DeepMind hopes its unrivaled collection of data, enabled by artificial intelligence, may advance development of precision medicines, new medical laboratory tests, and therapeutic treatments
‘Tis the season for giving, and one United Kingdom-based artificial intelligence (AI) research laboratory is making a sizeable gift. After using AI and machine learning to create “the most comprehensive map of human proteins,” in existence, DeepMind, a subsidiary of Alphabet Inc. (NASDAQ:GOOGL), parent company of Google, plans to give away for free its database of millions of protein structure predictions to the global scientific community and to all of humanity, The Verge reported.
Pathologists and clinical laboratory scientists developing proteomic assays understand the significance of this gesture. They know how difficult and expensive it is to determine protein structures using sequencing of amino acids. That’s because the various types of amino acids in use cause the [DNA] string to “fold.” Thus, the availability of this data may accelerate the development of more diagnostic tests based on proteomics.
“For decades, scientists have been trying to find a method to reliably determine a protein’s structure just from its sequence of amino acids. Attraction and repulsion between the 20 different types of amino acids cause the string to fold in a feat of ‘spontaneous origami,’ forming the intricate curls, loops, and pleats of a protein’s 3D structure. This grand scientific challenge is known as the protein-folding problem,” a DeepMind statement noted.
Enter DeepMind’s AlphaFold AI platform to help iron things out. “Experimental techniques for determining structures are painstakingly laborious and time consuming (sometimes taking years and millions of dollars). Our latest version [of AlphaFold] can now predict the shape of a protein, at scale and in minutes, down to atomic accuracy. This is a significant breakthrough and highlights the impact AI can have on science,” DeepMind stated.
Release of Data Will Be ‘Transformative’
In July, DeepMind announced it would begin releasing data from its AlphaFold Protein Structure Database which contains “predictions for the structure of some 350,000 proteins across 20 different organisms,” The Verge reported, adding, “Most significantly, the release includes predictions for 98% of all human proteins, around 20,000 different structures, which are collectively known as the human proteome. By the end of the year, DeepMind hopes to release predictions for 100 million protein structures.”
According to Edith Heard, PhD, Director General of the European Molecular Biology Laboratory (EMBL), the open release of such a dataset will be “transformative for our understanding of how life works,” The Verge reported.
“I see this as the culmination of the entire 10-year-plus lifetime of DeepMind,” company CEO and co-founder Demis Hassabis (above), told The Verge. “From the beginning, this is what we set out to do: to make breakthroughs in AI, test that on games like Go and Atari, [and] apply that to real-world problems, to see if we can accelerate scientific breakthroughs and use those to benefit humanity.” The release of DeepMind’s entire protein prediction database will certainly do that. Clinical laboratory scientists worldwide will have free access to use it in developing new precision medicine treatments based on proteomics. (Photo copyright: BBC.)
Free Data about Proteins Will Accelerate Research on Diseases, Treatments
Research into how protein folds and, thereby, functions could have implications to fighting diseases and developing new medicines, according to DeepMind.
“This will be one of the most important datasets since the mapping of the human genome,” said Ewan Birney, PhD, Deputy Director General of the EMBL, in the DeepMind statement. EMBL worked with DeepMind on the dataset.
DeepMind protein prediction data are already being used by scientists in medical research. “Anyone can use it for anything. They just need to credit the people involved in the citation,” said Demis Hassabis, DeepMind CEO and Co-founder, in The Verge.
In a blog article, Hassabis listed several projects and organizations already using AlphaFold. They include:
“As researchers seek cures for diseases and pursue solutions to other big problems facing humankind—including antibiotic resistance, microplastic pollution, and climate change—they will benefit from fresh insights in the structure of proteins,” Hassabis wrote.
Because of the deep financial backing that Alphabet/Google can offer, it is reasonable to predict that DeepMind will make progress with its AI technology that regularly adds capabilities and accuracy, allowing AlphaFold to be effective for many uses.
This will be particularly true for the development of new diagnostic assays that will give clinical laboratories better tools for diagnosing disease earlier and more accurately.
Research could lead to clinical laboratory tests in service of precision medicine therapies to reduce a person’s susceptibility to being targeted by blood-sucking insects
Ever wonder why some people attract mosquitoes while others do not? Could biting insects pick their victims by smell? Scientists in California believe the answers to these questions could lead to new precision medicine therapies and clinical laboratory tests.
The research revealed evidence that some blood-sucking insects may identify their prey by homing in on the “scent” of chemicals produced by bacteria located in the skin microbiome of animals and humans.
This is yet another example of research into one area of the human microbiome that might someday lead to a new clinical laboratory test, in this case to determine if a person is more likely to attracts biting insects. If there were such a test, precision medicine therapies could be developed that change an individual’s microbiome to discourage insects from biting that individual.
Then, the clinical laboratory test would have value because it helped diagnose a health condition that is treatable.
Curiosity regarding why mosquitoes seem to gravitate towards some humans over others was the original catalyst for the UCSD Medical School research. “You know when you go to a barbeque and your friend is getting bombarded by mosquitos, but you’re fine? There is some research to support the idea that the difference in mosquito attraction is linked to your skin microbiome—the unique community of bacteria living on your skin,” said Holly Lutz, PhD (above), first author of the UCSD study. “Keeping in mind that some people are more attractive to mosquitoes than others, I wondered what makes insects attracted to some bats but not others.” Lutz’s research could lead to clinical laboratory tests that drive precision medicine therapies to alter human skin microbiomes and make people less attractive to biting insects. (Photo copyright: The Field Museum of Natural History.)
Biting Flies Prefer Specific Bats
“In these caves, I’d see all these different bat species or even taxonomic families roosting side by side. Some of them were loaded with bat flies, while others had none or only a few,” Lutz said in Phys.org. “And these flies are typically very specific to different kinds of bats—you won’t find a fly that normally feeds on horseshoe bats crawling around on a fruit bat. I started wondering why the flies are so particular. Clearly, they can crawl over from one kind of bat to another, but they don’t really seem to be doing that.”
The researchers suspected that the bacteria contained in the skin microbiomes of individual bats could be influencing which bats the flies selected to bite. The bacteria produce a distinctive odor which may make certain bats more attractive to the flies.
The type of fly assessed for the study are related to mosquitoes and most of them are incapable of flight.
“They have incredibly reduced wings in many cases and can’t actually fly,” Lutz explained. “And they have reduced eyesight, so they probably aren’t really operating by vision. So, some other sensory mechanisms must be at play, maybe a sense of smell or an ability to detect chemical cues.”
To test their hypothesis, the research team collected skin and fur samples from the bodies and wings of a variety of bat species located in various caves around Kenya and Uganda. They collected their samples at 14 field sites from August to October in 2016. They then examined the DNA of the bats as well as the microbes residing on the animals’ skin and searched for the presence of flies.
“The flies are exquisitely evolved to stay on their bat,” said Carl Dick, PhD, a professor of biology at Western Kentucky University and one of the study’s authors. “They have special combs, spines, and claws that hold them in place in the fur, and they can run quickly in any direction to evade the biting and scratching of the bats, or the efforts by researchers to capture them,” he told Phys.org.
“You brush the bats’ fur with your forceps, and it’s like you’re chasing the fastest little spider,” Lutz said. “The flies can disappear in a split second. They are fascinatingly creepy.”
Genetic Sequencing DNA of Bat Skin Bacteria
After collecting their specimens, the researchers extracted DNA from the collected bacteria and performed genetic sequencing on the samples. They created libraries of the bacteria contained in each skin sample and used bioinformatics methods to identify the bacteria and compare the samples from bats that had flies versus those that did not.
“How the flies actually locate and find their bats has previously been something of a mystery,” Dick noted. “But because most bat flies live and feed on only one bat species, it’s clear that they somehow find the right host.”
The scientists discovered that different bat families did have their own distinctive skin microbiome, even among samples collected from different locations. They found that differences in the skin microbiomes of certain bats does contribute to whether those bats have parasites. But not all their questions were answered.
“We weren’t able to collect the actual chemicals producing cue—secondary metabolites or volatile organic compounds—during this initial work. Without that information, we can’t definitively say that the bacteria are leading the flies to their hosts,” Lutz said.
Next Steps
“So, next steps will be to sample bats in a way that we can actually tie these compounds to the bacteria. In science, there is always a next step,” she added.
This research illustrates that there may be a reason why certain animals and humans tend to be more attractive to insects than others. It is also possible that an individual’s skin microbiome may explain why some people are more prone to mosquito and other types of insect bites.
More research and clinical studies on this topic are needed, but it could possibly lead to a clinical laboratory test to determine if an individual’s skin microbiome could contribute to his or her potential to being bitten by insects. Such a test would be quite beneficial, as insects can carry a variety of diseases that are harmful to humans.
Perhaps a precision medicine therapy could be developed to alter a person’s microbiome to make them invisible to blood-sucking insects. That would be a boon to regions of the world were diseases like malaria are spread by insect bites.
WASE-COVID Study also found that use of artificial intelligence technology minimized variability among echocardiogram scan results
Many physicians—including anatomic pathologists—are watching the development of artificial intelligence (AI)-powered diagnostic tools that are intended to analyze images and analyze the data with accuracy comparable to trained doctors. Now comes news of a recent study that demonstrated the ability of an AI tool to analyze echocardiograph images and deliver analyses equal to or better than trained physicians.
Conducted by researchers from the World Alliance Societies of Echocardiography and presented at the latest annual sessions of the American College of Cardiology (ACC), the WASE-COVID Study involved assessing the ability of the AI platform to analyze digital echocardiograph images with the goal of predicting mortality in patients with severe cases of COVID-19.
To complete their research, the WASE-COVID Study scientists examined 870 patients with acute COVID-19 infection from 13 medical centers in nine countries throughout Asia, Europe, United States, and Latin America.
Human versus Artificial Intelligence Analysis
Echocardiograms were analyzed with automated, machine learning-derived algorithms to calculate various data points and identify echocardiographic parameters that would be prognostic of clinical outcomes in hospitalized patients. The results were then compared to human analysis.
All patients in the study had previously tested positive for COVID-19 infection using a polymerase chain reaction (PCR) or rapid antigen test (RAT) and received a clinically-indicated echocardiogram upon admission. For those patients ultimately discharged from the hospital, a follow-up echocardiogram was performed after three months.
“What we learned was that the manual tracings were not able to predict mortality,” Federico Asch, MD, FACC, FASE, Director of the Echocardiography Core Lab at MedStar Health Research Institute in Washington, DC, told US Cardiology Review in a video interview describing the WASE-COVID Study findings.
Asch is also Associate Professor of Medicine (Cardiology) at Georgetown University. He added, “But on the same echoes, if the analysis was done by machine—Ultromics EchoGo Core, a software that is commercially available—when we used the measurements obtained through this platform, we were able to predict in-hospital and out-of-hospital mortality both with ejection fraction and left ventricular longitudinal strain.”
“When compared to the manual reads, the AI algorithms had a much higher predictive value for mortality,” Federico Asch, MD (above), told US Cardiology Review. “Indeed, they were predictive where the manual ones were not.” These findings may have implications in the development and adoption of artificial intelligence driven clinical laboratory diagnostics and for predicting risk of COVID-19 deaths in hospitalized heart patients. Click here to review the entire video interview. (Photo copyright: US Cardiology Review.)
Nearly half of the 870 hospitalized patients were admitted to intensive care units, 27% were placed on ventilators, 188 patients died in the hospital, and 50 additional patients died within three to six months after being released from the hospital.
10 of 13 medical centers performed limited cardiac exams as their primary COVID in-patient practice and three out of the 13 centers performed comprehensive exams.
In-hospital mortality rates ranged from 11% in Asia, 19% in Europe, 26% in the US, to 27% in Latin America.
Left ventricular longitudinal strain (LVLS), right ventricle free wall strain (RVFWS), as well as a patient’s age, lactic dehydrogenase levels and history of lung disease, were independently associated with mortality. Left ventricle ejection fraction (LVEF) was not.
Fully automated quantification of LVEF and LVLS using AI minimized variability.
AI-based left ventricular analyses, but not manual, were significant predictors of in-hospital and follow-up mortality.
The WASE-COVID Study also revealed the varying international use of cardiac ultrasound (echocardiography) on COVID-19 patients.
“By using machines, we reduce variability. By reducing variability, we have a better capacity to compare our results with other outcomes, whether that outcome in this case is mortality or it could be changes over time,” Asch stated in the US Cardiology Review video. “What this really means is that we may be able to show associations and comparisons by using AI that we cannot do with manual [readings] because manual has more variation and is less reliable.”
He said the next steps will be to see if the findings hold true when AI is used in other populations of cardiac patients.
COVID-19 Pandemic Increased Need for Swift Analyses
An earlier WASE Study in 2016 set out to answer whether normal left ventricular heart chamber quantifications vary across countries, geographical regions, and cultures. However, the data produced by that study took years to review. Asch said the COVID-19 pandemic created a need for such analysis to be done more quickly.
“When the pandemic began, we knew that the clinical urgency to learn as much as possible about the cardiovascular connection to COVID-19 was incredibly high, and that we had to find a better way of securely and consistently reviewing all of this information in a timely manner,” he said in the Ultromics new release.
Coronary artery disease (CAD) is the most common form of heart disease and affects more than 16.5 million people over the age of 20. By 2035, the economic burden of CAD will reach an estimated $749 billion in the US alone, according to the Ultromics website.
“COVID-19 has placed an even greater pressure on cardiac care and looks likely to have lasting implications in terms of its impact on the heart,” said Ross Upton, PhD, Founder and CEO of Oxford, UK-based Ultromics, in a news release announcing the US Food and Drug Administration’s 510(k) clearance for the EchoGo Pro, which supports clinicians’ diagnosing of CAD. “The healthcare industry needs to quickly pivot towards AI-powered automation to reduce the time to diagnosis and improve patient care.”
Use of AI to analyze digital pathology images is expected to be a fast-growing element in the anatomic pathology profession, particularly in the diagnosis of cancer. As Dark Daily outlined in this free white Paper, “Anatomic Pathology at the Tipping Point? The Economic Case for Adopting Digital Technology and AI Applications Now,” anatomic pathology laboratories can expect adoption of AI and digital technology to gain in popularity among pathologists in coming years.
Determining how dogs do this may lead to biomarkers for new clinical laboratory diagnostics tests
Development of new diagnostic olfactory tools for prostate and other cancers is expected to result from research now being conducted by a consortium of researchers at different universities and institutes. To identify new biomarkers, these scientists are studying how dogs can detect the presence of prostate cancer by sniffing urine specimens.
Funded by a grant from the Prostate Cancer Foundation, the pilot study demonstrated that dogs could identify prostate samples containing cancer and discern between cancer positive and cancer negative samples.
Canine Olfactory Combined with Artificial Intelligence Analysis Approach
The part of a canine brain that controls smell is 40 million times greater than that of humans. Some dog breeds have 300 to 350 million sensory receptors, compared to about five million in humans. With their keen sense of smell, dogs are proving to be vital resources in the detection of some diseases.
The pilot study examined how dogs could be trained to detect prostate cancer in human urine samples.
Claire Guest, CEO and Chief Scientific Officer of UK-based Medical Detection Dogs and one of the study authors, is shown above with one of her cancer detecting dogs. In a Prostate Cancer Foundation article, she said, “Prostate cancer is not going to turn out to be a single note. What dogs are really good at discovering is a tune. Think of Beethoven’s Fifth Symphony, those first few notes. We suspect the cancer signature is something like that. It’s a pattern; the dogs are really good at recognizing the pattern. Machines that recognize the notes but can’t read the pattern are not reliable biomarkers,” she noted. The researchers believe the best solution for developing a clinical laboratory diagnostic that detects prostate cancer may be a combined approach using canine olfaction and AI neural networks. (Photo copyright: Janine Warwick/NPR.)
To perform the study, the researchers trained two dogs to sniff urine samples from men with high-grade prostate cancer and from men without the cancer. The two dogs used in the study were a four-year-old female Labrador Retriever named Florin, and a seven-year-old female wirehaired Hungarian Vizsla named Midas. The dogs were trained to respond to cancer-related chemicals, known as volatile organic compounds, or VOCs, the researchers added to the urine samples, and to not respond to the samples without the VOCs.
Both dogs performed well in their cancer detection roles, and both successfully identified five of seven urine samples from men with prostate cancer, correlating to a 71.4% accuracy rate. In addition, Florin correctly identified 16 of 21 non-aggressive or no cancer samples for an accuracy rate of 76.2% and Midas did the same with a 66.7% accuracy rate.
“We wondered if having the dogs detect the chemicals, combined with analysis by GC-MS, bacterial profiling, and an artificial intelligence (AI) neural network trained to emulate the canine cancer detection ability, could significantly improve the diagnosis of high-grade prostate cancer,” said Alan Partin, MD, PhD, Professor of Urology, Pathology and Oncology, Johns Hopkins University School of Medicine and one of the authors of the study, told Futurity.
The researchers determined that canine olfaction was able to distinguish between positive and negative prostate cancer in the samples, and the VOC and microbiota profiling analyses showed a qualitative difference between the two groups. The multisystem approach demonstrated a more sensitive and specific way of detecting the presence of prostate cancer than any of the methods used by themselves.
In their paper, the researchers concluded that “this study demonstrated feasibility and identified the challenges of a multiparametric approach as a first step towards creating a more effective, non-invasive early urine diagnostic method for the highly aggressive histology of prostate cancer.”
Can Man’s Best Friend be Trained to Detect Cancer and Save Lives?
Prostate cancer is the second leading cause of cancer deaths among men in the developed world. And, according to data from the National Cancer Institute, standard clinical laboratory blood tests, such as the prostate-specific antigen (PSA) test for early detection, sometimes miss the presence of cancer.
Establishing an accurate, non-invasive method of sensing the disease could help detect the disease sooner when it is more treatable and save lives.
The American Cancer Society estimates that there will be about 248,530 new cases of prostate cancer diagnosed in 2021 and that there will be approximately 34,130 deaths resulting from the disease during the same year.
Of course, more testing will be needed before Man’s best friend can be put to work detecting cancer in medical environments. But if canines can be trained to detect the disease early, and in a non-invasive way, more timely diagnosis and treatment could result in higher survival rates.
Meanwhile, as researchers identify the elements dogs use to detect cancer and other diseases, this knowledge can result in the creation of new biomarkers than can be used in clinical laboratory tests.
Nanorate sequencing allows researchers to identify changes to individual genetic sequencing letters among millions of DNA letters contained in a single cell
Detecting genetic mutations in cells requires genomic sequencing that, until now, has not been accurate enough to spot minute changes in DNA sequences. Many clinical laboratory scientists know this restricted the ability of genetic scientists to identify cancerous mutations early in individual cells.
Now, researchers at the Wellcome Sanger Institute in the United Kingdom have developed a new method of genetic sequencing that “makes it possible to more accurately investigate how genetic changes occur in human tissues,” according to Genetic Engineering and Biotechnology News (GEN).
This development suggests a new, more sensitive tool may soon be available for anatomic pathologists to speed evaluation of pre-cancerous and cancerous tissues, thereby achieving earlier detection of disease and clinical intervention.
Called Nanorate Sequencing (NanoSeq for short), the new technology enables researchers to detect genetic changes in any human tissues “with unprecedented accuracy,” according to a news release.
How Somatic Mutations Drive Cancer, Aging, and Other Diseases
NanoSeq enables the detection of new mutations in most human cells—the non-dividing cells—GEN explained, calling Wellcome Sangar Institute’s new technology a “breakthrough” in the use of duplex sequencing.
Until now, genomic sequencing has not been “accurate enough” for this level of detection, Sanger stated in the news release. Thus, there was little opportunity to enhance exploration of new mutations in the majority of human cells.
Further, the findings of the Sanger study suggest that cell division may not be the primary cause of somatic mutations (changes in the DNA sequence of a biological cell).
In their paper, the researchers discussed the importance of somatic mutations. “Somatic mutations drive the development of cancer and may contribute to aging and other diseases. Despite their importance, the difficulty of detecting mutations that are only present in single cells or small clones has limited our knowledge of somatic mutagenesis to a minority of tissues.
“Here, to overcome these limitations, we developed Nanorate Sequencing (NanoSeq), a duplex sequencing protocol with error rates of less than five errors per billion base pairs in single DNA molecules from cell populations. This rate is two orders of magnitude lower than typical somatic mutation loads, enabling the study of somatic mutations in any tissue independently of clonality,” the researchers wrote in Nature.
Refining Duplex Sequencing and Improving PCR Testing
In their study, Sanger researchers assessed duplex sequencing and found errors concentrated at DNA fragment ends. To them, this suggested “flaws” in preparation for DNA sequencing.
Duplex sequencing is an established technique “which sequences both strands of a DNA molecule to remove sequencing and polymerase chain reaction (PCR) errors,” explained a Science Advisory Board article.
“Detecting somatic mutations that are only present in one or a few cells is incredibly technically challenging. You have to find a single letter change among tens of millions of DNA letters and previous sequencing methods were simply not accurate enough,” said Robert Osborne, PhD (above), former Principal Staff Scientist at Sanger who led development of NanoSeq, in the news release. Osborne is now COO of Biofidelity, a cancer diagnostics developer in Cambridge, United Kingdom. This research may eventually give clinical laboratories and surgical pathologists useful new tools that enable earlier, more accurate diagnosis of cancer. (Photo copyright: Cambridge Independent.)
Re-evaluating Mutagenesis and Cell Division with NanoSeq
It took the Sanger researchers four years to create NanoSeq. They “carefully refined” duplex sequencing methods using more specific enzymes to aid DNA cutting and bioinformatics analysis, Clinical OMICS noted.
Then, they put NanoSeq’s sensitivity to the test. They wanted to know if its low error rate meant that NanoSeq could enable study of somatic mutations in any tissue. This would be important, they noted, because genetic mutations naturally occur in cells in a range of 15 to 40 mutations per year with some changes leading to cancer.
The scientists compared the rate and pattern of mutation in both stem cells (renewing cells supplying non-dividing cells) and non-dividing cells (the majority of cells) in blood, colon, brain, and muscle tissues.
The Sanger study found:
Mutations in slowly dividing stem cells are on track with progenitor cells, which are more rapidly dividing cells.
Cell division may not be the “dominant process causing mutations in blood cells.”
Analysis of non-dividing neurons and rarely-dividing muscle cells found “mutations accumulate throughout life in cells without cell division and at a similar pace” to blood cells.
“It is often assumed that cell division is the main factor in the occurrence of somatic mutations, with a greater number of divisions creating a greater number of mutations. But our analysis found that blood cells that had divided many times more than others featured the same rates and patterns of mutation. This changes how we think about mutagenesis and suggests that other biological mechanisms besides cell divisions are key,” said Federico Abascal, PhD, First Author and Sanger Postdoctoral Fellow, in the news release.
Using NanoSeq to Scale Up Somatic Mutation Analyses
“NanoSeq will also make it easier, cheaper, and less invasive to study somatic mutation on a much larger scale. Rather than analyzing biopsies from small numbers of patients and only being able to look at stem cells or tumor tissue, now we can study samples from hundreds of patients and observe somatic mutations in any tissue,” said Inigo Martincorena, PhD, Senior Author and Sanger Group Leader, in the news release.
More research is needed before NanoSeq finds its way to diagnosing cancer by anatomic pathology groups. Still, for diagnostics professionals and clinical laboratory leaders, NanoSeq is an interesting development. It appears to be a way for scientists to see genetic changes in single cells and mutations in a handful of cells that evolve into cancerous tumors, as compared to those that do not.
The Sanger scientists plan to pursue larger follow-up NanoSeq studies.
Although there are healthcare providers who see the potential in microbiome testing, many clinical laboratories are not yet ready to embrace microbiome-based testing
In an unlikely string of events, no less than Nordstrom, the national department store chain, announced in September that it would offer microbiome-based test claimed to “check gut health.” Apparently, its customers were interested in this clinical laboratory test, as the Nordstrom website currently indicates that the “Health Intelligence Test Kit by Viome” is already sold out!
What does it say about consumer interest in clinical laboratory self-testing that Nordstrom has decided to offer at-home microbiome tests to its store customers? Can it be assumed that Nordstrom conducted enough marketing surveys of its customers to determine: a) that they were interested in microbiome testing; and b) they would buy enough microbiome tests that Nordstrom would benefit financially from either the mark-up on the tests or from the derived goodwill for meeting customer expectations?
Whatever the motivation, the retail giant recently announced it had partnered with Viome Life Sciences to sell Viome’s microbiome testing kits to its customers online, and in 2022, at some Nordstrom retail locations. These tests are centered around helping consumers understand the relationship between their microbiome and nutrition.
Pathologists and clinical laboratories will want to track Nordstrom’s success or failure in selling microbiome-based assays to its consumers. Microbiomics is in its infancy and remains a very unsettled area of diagnostics. Similarly, Viome, a self-described precision health and wellness company that conducts mRNA analysis at scale, will need to demonstrate that its strategy of developing precision medicine diagnostics and therapeutics based on the human microbiome has clinical relevance.
Helping Consumers with ‘Precision Nutrition’
In a September news release, Viome founder and CEO Naveen Jain, a serial entrepreneur, said, “Both Viome and Nordstrom believe that true health and beauty start from within. There is no such thing as a universal healthy food or healthy supplement. What is right for one person can be wrong for someone else, especially when it comes to nutrition which is key to human longevity and vitality. Precision nutrition is the future!”
“Precision medicine seeks to improve the personalized treatment of diseases, and precision nutrition is specific to dietary intake. Both develop interventions to prevent or treat chronic diseases based on a person’s unique characteristics like DNA, race, gender, health history, and lifestyle habits. Both aim to provide safer and more effective ways to prevent and treat disease by providing more accurate and targeted strategies.
“Precision nutrition assumes that each person may have a different response to specific foods and nutrients, so that the best diet for one individual may look very different than the best diet for another.
“Precision nutrition also considers the microbiome, trillions of bacteria in our bodies that play a key role in various daily internal operations. What types and how much bacteria we have are unique to each individual. Our diets can determine which types of bacteria live in our digestive tracts, and according to precision nutrition the reverse is also true: the types of bacteria we house might determine how we break down certain foods and what types of foods are most beneficial for our bodies.”
Medical Laboratory Testing, not Guessing
Viome Life Sciences is a microbiome and RNA analysis company based in Bellevue, Wash. The test kit that Nordstrom is selling is called the Health Intelligence Test. It is an at-home mRNA test that can provide users with some insights regarding their health. Consumers use the kit to collect blood and fecal samples, then return those samples to Viome for testing.
In a press release announcing its collaboration with Nordstrom, Viome said, “In a world overwhelmed by information relating to diet and supplement advice, Viome believes in testing, not guessing and empowering its users with actionable insights. To date, Viome has helped over 250,000 individuals improve their health through precision nutrition powered by microbial and human gene expression insights.”
Nordstrom began offering Viome’s Health Intelligence Test kit for $199 on its website starting in September. As of this writing and noted above, the kits are sold out. Nordstrom plans to stock the kit in select stores starting in 2022.
Viome’s Health Intelligence Test kit (above) looks at the microbiome to determine gut health, cellular health, healthy aging, immune health, and stress responses. Test results offer consumers personalized nutritional suggestions and recommendations for supplements, probiotics, and prebiotics based on an individual’s biology. Test are performed by Viome’s own clinical laboratories and results sent directly to Nordstrom’s customers. (Photo copyright: Viome Life Sciences.)
Individuals who purchase the test submit blood and stool samples to Viome’s lab which performs an analysis of gene activity patterns in the user’s cells and microbiome. Viome provides the results to consumers within two to three weeks.
“This partnership is a giant step towards making our technology more accessible, so people can understand what’s right for their unique body,” Jain said in the news release. “We are inspired each day by the incredible changes our customers are seeing in their health including improvements in digestion, weight, stress, ability to focus, and more.”
According to the news release, Viome conducted blind studies earlier this year that revealed significant successes based on their precision nutritional approach to wellness. Study participants, Viome claims, improved their outcomes to four diseases through nutrition:
Is Microbiome Diagnostics Testing Ready for Clinical Use?
Microbiomics is a relatively new field of diagnostics research. Much more research and testing will be needed to prove its clinical value and efficacy in healthcare diagnostics. Nevertheless, companies are offering microbiomics testing to consumers and that has some healthcare providers concerned.
In the GeekWire article, David Suskind, MD, a gastroenterologist at Seattle Children’s Hospital and Professor of Pediatrics at the University of Washington, described Viome’s study methodology as “questionable,” adding, “I think this is a very interesting and exciting space and I do think there are definite potential implications, down the road. [However] we are not there in terms of looking at microbiome and making broad recommendation for individuals, as of yet.”
Will at-home clinical laboratory testing kits that analyze an individual’s microbiome someday provide data that help people lead healthier lives and ward off diseases? That’s Jain’s prediction.
In an article published in Well+Good, Jain said, “COVID-19 has, of course, been such a dark time, but one positive that did come from it is that more people are taking control of their own health. I really believe that the future of healthcare will be delivered not at the hospital, but at home.”
If this collaboration between Nordstrom and Viome proves successful, similar partnerships between at-home diagnostics developers and established retail chains may become even more common. And that should be on the radars of pathologists and clinical laboratories.
