patient's body is reacting to an infection. "As a clinician, this gives you a better idea, when we identify a pathogen whether it is really the cause of the disease," says Carrie L. Byington, MD, professor of pediatrics of the U of U and co-director of the Center for Clinical and Translational Science. The tool will also show if the patient is responding to a bacterial or viral infection when we don't find a pathogen or when we find multiple potential causes.She states that she sees the exceptional value of this tool for treating children, who experience more life-threatening infections early in life. "Seeing how a host [patient] reacts is extremely valuable; I believe this is a paradigm shift in how we diagnose people. culled from R&D Magazine.

A SMART PHONE-SIZED DEVICE CAN DIAGNOSE CANCER IN 20 MINUTES.

Advances in disease diagnostics now offer clinicians a staggering degree of accuracy. But access to results generally requires a well-equipped lab and a few weeks’ waiting time. This could soon change thanks to a new, low-cost diagnostic DNA analyzer the size of a smartphone. Q-Poc, billed as a “handheld lab”, is the idea of British-based tech firm QuantuMDx, which says the analyzer can accurately diagnose everything from cancers to infectious diseases in a matter of minutes. Currently in the alpha testing stage, the company hopes to get the product in the hands of doctors by early 2018. “We’re now at the point that we have a working prototype that can perform a highly sensitive tuberculosis test from a sample through to results in 15-20 minutes,” says Jonathan O’Halloran, the company’s co-founder. “The technology is now being ramped up to beta stage and we hope to start manufacturing towards the end of this year.” The handheld apparatus, which runs on a solar-powered battery or wind-up device, is designed to read biological samples submitted via a credit card-size cartridge (think of it as a sophisticated Game Boy). It can work with a range of sample types. Swabs can be used to detect sexually-transmitted infections, while sputum is used to detect tuberculosis. Q-Poc differs from most conventional point-of-care diagnostic tools in that it analyses the DNA of pathogens rather than the proteins within the sample. The device depends on microfluidic technology , which essentially allows fluids to pass through different microscopic channels of different diameters. A chemical process then breaks down the sample into a molecular soup , which is then forced through a nanoscale-based filter system. The filter is coated with a negatively charged polymer, which repels the DNA as other molecules are held back, thereby isolating the DNA for analysis. “It sounds simple, but it is absolutely groundbreaking,” says the 40-year-old O’Halloran, who has a background in molecular genetics. “Nothing out there on the market can come close to its speed and proficiency.” The potential of O’Halloran’s invention to “change the face of healthcare globally” saw him named 2015 European Chief Technology Officer of the Year (small business category) by Eirma, an industrial research association. The award’s judges gave particular praise to the technology’s developing world focus, especially at a time when the threat of drug resistant superbugs are on the rise. read more;http://www.theguardian.com/sustainable-business/2016/apr/21/quantumdx-cancer-diagnostics-medicine-africa-tuberculosis