The AI protein-structure-prediction system may ‘revolutionize life sciences by enabling researchers to better understand disease,’ researchers say
Genomics leaders watched with enthusiasm as artificial intelligence (AI) accelerated discoveries that led to new clinical laboratory diagnostic tests and advanced the evolution of personalized medicine. Now Google’s London-based DeepMind has taken that a quantum step further by demonstrating its AI can predict the shape of proteins to within the width of one atom and model three-dimensional (3D) structures of proteins that scientist have been trying to map accurately for 50 years.
Pathologists and clinical laboratory professionals know that it is estimated that there are around 30,000 human genes. But the human proteome has a much larger number of unique proteins. The total number is still uncertain because scientists continue to identify new human proteins. For this reason, more knowledge of the human protein is expected to trigger an expanding number of new assays that can be used by medical laboratories for diagnostic, therapeutic, and patient-monitoring purposes.
DeepMind’s AI tool is called AlphaFold and the protein-structure-prediction system will enable scientists to quickly move from knowing a protein’s DNA sequence to determining its 3D shape without time-consuming experimentation. It “is expected to accelerate research into a host of illnesses, including COVID-19,” BBC News reported.
This protein-folding breakthrough not only answers one of biology’s biggest mysteries, but also has the potential to revolutionize life sciences by enabling researchers to better understand disease processes and design personalized therapies that target specific proteins.
In November, DeepMind’s AlphaFold won the 14th Community Wide Experiment on Critical Assessment of Techniques for Protein Structure Prediction (CASP14), a biennial competition in which entrants receive amino acid sequences for about 100 proteins whose 3D structures are unknown. By comparing the computational predictions with the lab results, each CASP14 competitor received a global distance test (GDT) score. Scores above 90 out of 100 are considered equal to experimental methods. AlphaFold produced models for about two-thirds of the CASP14 target proteins with GDT scores above 90, a CASP14 press release states.
According to MIT Technology Review, DeepMind’s discovery is significant. That’s because its speed at predicting the structure of proteins is unprecedented and it matched the accuracy of several techniques used in clinical laboratories, including:
Unlike the laboratory techniques, which, MIT noted, are “expensive and slow” and “can take hundreds of thousands of dollars and years of trial and error for each protein,” AlphaFold can predict a protein’s shape in a few days.
“AlphaFold is a once in a generation advance, predicting protein structures with incredible speed and precision,” Arthur D. Levinson, PhD, Founder and CEO of Calico Life Sciences, said in a DeepMind blogpost. “This leap forward demonstrates how computational methods are poised to transform research in biology and hold much promise for accelerating the drug discovery process.”
Science reported that AlphaFold, which scored a median of 87—25 points above the next best predictions—did so well that CASP14 organizers worried DeepMind may have been somehow cheated. To validate the results, they asked AlphaFold to complete a “special challenge”—modeling a membrane protein from an ancient species of microbes called archaea, which they had been unable to model satisfactorily using X-ray crystallography. AlphaFold returned a detailed image of a three-part protein with two long helical arms in the middle. “It’s almost perfect,” Andrei Lupas, PhD, Director at the Max Planck Institute for Developmental Biology, told Science. “They could not possibly have cheated on this. I don’t know how they do it.” (Graphic copyright: DeepMind/Nature.)
“Even tiny rearrangements of these vital molecules can have catastrophic effects on our health, so one of the most efficient ways to understand disease and find new treatments is to study the proteins involved,” Moult said in the CASP14 press release. “There are tens of thousands of human proteins and many billions in other species, including bacteria and viruses, but working out the shape of just one requires expensive equipment and can take years.”
Science reported that the 3D structures of only 170,000 proteins have been solved, leaving roughly 200 million proteins that have yet to be modeled. Therefore, AlphaFold will help researchers in the fields of genomics, microbiomics, proteomics, and other omics understand the structure of protein complexes.
“Being able to investigate the shape of proteins quickly and accurately has the potential to revolutionize life sciences,” Andriy Kryshtafovych, PhD, Project Scientist at University of California, Davis, Genome Center, said in the press release. “Now that the problem has been largely solved for single proteins, the way is open for development of new methods for determining the shape of protein complexes—collections of proteins that work together to form much of the machinery of life, and for other applications.”
Clinical laboratories play a major role in the study of human biology. This breakthrough in genomics research and new insights into proteomics may provide opportunities for medical labs to develop new diagnostic tools and assays that better identify proteins of interest for diagnostic and therapeutic purposes.
Many companies want to adapt consumer wearables to monitor health conditions, including biomarkers tested by medical laboratories
Clinical laboratory managers know that wearable devices for monitoring biophysical functions or measuring biomarkers are becoming more complex and capable thanks to advances in miniaturization, informatics, software, and artificial intelligence machine learning that enable new functions to be developed and proved to be accurate.
In September, Fitbit (NYSE:FIT), took that a step further. The San Francisco-based maker of personal fitness technology, “received 510(k) clearance from the US Food and Drug Administration (FDA), as well as Conformité Européenne (CE marking) in the European Union, for its electrocardiogram (ECG) app to assess heart rhythm for atrial fibrillation (AFib),” according to a press release.
The fact that Google is currently in the process of acquiring Fitbit for $2.1 billion may indicate that wearable devices to help physicians and patients diagnose and monitor health conditions will be big business in the future.
The new ECG app is available on Fitbit Sense (above), an “advanced health smartwatch.” To use the app, wearers place their finger and thumb to the stainless-steel corners on the watch and remain still for 30 seconds. The app analyzes the heart’s rhythm for signs of AFib. Individuals can take readings of their heart rhythm at any time, monitor for irregularities, and save and share the data. (Photo copyright: Fitbit.)
Helping Doctors ‘Stay Better Connected’ to Their Patients
“Helping people understand and manage their heart health has always been a priority for Fitbit, and our new ECG app is designed for those users who want to assess themselves in the moment and review the reading later with their doctor,” said Eric Friedman, Fitbit co-founder and Chief Technology Officer, in the press release.
Prior to submitting the device for approval to regulatory agencies, Fitbit conducted the clinical trial in regions throughout the US to evaluate the device’s ability to accurately detect AFib from normal sinus rhythm and generate ECG traces. The researchers proved that their algorithm was able to detect 98.7% of AFib cases (sensitivity) and was able to accurately identify normal sinus rhythms (specificity) in 100% of the cases.
Venkatesh Raman, MD, interventional cardiologist and Medical Director of the Cardiac Catheterization Lab at 609-bed MedStar Georgetown University Hospital, was Principal Investigator for the clinical study on Fitbit’s ECG app. “Physicians are often flying blind as to the day-to-day lives of our patients in between office visits. I’ve long believed in the potential for wearable devices to help us stay better connected, and use real-world, individual data to deliver more informed, personalized care,” he said in the press release.
“Given the toll that AFib continues to take on individuals and families around the world,” Raman continued, “I’m very enthusiastic about the potential of this tool to help people detect possible AFib—a clinically important rhythm abnormality—even after they leave the physician’s office.”
Fitbit ECG App Receives European CE Marking
In addition to receiving approval for the Fitbit ECG app in the US, the device also received CE marking (Conformité Européenne) for use in some European countries.
In October 2020, the app was made available to Fitbit Sense users in the US, Austria, Belgium, Czech Republic, France, Germany, Ireland, Italy, Luxembourg, the Netherlands, Poland, Portugal, Romania, Spain, Sweden, Switzerland, and the United Kingdom. The device also received approval for use in Hong Kong and India.
It is estimated that more than 33.5 million people globally have AFib, an irregular heart rhythm (arrhythmia) that can lead to stroke, blood clots, or heart failure. The American Heart Association estimates that at least 2.7 million Americans currently live with the condition. The most common symptoms experienced by those with the condition are:
Irregular heartbeat,
Heart palpitations (rapid, fluttering, quivering or pounding),
Lightheadedness,
Extreme fatigue,
Shortness of breath, and
Chest pain.
Risk factors for AFib include advancing age, high blood pressure, obesity, diabetes, European ancestry, hyperthyroidism, chronic kidney disease, alcohol use, smoking, and known heart issues such as heart failure, ischemic heart disease, and enlargement of the chambers on the left side of the heart.
According to the Centers for Disease Control and Prevention (CDC), there are more than 454,000 hospitalizations annually in the US that list AFib as the primary diagnosis. In 2018, AFib was mentioned on 175,326 death certificates with the condition being the underlying cause of death in 25,845 of those cases.
The CDC reports that cases are increasing and projects that by 2030 12.1 million people in the US will have AFib. Many people are asymptomatic of the illness and do not know they have it, which can make AFib more difficult to diagnose.
“Early detection of AFib is critical, and I’m incredibly excited that we are making these innovations accessible to people around the world to help them improve their heart health, prevent more serious conditions, and potentially save lives,” Friedman said, in a statement.
Clinical laboratory managers should monitor these developments closely. Fitbit’s FDA clearance and CE Marking of its ECG app suggest this trend is accelerating.
Privacy concerns have one tech giant suggesting alternatives to sharing potentially identifiable location tracking data
Expect an interesting debate on the use of location tracking as a way to manage this and future pandemics. It is a debate that has implications for clinical laboratories. After all, if location tracking identifies individuals who may have been exposed to an infectious disease, will health authorities want those individuals to be immediately tested?
Location tracking has been around for quite some time. Anyone who owns a smartphone knows that digital map and navigation software applications (apps) locate our position and track our movements. That’s how they work. Maps are good. But does collecting and sharing location tracking data violate personal privacy laws that some Silicon Valley tech giants want to use to help public health officials track disease? Maybe.
Google, Facebook, and other tech companies have been talking to the US federal government about ways to use location tracking data from smartphones and online software applications to combat the spread of SARS-CoV-2, the coronavirus that causes the COVID-19 illness, reported the Washington Post.
The tracking data could be used by public health officials
to spot disease outbreaks in populations and predict how it might spread. Analyzing
the data generated by smartphone tracking and reporting apps also could be used
to identify individuals who may have been exposed to the coronavirus, and who should
get clinical laboratory tests to determine if they need medical intervention.
However, Google is apparently resistant to using its collected location data to track and identify individuals. Instead, Google Health’s Head of Communications and Public Affairs, Johnny Luu, said Google was “exploring ways that aggregated anonymized location information could help in the fight against COVID-19. One example could be helping health authorities determine the impact of social distancing, similar to the way we show popular restaurant times and traffic patterns in Google Maps,” said Luu in a statement. He stressed, though, that any such arrangement “would not involve sharing data about any individual’s location, movement, or contacts,” reported the Washington Post.
Can Privacy be Maintained While Tracking Disease?
Google’s sister company, Verily, launched a screening website in March for people who believe they may have COVID-19. The pilot program is only available to some California residents. Users of the service complete a series of online questions to determine their coronavirus risk and whether or not they should seek medical attention.
To use the service, individuals must log into the site using
a Google account and sign a consent authorization form which states data
collected may be shared with public health officials, a move that has received
criticism.
Jacob Snow, JD, a technology and civil liberties attorney with the American Civil Liberties Union (ACLU) of Northern California, expressed concerns about Verily’s program. “COVID-19 testing is a vital public necessity right now—a core imperative for slowing this disease,” he told CNET. “Access to critical testing should not depend on creating an account and sharing information with what is, essentially, an advertising company.
“This is how privacy invasions have the potential to
disproportionately harm the vulnerable,” he continued. “Google should release
this tool without those limits, so testing can proceed as quickly as possible.”
Facebook, on the other hand, has had a Disease Prevention Map program in place for about a year. This program provides location information provided by individuals who choose to participate to health organizations around the globe.
“Disease prevention maps have helped organizations respond to health emergencies for nearly a year and we’ve heard from a number of governments that they’re supportive of this work,” said Laura McGorman, Policy Lead, Data for Good at Facebook, in a statement, reported CNET. “In the coronavirus context, researchers and nonprofits can use the maps, which are built with aggregated and anonymized data that people opt in to share, to understand and help combat the spread of the virus.”
Researchers at Carnegie Mellon University worked with Facebook to create the COVID-19 Symptom Map (above), which is based on aggregated data drawn from self-reported symptoms Facebook. The map, which updates regularly, is viewable by day, counties, hospital referral regions, and COVID-19 symptoms. “This is work that social networks are well-situated to do. By distributing surveys to large numbers of people whose identities we know, we can quickly generate enough signal to correct for biases and ensure sampling is done properly,” wrote Mark Zuckerberg, Facebook founder and CEO, in a Washington Post op-ed about the Carnegie Mellon’s results, reported MobiHealthNews. (Graphic copyright: Facebook/Business Insider.)
Privacy Organizations Voice Concerns
Privacy and civil liberties issues regarding the collection
and use of smartphone data to curtail the pandemic are of concern to some organizations.
There may be legal and ethical implications present when using personal data in
this manner.
Al Gidari, JD, Director of Privacy, Center for Internet and Society at Stanford University Law School, says the balance between privacy and pandemic policy is a delicate one, reported the Washington Post. “The problem here is that this is not a law school exam. Technology can save lives, but if the implementation unreasonably threatens privacy, more lives may be at risk,” he said.
In response to public privacy concerns following the Washington
Post’s report, representatives for Google and Facebook said the companies
have not shared any aggregated and anonymized data with the government
regarding contact
tracing and COVID-19, reported the Washington Post.
Google reiterated that any related projects are still in their early stages and that they are not sure what their participation level might look like. And, CEO Mark Zuckerberg stated that Facebook “isn’t prepared to turn over people’s location data en masse to any governments for tracking the coronavirus outbreak,” reported CNET.
“I don’t think it would make sense to share people’s data in a way where they didn’t have the opportunity to opt in to do that,” Zuckerberg said.
The potential use of location tracking data, when combined
with other information, is one example of how technology can leverage non-medical
information and match it with clinical data to watch population trends.
As of April 23, there were 2,637,911 confirmed cases of COVID-19 and 184,235 deaths from the coronavirus worldwide, according to www.worldometers.info/coronavirus. And, cases of coronavirus disease have been reported in 213 countries according to the World Health Organization (WHO).
As testing increases, more cases will be reported and it is
unknown how long the virus will continue to spread, so advocates of location
tracking and similar technologies that can be brought to bear to save lives during
a disease outbreak may be worth some loss of privacy.
Pathologists and medical laboratory professionals may want
to monitor the public debate over the appropriate use of location tracking.
After all, at some future point, clinical laboratory test results of
individuals might be added to location tracking programs to help public health
authorities better monitor where disease outbreaks are occurring and how they are
spreading.
Strategists agree that big tech is disrupting healthcare,
so how will clinical laboratories and anatomic pathology groups serve virtual
healthcare customers?
Visionary XPRIZE founder Peter Diamandis, MD, sees big tech as “the doctor of the future.” In an interview with Fast Company promoting his new book, “The Future Is Faster Than You Think,” Diamandis, who is the Executive Chairman of the XPRIZE Foundation, said that the healthcare industry is “phenomenally broken” and that Apple, Amazon, and Google could do “a thousandfold” better job.
Diamandis, who also founded Singularity University, a global learning and innovation community that uses exponential technologies to tackle worldwide challenges, according to its website, said, “We’re going to see Apple and Amazon and Google and all the data-driven companies that are in our homes right now become our healthcare providers.”
If this prediction becomes reality, it will bring significant changes in the traditional ways that consumers and patients have selected providers and access healthcare services. In turn, this will require all clinical laboratories and pathology groups to develop business strategies in response to these developments.
Amazon Arrives in Healthcare Markets
Several widely-publicized business initiatives by Amazon, Google, and Apple substantiate these predictions. According to an Amazon blog, healthcare insurers, providers, and pharmacy benefit managers are already operating HIPAA-eligible Amazon Alexa for:
Alexa also enables HIPAA-compliant blood glucose updates as part of the Livongo for Diabetes program. “Our members now have the ability to hear their last blood glucose check by simply asking Alexa,” said Jennifer Schneider, MD, President of Livongo, a digital health company, in a news release.
And Cigna’s “Answers By Cigna” Alexa “skill” gives members who install the option responses to 150 commonly asked health insurance questions, explained a Cigna news release.
“Google plans to disrupt healthcare and use data and artificial intelligence,” Toby Cosgrove, Executive Advisor to the Google Cloud team and former Cleveland Clinic President, told B2B information platform PYMNTs.com.
PYMNTs speculated that Google, which recently acquired Fitbit, could be aiming at connecting consumers’ Fitbit fitness watch data with their electronic health records (EHRs).
“Ultimately what’s best is human and AI collaboratively,” Peter Diamandis, MD, founder of XPRIZE Foundation and Singularity University told Fast Company. “But I think for reading x-rays, MRIs, CT scans, genome data, and so forth, that once we put human ego aside, machine learning is a much better way to do that.” (Photo copyright: SALT.)
Apple Works with Insurers, Integrating Health Data
The Apple Watch health app also enables people to access medical laboratory test results and vaccination records, and “sync up” information with some hospitals, Business Insider explained.
Virtual Care, a Payer Priority: Survey
Should healthcare providers feel threatened by the tech giants? Not necessarily. However, employers and payers surveyed by the National Business Group on Health (NBGH), an employer advocacy organization, said they want to see more virtual care solutions, a news release stated.
“One of the challenges employers face in managing their healthcare costs is that healthcare is delivered locally, and change is not scalable. It’s a market-by-market effort,” said Brian Marcotte, President and CEO of the NBGH, in the news release. “Employers are turning to market-specific solutions to drive meaningful changes in the healthcare delivery system.
“Virtual care solutions bring healthcare to the consumer
rather than the consumer to healthcare,” Marcotte continue. “They continue to
gain momentum as employers seek different ways to deliver cost effective,
quality healthcare while improving access and the consumer experience.”
“In AI, there are three trends to watch,” said health strategist Ted Schwab (above) while speaking at the 2019 Executive War College. “The first major AI trend will affect clinical laboratories and pathologists. It involves how diagnosis will be done on the Internet and via telehealth. The second AI trend is care delivery, such as what we’ve seen with Amazon’s Alexa—you should know that Amazon’s business strategy is to disrupt healthcare. And the third AI trend involves biological engineering,” he concluded. (Photo copyright: Dark Daily.)
“If you use Google in the United States to check symptoms,
you’ll get five-million to 11-million hits,” Schwab told The Dark Report.
“Clearly, there’s plenty of talk about symptom checkers, and if you go online
now, you’ll find 350 different electronic applications that will give you
medical advice—meaning you’ll get a diagnosis over the internet. These
applications are winding their way somewhere through the regulatory process.
“The FDA just released a report saying it plans to regulate
internet doctors, not telehealth doctors and not virtual doctors,” he
continued. “Instead, they’re going to regulate machines. This news is
significant because, today, within an hour of receiving emergency care, 45% of
Americans have googled their condition, so the cat is out of the bag as it
pertains to us going online for our medical care.”
Be Proactive, Not Reactive, Health Leaders Say
Healthcare leaders need to work on improving access to primary care, instead of becoming defensive or reactive to tech companies, several healthcare CEOs told Becker’s Hospital Review.
Clinical laboratory leaders are advised to keep an eye on
these virtual healthcare trends and be open to assisting doctors engaged in
telehealth services and online diagnostic activities.
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.
