Half of the genes identified were found to be singletons, unique to specific individuals, offering the possibility of developing precision medicine therapies targeted to specific patients, as well as clinical laboratory tests
Microbiologists and other medical laboratory scientists may soon have more useful biomarkers that aid in earlier, more accurate detection of disease, as well as guiding physicians to select the most effective therapies for specific patients, a key component of Precision Medicine.
The scientists also found that more than half of the bacterial genes examined occurred only once (called “singletons”) and were specific to each individual. A total of 11.8 million of these singletons came from oral samples and 12.6 million of them derived from gut samples, a Harvard news release noted.
In a paper published in Cell Host and Microbe the researchers state, “Despite substantial interest in the species diversity of the human microbiome and its role in disease, the scale of its genetic diversity, which is fundamental to deciphering human-microbe interactions, has not been quantified.”
To determine this quantity, the researchers conducted a meta-analysis of metagenomes from the human mouth and gut among 3,655 samples from 13 unique studies. Of their findings, they wrote, “We found staggering genetic heterogeneity in the dataset, identifying a total of 45,666,334 non-redundant genes (23,961,508 oral and 22,254,436 gut) at the 95% identity level.”
The scientists also found that while genes commonly found in
all the samples seemed to drive the basic functions of a microbe’s survival,
the singletons perform more specialized functions within the body, such as
creating barriers to protect the micro-organisms from external onslaughts and
helping to build up resistance to antibiotics.
“Some of these unique genes appear to be important in solving evolutionary challenges,” said Braden Tierney, a PhD student at Harvard Medical School and one of the authors of the study, in the news release. “If a microbe needs to become resistant to an antibiotic because of exposure to drugs, or suddenly faces a new selective pressure, the singleton genes may be the wellspring of genetic diversity the microbe can pull from to adapt,” he concluded.
‘More Genes in the Human Microbiome than Stars in the
Universe’
According to their published paper, the team of microbiologists and bioinformaticians pinpointed more than 46 million bacterial genes contained within 3,655 Deoxyribonucleic acid (DNA) samples. They identified 23,961,508 non-redundant genes in the oral samples and 22,254,436 non-redundant genes in the intestinal samples.
While similar research in the past has targeted bacteria in
either the gut or the mouth, the scientists believe their study is the first
that analyzed DNA collected from both areas simultaneously.
The graphic above, taken from the Harvard Medical School study, illustrates the ratio of singleton vs. non-singleton bacteria contained in human microbiome. The sheer amount of diversity seems to have impressed the scientists. “There may be more genes in the collective human microbiome than stars in the observable universe, and at least half of these genes appear to be unique to each individual,” the Harvard news release states. This diversity could lead to new precision medicine treatments and clinical laboratory diagnostics. (Graphic copyright: Harvard Medical School.)
“Just like no two siblings are genetically identical, no two bacterial strains are genetically identical, either,” said study co-author Chirag Patel, PhD, Assistant Professor of Biomedical Informatics at Harvard’s Blavatnik Institute. “Two members of the same bacterial strain could have markedly different genetic makeup, so information about bacterial species alone could mask critical differences that arise from genetic variation.”
The scientists also endeavored to determine the number of
genes that reside in the human microbiome but found the precise number difficult
to identify. One calculation estimated that number to be around 232 million,
while another suggested the number could be substantially higher.
“Whatever it may be, we hope that our catalog, along with a
searchable web application, will have many practical uses and seed many directions
of research in the field of host-microbe relationships,” stated Patel in the
news release.
New Diagnostics for Clinical Laboratories?
This type of research could have lasting effects on clinical
laboratories. As the volume of data generated by diagnostic testing of microbes
in patients opens new understanding of how these factors affect human disease
and create differences from one individual to another, the increased number of
genes and gene mutations mean that microbiology laboratories will increase
their use of information technology and analytical software tools.
“Ours is a gateway study, the first step on a what will
likely be a long journey toward understanding how differences in gene content
drive microbial behavior and modify disease risk,” said Tierney in the Harvard
news release.
That’s good news, because new biomarkers derived from such
research will help microbiologists and other clinical laboratory scientists
more accurately detect disease and identify the best therapies for individual
patients.
Low prices to encourage consumers to order its WGS service is one way Veritas co-founder and genetics pioneer George Church hopes to sequence 150,000 genomes by 2021
By announcing an annotated whole-genome sequencing (WGS) service to consumers for just $599, Veritas Genetics is establishing a new price benchmark for medical laboratories and gene testing companies. Prior to this announcement in July, Veritas priced its standard myGenome service at $999.
“There is no more comprehensive genetic test than your whole genome,” Rodrigo Martinez, Veritas’ Chief Marketing and Design Officer, told CNBC. “So, this is a clear signal that the whole genome is basically going to replace all other genetic tests. And this [price drop] gets it closer and closer and closer.”
Pathologists and clinical laboratory managers will want to watch to see if Veritas’ low-priced, $599 whole-genome sequencing becomes a pricing standard for the genetic testing industry. Meanwhile, the new price includes not only the sequencing, but also an expert analysis of test results that includes information on more than 200 conditions, Veritas says.
“The focus in our industry is shifting from the cost of sequencing genomes to interpretation capabilities and that’s where our secret sauce is,” said Veritas CEO Mirza Cifric in a news release. “We’ve built and deployed a world class platform to deliver clinically-actionable insights at scale.” The company also says it “achieved this milestone primarily by deploying internally-developed machine learning and AI [artificial intelligence] tools as well as external tools—including Google’s DeepVariant—and by improving its in-house lab operations.”
The myGenome service offers 30x WGS, which Veritas touts in company documentation as the “gold standard” for sequencing, compared to the less-precise 0.4x WGS.
The myGenome service is available only in the United States.
Will Whole-Genome Sequencing Replace Other Genetic Tests?
Veritas was co-founded by George Church, PhD, a pioneer of personal genomics through his involvement with the Harvard Personal Genome Project at Harvard Medical School. In a press release announcing the launch of myGenome in 2016, Veritas described its system as “the world’s first whole genome for less than $1,000, including interpretation and genetic counseling.”
Church predicts that WGS will someday replace other genetic tests, such as the genotyping used by personal genomics and biotechnology company 23andMe.
“Companies like 23andMe that are based on genotyping technology basically opened the market over the last decade,” Martinez explained in an interview with WTF Health. “They’ve done an incredible job of getting awareness in the general population.”
However, he goes on to say, “In genotyping technology, you
are looking at very specific points of the genome, less than half of one
percent, a very small amount.”
Martinez says Veritas is sequencing all 6.4 billion letters
of the genome. And, with the new price point, “we’re closer to realizing that
seismic shift,” he said in the news release.
“This is the inflection point,” Martinez told CNBC.
“This is the point where the curve turns upward. You reach a critical mass when
you are able to provide a product that gives value at a specific price point.
This is the beginning of that. That’s why it’s seismic.”
Rodrigo Martinez (above), Veritas’ Chief Marketing and Design Officer, told CNBC, “The only way we’re going to be able to truly extract the value of the genome for a healthier society is going to be analyzing millions of genomes that have been sequenced. And the only way we can get there is by reducing the price so that more consumers can sequence their genome.” Photo copyright: Twitter.)
Payment Models Not Yet Established by Government, Private
Payers
However, tying WGS into personalized medicine that leads to actionable diagnoses may not be easy. Robin Bennett, PhD (hon.), a board certified senior genetic counselor and Professor of Medicine and Medical Genetics at UW School of Medicine, told CNBC, “[Healthcare] may be moving in that direction, but the payment for testing and for services, it hasn’t moved in the preventive direction. So, unless the healthcare system changes, these tests may not be as useful because … the healthcare system hasn’t caught up to say, ‘Yes, we support payment for this.’”
“Insurers are looking for things where, if you get the
information, there’s something you can do with it and that both the provider
and the patient are willing and able to use that information to do things that
improve their health,” Phillips told CNBC. “Insurers are very interested
in using genetic testing for prevention, but we need to . . . demonstrate that
the information will be used and that it’s a good trade-off between the
benefits and the costs.”
Sequencing for Free If You Share Your Data
Church may have an answer for that as well—get biopharmaceutical companies to foot the bill. Though Veritas’ new price for their myGenome service is significantly lower than before, it’s not free. That’s what Nebula Genomics, a start-up genetics company in Massachusetts co-founded by Church, offers people willing to share the data derived from their sequencing. To help biomedical researchers gather data for their studies, Nebula provides free or partially-paid-for whole-genome sequencing to qualified candidates.
“Nebula will enable individuals to get sequenced at much
lower cost through sequencing subsidies paid by the biopharma industry,” Church
told BioSpace.
“We need to bring the costs of personal genome sequencing close to zero to
achieve mass adoption.”
So, will lower-priced whole-genome sequencing catch on?
Perhaps. It’s certainly popular with everyday people who want to learn their
ancestry or predisposition to certain diseases. How it will ultimately affect
clinical laboratories and pathologists remains to be seen, but one thing is
certain—WGS is here to stay.
Next step is to design Web portal offering low-cost ‘polygenic risk score’ to people willing to upload genetic data received from DNA testing companies such as 23andMe
Their study, published last month in Nature Genetics, found that a genome analysis called polygenic risk scoring can identify individuals with a high risk of developing one of five potentially deadly diseases:
Polygenic Scoring Predicts Risk of Disease Among General Population
To date, most genetic testing has been “single gene,” focusing on rare mutations in specific genes such as those causing sickle cell disease or cystic fibrosis. This latest research indicates that polygenic predictors could be used to discover heightened risk factors in a much larger portion of the general population, enabling early interventions to prevent disease before other warning signs appear. The ultimate goal of precision medicine.
“We’ve known for long time that there are people out there at high risk for disease based just on their overall genetic variation,” senior author Sekar Kathiresan, MD, co-Director of the Medical and Population Genetics Program at the Broad Institute, and Director, Center for Genomic Medicine at Massachusetts General Hospital, said in a Broad Institute news release. “Now, we’re able to measure that risk using genomic data in a meaningful way. From a public health perspective, we need to identify these higher-risk segments of the population, so we can provide appropriate care.”
“What I foresee is in five years, each person will know this risk number—this ‘polygenic risk score’—similar to the way each person knows his or her cholesterol,” Sekar Kathiresan, MD (above), Co-Director of the Medical and Population Genetics Program at the Broad Institute, and Director, Center for Genomic Medicine at Massachusetts General Hospital, told the Associated Press (AP). He went on to say a high-risk score could lead to people taking other steps to lower their overall risk for specific diseases, while a low-risk score “doesn’t give you a free pass” since an unhealthy lifestyle can lead to disease as well. (Photo copyright: Massachusetts General Hospital.)
The researchers conducted the study using data from more than 400,000 individuals in the United Kingdom Biobank. They created a risk score for coronary artery disease by looking for 6.6 million single-letter genetic changes that are more prevalent in people who have had early heart attacks. Of the individuals in the UK Biobank dataset, 8% were more than three times as likely to develop the disease compared to everyone else, based on their genetic variation.
In absolute terms, only 0.8% of individuals with the very lowest polygenic risk scores had coronary artery disease, compared to 11% for people with the highest scores, the Broad Institute news release stated.
“The results should be eye-opening for cardiologists,” Charles C. Hong, MD, PhD, Director of Cardiovascular Research at the University of Maryland School of Medicine, told the AP. “The only disappointment is that this score applies only to those with European ancestry, so I wonder if similar scores are in the works for the large majority of the world population that is not white.”
In its news release, the Broad Institute noted the need for additional studies to “optimize the algorithms for other ethnic groups.”
The Broad Institute’s results suggest, however, that as many as 25 million people in the United States may be at more than triple the normal risk for coronary artery disease. And millions more may be at similar elevated risk for the other conditions, based on genetic variations alone.
Reanalyzing Data from DNA Testing Companies
The researchers are building a website that would enable users to receive a low-cost polygenic risk score—such as calculating inherited risk score for many common diseases—by reanalyzing data users previously receive from DNA testing companies such as 23andMe.
Kathiresan told Forbes his goal is for the 17 million people who have used genotyping services to submit their data to the web portal he is building. He told the magazine he’s hoping “people will be able to get their polygenic scores for about as much as the cost of a cholesterol test.”
Some Experts Not Impressed with Broad Institute Study
But not all experts believe the Broad Institute/MGH/Harvard Medical School study deserves so much attention. Ali Torkamani, PhD, Director of Genomics and Genome Informatics at the Scripps Research Translational Institute, offered a tepid assessment of the Nature Genetics study.
In an article in GEN that noted polygenic risk scores were receiving “the type of attention reserved for groundbreaking science,” Torkamani said the recent news is “not particularly” a big leap forward in the field of polygenic risk prediction. He described the results as “not a methodological advance or even an unexpected result,” noting his own group had generated similar data for type 2 diabetes in their analysis of the UK dataset.
Nevertheless, Kathiresan is hopeful the study will advance disease treatment and prevention. “Ultimately, this is a new type of genetic risk factor,” he said in the news release. “We envision polygenic risk scores as a way to identify people at high or low risk for a disease, perhaps as early as birth, and then use that information to target interventions—either lifestyle modifications or treatments—to prevent disease.”
This latest research indicates healthcare providers could soon be incorporating polygenic risking scoring into routine clinical care. Not only would doing so mean another step forward in the advancement of precision medicine, but clinical laboratories and pathology groups also would have new tools to help diagnose disease and guide treatment decisions.
New metalens technology from MGH and SEAS researchers gives greater endoscopic optical imaging resolution and sample detail for anatomic pathologists performing diagnostics
Anatomic pathologists and clinical laboratories know that biopsy samples are necessary to diagnose many diseases. But, current endoscopic imaging techniques used by physicians sometimes fail to clearly visualize disease sites. Consequently, biopsies collected during these procedures may make it harder for pathologists and physicians to diagnose certain diseases and health conditions.
That’s according to an article in Nature Photonics that reported on the research team’s study, published in Phys.org.
These nano-optics involved “flat metalenses” that promise to sharpen clarity and increase resolution of endoscopic imaging technology In turn, this contributes to more accurate pathology diagnostics and improve patient outcomes, while furthering the aims of precision medicine.
“Metalenses based on flat optics are a game changing new technology because the control of image distortions necessary for high resolution imaging is straightforward compared to conventional optics, which requires multiple complex shaped lenses,” Federico Capasso, PhD, Robert L. Wallace Professor of Applied Physics and Vinton Hayes Senior Research Fellow in Electrical Engineering at SEAS, and co-senior author of the study paper, told Nature Photonics. “I am confident that this will lead to a new class of optical systems and instruments with a broad range of applications in many areas of science and technology.”
The image above shows a flat metalens taken using a scanning electron microscope. Anatomic pathologists and medical laboratories will benefit from the better quality biopsy specimens collected because of the sharper clarity and increased resolution of endoscopes built with the new nano-optics. (Photo copyright: Harvard SEAS.)
Researchers demonstrated the nano-optic endoscope’s ability to deeply penetrate and capture images at high resolutions in various tissues, including:
Swine and sheep airways;
Human lung tissue; and,
Fruit flesh.
In the human lung tissue, “[T]he researchers were able to clearly identify structures that correspond to fine, irregular glands indicating the presence of adenocarcinoma, the most prominent type of lung cancer,” according to Phys.org.
Improving Endoscopic Imaging through Metalenses
The improved image resolution is due to the flat metalens configuration. “Currently, we are at the mercy of materials that we have no control over to design high-resolution lenses for imaging,” Yao-Wei Huang, PhD, Post-Doctoral Fellow at Harvard’s John A. Paulson School of Engineering and Applied Sciences and co-first author of the paper, told Phys.org.
Yao-Wei Huang, PhD (above), is a Post-Doctoral Fellow at Harvard’s John A. Paulson School of Engineering and Applied Sciences and co-first author of the study paper. “The main advantage of the metalens is that we can design and tailor its specifications to overcome spherical aberrations and astigmatism and achieve very fine focus of the light. As a result, we achieve very high resolution with extended depth of field without the need for complex optical components.” (Photo copyright: Harvard School of Engineering and Applied Sciences.)
The researchers note that current endoscopes using gradient-index (GRIN) lens-prism configurations and angle-polished ball lenses are used in a range of clinical applications due to their basic design. However, this benefit comes with shortfalls. “The ability of the nano-optic endoscope to obtain high-resolution images of sub-surface tissue structures in vivo is likely to increase the clinical utility of OCT [optical coherence tomography] in detection, diagnosis, and monitoring of diseases,” they state in their paper.
“The ability to control other properties of output light, such as the polarization state, enables a host of other applications—implausible to achieve using conventional catheters,” they continue. “Several tissues—such as smooth muscle, collagen (either innate or in fibrosis), and blood vessels—have constituent structures highly organized in one particular direction. Polarization-sensitive imaging can differentiate these structures from surrounding tissue by detecting their innate birefringence and optic axis.”
They further note that nano-optic endoscopes may yield benefits to other endoscopic optical imaging modalities such as confocal endomicroscopy.
Additional clinically-oriented studies will be required to assess how nano-optic endoscopes can elevate the capabilities of endoscopic OCT in examining fine pathological changes in luminal tissues.
Implications for Clinical Laboratories and Pathology Groups
The technology is still in the research stage with more trials needed to confirm the viability and accuracy of the approach. “This preclinical evaluation of the nano-optic endoscope indicated no significant flaws in the design for in vivo endoscopic imaging,” researchers note.
However, should nano-optic catheters gain clearance and change the endoscopy landscape as researchers predict, medical laboratories and pathologists might enjoy higher resolution images with greater information of the sample site—both key components of accurate diagnosis.
“Clinical adoption of many cutting-edge endoscopic microscopy modalities has been hampered due to the difficulty of designing miniature catheters that achieve the same image quality as bulky desktop microscopes,” Melissa Suter, PhD, Assistant Professor of Medicine at MGH and Harvard Medical School (HMS) and co-senior author of the study told Nature Photonics. “The use of nano-optic catheters that incorporate metalenses into their design will likely change the landscape of optical catheter design, resulting in a dramatic increase in the quality, resolution, and functionality of endoscopic microscopy. This will ultimately increase clinical utility by enabling more sophisticated assessment of cell and tissue microstructure in living patients.”
This research project at Massachusetts General Hospital and Harvard John A. Paulson School of Engineering and Applied Sciences is another example of how advances in technologies unrelated to surgical pathology can eventually contribute to improvements in how pathologists diagnose disease and help physicians identify the most promising therapies for their patients.
Wall Street Journal reports IBM losing Watson-for-Oncology partners and clients, but scientists remain confident artificial intelligence will revolutionize diagnosis and treatment of disease
What happens when a healthcare revolution is overhyped? Results fall short of expectations. That’s the diagnosis from the Wall Street Journal (WSJ) and other media outlets five years after IBM marketed its Watson supercomputer as having the potential to “revolutionize” cancer diagnosis and treatment.
“Watson can read all of the healthcare texts in the world in seconds,” John E. Kelly III, PhD, IBM Senior Vice President, Cognitive Solutions and IBM Research, told Wired in 2011. “And that’s our first priority, creating a ‘Dr. Watson,’ if you will.”
However, despite the marketing pitch, the WSJ investigation published in August claims IBM has fallen far short of that goal during the past seven years. The article states, “More than a dozen IBM partners and clients have halted or shrunk Watson’s oncology-related projects. Watson cancer applications have had limited impact on patients, according to dozens of interviews with medical centers, companies and doctors who have used it, as well as documents reviewed by the Wall Street Journal.”
Anatomic pathologists—who use tumor biopsies to diagnose cancer—have regularly wondered if IBM’s Watson would actually help physicians do a better job in the diagnosis, treatment, and monitoring of cancer patients. The findings of the Wall Street Journal show that Watson has yet to make much of a positive impact when used in support of cancer care.
The WSJ claims Watson often “didn’t add much value” or “wasn’t accurate.” This lackluster assessment is blamed on Watson’s inability to keep pace with fast-evolving treatment guidelines, as well as its inability to accurately evaluate reoccurring or rare cancers. Despite the more than $15 billion IBM has spent on Watson, the WSJ reports there is no published research showing Watson improving patient outcomes.
“The discomfort that I have—and that others have had with using it—has been the sense that you never know how much faith you can put in those results,” Wartman said.
Rudimentary Not Revolutionary Intelligence, STAT Notes
IBM’s Watson made headlines in 2011 when it won a head-to-head competition against two champions on the game show “Jeopardy.” Soon after, IBM announced it would make Watson available for medical applications, giving rise to the idea of “Dr. Watson.”
In a 2017 investigation, however, published on STAT, Watson is described as in its “toddler stage,” falling far short of IBM’s depiction of Watson as a “digital prodigy.”
“Perhaps the most stunning overreach is in [IBM’s] claim that Watson-for-Oncology, through artificial intelligence, can sift through reams of data to generate new insights and identify, as an IBM sales rep put it, ‘even new approaches’ to cancer care,” the STAT article notes. “STAT found that the system doesn’t create new knowledge and is artificially intelligent only in the most rudimentary sense of the term.”
STAT reported it had taken six years for data engineers and doctors to train Watson in just seven types of cancers and keep the system updated with the latest knowledge.
“IBM spun a story about how Watson could improve cancer treatment that was superficially plausible—there are thousands of research papers published every year and no doctor can read them all,” Howard told HealthNewsReview.org. “However, the problem is not that there is too much information, but rather there is too little. Only a handful of published articles are high-quality, randomized trials. In many cases, oncologists have to choose between drugs that have never been directly compared in a randomized trial.”
Howard argues the news media needs to do a better job vetting stories touting healthcare breakthroughs.
“Reporters are often susceptible to PR hype about the potential of new technology—from Watson to ‘wearables’—to improve outcomes,” Howard said. “A lot of stories would turn out differently if they asked a simple question: ‘Where is the evidence?’”
Peter Greulich, a retired IBM manager who has written extensively on IBM’s corporate challenges, told STAT that IBM would need to invest more money and people in the Watson project to make it successful—an unlikely possibility in a time of shrinking revenues at the corporate giant.
“IBM ought to quit trying to cure cancer,” he said. “They turned the marketing engine loose without controlling how to build and construct a product.”
AI Could Still Revolutionize Precision Medicine
Despite the recent negative headlines about Watson, AI continues to offer the promise of one day changing how pathologists and physicians work together to diagnose and treat disease. Isaac Kohane, MD, PhD, Chairman of the Biomedical Informatics Program at Harvard Medical School, told Bloomberg that IBM may have oversold Watson, but he predicts AI one day will “revolutionize medicine.”
“It’s anybody’s guess who is going to be the first to the market leader in this space,” he said. “Artificial intelligence and big data are coming to doctors’ offices and hospitals. But it won’t necessarily look like the ads on TV.”
How AI and precision medicine plays out for clinical laboratories and anatomic pathologists is uncertain. Clearly, though, healthcare is on a path toward increased involvement of computerized decision-making applications in the diagnostic process. Regardless of early setbacks, that trend is unlikely to slow. Laboratory managers and pathology stakeholders would be wise to keep apprised of these developments.
