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.
The 80 scientists and engineers that comprise the consortium believe synthetic biology can address key challenges in health and medicine, but technical hurdles remain
Synthetic biology now has a 20-year development roadmap. Many predict this fast-moving field of science will deliver valuable products that can be used in diagnostics—including clinical laboratory tests, therapeutics, and other healthcare products.
Eighty scientists from universities and companies around the world that comprise the Engineering Biology Research Consortium (EBRC) recently published the 20-year roadmap. They designed it to “provide researchers and other stakeholders (including government funders)” with what they hope will be “a go-to resource for engineering/synthetic biology research and related endeavors,” states the EBRC Roadmap website.
Medical laboratories and clinical pathologists may soon have new tools and therapies for targeting specific diseases. The EBRC defines synthetic biology as “the design and construction of new biological entities such as enzymes, genetic circuits, and cells or the redesign of existing biological systems. Synthetic biology builds on the advances in molecular, cell, and systems biology and seeks to transform biology in the same way that synthesis transformed chemistry and integrated circuit design transformed computing.”
Synthetic biology is an expanding field and there are predictions that it may produce research findings that can be adapted for use in clinical pathology diagnostics and treatment for chronic diseases, such as cancer.
Another goal of the roadmap is to encourage federal
government funding for synthetic biology.
“The question for government is: If all of these avenues are now open for biotechnology development, how does the US stay ahead in those developments as a country?” said Douglas Friedman, EBRC’s Executive Director, in a news release. “This field has the ability to be truly impactful for society and we need to identify engineering biology as a national priority, organize around that national priority, and take action based on it.”
Designing or Redesigning Life Forms for Specific
Applications
Synthetic biology is an interdisciplinary field that combines
elements of engineering, biology, chemistry, and computer science. It enables
the design and construction of new life forms—or redesign of existing ones—for
a multitude of applications in medicine and other fields.
Another recent example comes from the Wyss Institute at Harvard. Scientist there developed a direct-to-consumer molecular diagnostics platform called INSPECTR that, they say, uses programmable synthetic biosensors to detect infectious pathogens or host cells.
The Wyss Institute says on its website that the platform can
be packaged as a low-cost, direct-to-consumer test similar to a home pregnancy
test. “This novel approach combines the specificity, rapid development, and
broad applicability of a molecular diagnostic with the low-cost, stability, and
direct-to-consumer applicability of lateral flow immunoassays.”
In March, Harvard announced that it had licensed the technology to Sherlock Biosciences.
Howard Salis, PhD (above), Associate Professor of biological engineering and chemical engineering at Pennsylvania State University (Penn State), co-chaired the EBRC Roadmapping Working Group that produced the roadmap. In a Penn State news story, Salis explained synthetic biology’s potential. “There are both traditional and startup companies leveraging synthetic biology technologies to develop novel biotech products,” he said. “Organisms that produce biorenewable materials; diagnostics to detect the Zika virus, Ebola and tuberculosis; and soil bacteria that fix nitrogen into ammonia for improved plant growth.” (Photo copyright: Twitter.)
Fundamental Challenges with Synthetic Biology
The proponents of synthetic biology hope to make it easier
to design and build these systems, in much the same way computer engineers
design integrated circuits and processors. The EBRC Roadmap may help scientist
worldwide achieve this goal.
However, in “What is Synthetic/Engineering Biology?” the EBRC also identifies the fundamental challenges facing the field. Namely, the complexity and unpredictability inherent in biology, and a limited understanding of how biological components interact.
The EBRC roadmap report, “Engineering Biology: A Research
Roadmap for the Next-Generation Bioeconomy,” covers five categories of applications:
Health and medicine are of primary interest to pathologists.
Synthetic Biology in Health and Medicine
The Health and Medicine section of the report identifies
four broad societal challenges that the EBRC believes can be addressed by
synthetic biology. For each, the report specifies engineering biology
objectives, including efforts to develop new diagnostic technologies. They
include:
Existing and emerging infectious diseases: Objectives include development of tools for treating infections, improving immunity, reducing dependence on antibiotics, and diagnosing antimicrobial-resistant infections. The authors also foresee tools for rapid characterization and response to “known and unknown pathogens in real time at population scales.”
Non-communicable diseases and disorders, including cancer, heart disease, and diabetes: Objectives include development of biosensors that will measure metabolites and other biomolecules in vivo. Also: tools for identifying patient-specific drugs; tools for delivering gene therapies; and genetic circuits that will foster tissue formation and repair.
Environmental health threats, such as toxins, pollution, and injury: Objectives include systems that will integrate wearable tech with living cells, improve interaction with prosthetics, prevent rejection of transplanted organs, and detect and repair of biochemical damage.
Healthcare access and personalized medicine: The authors believe that synthetic biology can enable personalized treatments and make new therapies more affordable.
Technical Themes
In addition to these applications, the report identifies
four “technical themes,” broad categories of technology that will spur the
advancement of synthetic biology:
Gene editing, synthesis, and assembly: This refers to tools for producing chromosomal DNA and engineering whole genomes.
Biomolecule, pathway, and circuit engineering: This “focuses on the importance, challenges, and goals of engineering individual biomolecules themselves to have expanded or new functions,” the roadmap states. This theme also covers efforts to combine biological components, both natural and non-natural, into larger, more-complex systems.
Host and consortia engineering: This “spans the development of cell-free systems, synthetic cells, single-cell organisms, multicellular tissues and whole organisms, and microbial consortia and biomes,” the roadmap states.
Data Integration, modeling, and automation: This refers to the ability to apply engineering principles of Design, Build, Test and Learn to synthetic biology.
The roadmap also describes the current state of each
technology and projects likely milestones at two, five, 10, and 20 years into
the future. The 2- and 5-year milestones are based on “current or recently
implemented funding programs, as well as existing infrastructure and facilities
resources,” the report says.
The longer-term milestones are more ambitious and may
require “significant technical advancements and/or increased funding and
resources and new and improved infrastructure.”
Synthetic biology is a significant technology that could
bring about major changes in clinical pathology diagnostics and treatments.
It’s well worth watching.
At The Dark Report’s annual Lab Quality Confab for clinical laboratory administrators, managers, and quality team members, experts outline how disruption in healthcare requires labs to improve processes and cut costs
This is an opportunity for clinical laboratory directors,
pathologists, and other lab professionals, to comment on the proposed revisions
to CLIA before or during the upcoming CLIAC meeting on Nov. 6.
The agenda for the meeting is posted on the CDC’s website.
Public to be Heard on CLIA Regulations
“For the first time in its 26-year history, the council has
called for three workgroups to address how to revise CLIA,” Salerno said. The
workgroups will address these topics:
“It’s a dramatic step for the government to ask the
laboratory community how to revise the CLIA regulations,” Salerno commented.
Chartered in 1992, the advisory council meets twice a year, once in April and
once in November.
In the coming weeks, Dark Daily will publish more
information on how clinical laboratory professionals can comment on the
important issue of CLIA revisions.
Digital slides from Salerno’s keynote address are posted on LQC’s presentations website.
Clinical Laboratory Testing is Increasing in Value,
Keynote Speaker Says
As a service to clinical laboratories, Salerno outlined many
of the services the CDC’s Division of Laboratory Systems provides for free to
clinical labs, including information on such topics as:
During his remarks at the 13th Annual Lab Quality Confab in Atlanta, Salerno had good news for the clinical laboratory professionals in attendance. He said that lab testing was becoming a more valued commodity in healthcare because physicians and other providers were growing increasingly confident in lab test results. [Photo copyright: The Dark Report.]
Healthcare System Disruption Impacts Providers, Including
Clinical Laboratories
Other keynote speakers addressed how disruption in the US
healthcare systems affects provider organizations in significant ways. For
clinical laboratories, such disruption has resulted in reduced payment and
demands for quality improvement and shorter turnaround times.
For all these reasons, quality
management systems may be every clinical laboratory’s best strategy to
survive and thrive, the keynote speakers said.
The first keynoter was Robert L. Michel, Editor-in-Chief and Publisher of The Dark Report. Michel’s remarks focused on how price cuts from Medicare, Medicaid, private payers, and the drive for value-based payment, are requiring labs to do more with less. For this reason, quality management systems are necessary for all labs seeking to improve results, eliminate errors, and cut costs, he said.
“The people closest to the work know how to fix these
problems,” he added. “That’s why labs know they must train their staff to
identify problems and then report them up the chain so they can be fixed,”
Michel commented. “Labs that are best at listening to their employees are
getting very good at identifying problems by measuring results and monitoring
and reporting on their own performance.”
Michel identified three principle factors that are
disrupting healthcare:
The shift from reactive care in which the health system cares for sick patients to proactive care in which the health system aims to keep patients healthy and out of the hospital and other costly sites of care.
The transition away from fee-for-service payment that encourages providers to do more for patients, whether more care is needed or not, to value-based payment that aims to reward providers for keeping patients healthy.
The consolidation among hospitals, health systems, physicians, and other providers. A trend that requires clinical laboratories to find new partners and new ways to improve lab services and reduce costs.
Informatics Performance Data Help Clinical Laboratories
Respond to Change
“The attributes of new and successful labs are that they will have faster workflow and shorter cycle times for clinical lab tests and anatomic pathology specimen results,” Michel explained. “That means that labs will attack non-value-added processes by implementing continuous improvement strategies [such as Lean and Six Sigma] and by the sophisticated use of informatics.”
Making use of performance data enables clinical laboratory
directors to make changes in response to disruptions that affect healthcare.
“If you have good informatics, then seven or eight of every 10 decisions you
make will be good decisions, and with the other two and three decisions, you’ll
have time to pull back and adjust,” Michel commented.
The second keynote speaker, Jeremy Schubert, MBA, MPH, Division Vice President of Abbott, reiterated what Michel said about how the health system is moving away from fee-for-service payment. Instead of focusing on caring for sick patients exclusively, he said, health insurers are paying all healthcare providers to keep patients healthy.
“Healthcare today is about the whole life course of the
individual,” Schubert explained. “Patients no longer want healthcare only when
they’re sick. Instead, they want to be healthy. And health creation is not just
about a person’s physical health. It’s about their mental health, their
emotional health, and their social wellbeing.
“In fact,” he continued, “you can learn more about a
person’s health from their Zip code than from their genetic code.”
That is essentially what TriCore Reference Laboratories (TriCore) has been doing in New Mexico, Schubert added. During his presentation, Michel mentioned TriCore as being one of four clinical laboratories participating in Project Santa Fe, a non-profit organization that promotes the movement from Clinical Lab 1.0 to Clinical Lab 2.0. (See “TriCore Forges Ahead to Help Payers Manage Population Health,” The Dark Report, May 20, 2019.)
“If you want to be a quality engine in healthcare you have
to be operating at Lab 2.0. Who is best qualified to interpret information?
It’s the lab,” Schubert said. Then he challenged labs to begin pursuing the
goal of achieving Lab 3.0, saying “Lab 3.0 is being able to interface with the
patient to address each patient’s problems.”
The 13th Annual Lab Quality Confab (LQC) in Atlanta continues through the 17th with post-event workshops in Six Sigma and mastering quality management systems. In attendance are 300 clinical laboratory administrators, managers, and quality team members who are learning a complete array of professional training methods.
To register to attend, click here or enter https://www.labqualityconfab.com/register into your browser, or call 707-829-9485, or e-mail lqcreg@amcnetwork.com.
As demand rises, Canadian clinical laboratories must learn to juggle test systems automation, funding challenges, and staffing shortages
Canada’s clinical laboratories are deeply affected by many of the trends impacting the Canadian healthcare system overall. Deployment of new technologies, such as test automation and artificial intelligence (AI) for example, are forcing Canadian labs to adapt during times of changing demographics and funding pressures.
Thus, the Canadian Diagnostic Executive Forum (CDEF), which takes place October 24-25 at the Westin Harbour Castle Hotel in Toronto, will provide an opportunity for clinical laboratory leaders to learn how to leverage technology and create positive change in their medical laboratory operations.
Change Management and Clinical Laboratory Leaders
The development of disruptive new technologies is becoming the norm and the laboratory’s role in healthcare delivery is growing. That’s why change management has become a focus of clinical laboratory leaders.
Sheila Woodcock, Convenor, WG 1 Quality and Competence in the Medical Laboratory at ISO/TC 212, and President and Principal Consultant at QSE Consulting Inc., Nova Scotia, Canada, says “allocation of resources” is a challenge for senior diagnostic executives juggling financial, technology, and staffing decisions.
In an exclusive interview with Dark Daily, Woodcock
said, “The number one lab challenge today is not having enough money; second is
not having enough people. Because if you don’t have enough money, even if there
are people out there, you can’t hire them. Money, people, and trying to keep up
with all the technological innovations bombarding us nowadays are the main
reasons to make changes.”
From deployment of digital pathology services and point-of-care (POC) testing to the introduction of automation and AI, innovation is happening at a rapid pace. It may or may not increase medical laboratory efficiency or support precision medicine, but it definitely alters laboratory infrastructure.
“Change is nearly constant in the clinical laboratory and
the healthcare network worlds, and there are many complexities that go with
that,” Woodcock said. “With the implementation of new technologies, and the
rapidly advancing world of automation in clinical laboratories that have never before
been automated, how do we ensure that when we automate new technology it
doesn’t negatively impact the quality of the testing process?”
Disruptive Changes are Redefining Clinical Laboratories
As Clinical Lab Products (CLP) points out, medical laboratories have become a reservoir of data that can “guide fact-based decisions to improve operational, financial, and clinical performance throughout their institutions.” As a result, clinical laboratories are increasingly shedding their “traditional and narrowly defined roles” in which “physicians order tests and labs report results.”
Emerging technologies also are ushering change outside of the medical laboratory. Drones soon may routinely transport patient specimens across healthcare networks. Dark Daily has reported on several new drone transport systems under development around the globe. One such system in the US involves UPS, the FAA, and WakeMed. Such high-tech specimen tracking and delivery systems could lead to fewer spoiled samples and possibly save lives, and clinical laboratories are at the heart of these innovations.
Kevin D. Orr (above), Senior Director, Hospital Business at In-Common Laboratories, told Dark Daily that laboratory leaders need to keep up with technology breakthroughs. However, knowing which tools and strategies are worth implementing is not so easy. Orr says diagnostic executives should take advantage of opportunities to “network to understand what is going on in everybody’s backyard, and to leverage some of the strategies, tools, and technologies innovators have used elsewhere.” (Photo copyright: LinkedIn.)
Kevin D. Orr, Senior Director, Hospital Business at In-Common Laboratories, believes technology may help laboratories overcome one major issue—a growing demand for testing services at a time when the laboratory workforce is shrinking, and provincial and territorial global funding is not keeping pace with diagnostic utilization rates. Orr points to digital pathology as an example of a technology that may enable labs to “do more with less” in terms of both funding and staffing.
“As people get older, there’s more demand for healthcare
services and because of that more clinical laboratory testing has to be done,”
Orr told Dark Daily. “The peak of the Baby Boomers is starting to get
sick now. We need to focus on innovations and technologies clinical
laboratories are employing to address the overarching issue of doing more with
less.”
How Clinical Laboratories Should Demonstrate Value
Woodcock, however, maintains that clinical laboratories also
need to do a better job of lobbying for funding, so they have the money needed
to implement new technologies.
“Traditionally, when labs are told they have cutbacks, they
do their utmost to work within what they have been assigned. But other
departments might be jumping up and down, getting more attention, and getting
more funding,” she said. “One of the things lab people have to learn—and are
getting better at as time goes on—is giving the lab a voice and making known
the contributions the lab makes to diagnosis and treatment of patients in a
facility.”
The Canadian Diagnostic Executive Forum on October 24-25 at
the Westin Harbour Castle Hotel in Toronto provides such an opportunity for
laboratory leaders to learn how to leverage technology to create positive
change in lab operations.
“We want to inspire people,” Orr told Dark Daily. “We
want people to leave this conference excited about what diagnostics is doing
and where it’s headed and what other people are doing. We want to show them the
bright light at the end of the tunnel, because sometimes when you’re dealing
with the negative aspects of no money or no staff or no this or that, it gets
pretty awful. We want to breathe some life and show them the rainbow and that the
light at the end of the tunnel could be just around the corner.”
The CDEF conference will be hosted by In-Common Laboratories, in conjunction with The Dark Report, Dark Daily’s sister publication. This two-day event will be packed with thought-provoking sessions on digital pathology, next-generation technology, precision medicine, blockchain, sample tracking, and artificial intelligence, as well as updates from across Canada on the latest innovations and technologies being implemented in medical laboratories.
The UE study sheds light on the types of bacteria in
wastewater that goes down hospital pipes to sewage treatment plants. The study
also revealed that not all infectious agents are killed after passing through
waste treatment plants. Some bacteria with antimicrobial (or antibiotic)
resistance survive to enter local food sources.
The scientists concluded that the amount of AMR genes found
in hospital wastewater was linked to patients’ length-of-stays and consumption
of antimicrobial resistant bacteria while in the hospital.
In a paper the University of Edinburgh published on medRxiv, the researchers wrote: “There was a higher abundance of antimicrobial-resistance genes in the hospital wastewater samples when compared to Seafield community sewage works … Sewage treatment does not completely eradicate antimicrobial-resistance genes and thus antimicrobial-resistance genes can enter the food chain through water and the use of [processed] sewage sludge in agriculture. As hospital wastewater contains inpatient bodily waste, we hypothesized that it could be used as a representation of inpatient community carriage of antimicrobial resistance and as such may be a useful surveillance tool.”
Additionally, they wrote, “Using metagenomics to identify
the full range of AMR genes in hospital wastewater could represent a useful
surveillance tool to monitor hospital AMR gene outflow and guide environmental
policy on AMR.”
Antimicrobial stewardship programs are becoming increasingly critical to preventing the spread of AMR bacteria. “By having those programs, [there are] documented cases of decreased antibiotic resistance within organisms causing these infections,” Paul Fey, PhD, of the University of Nebraska Medical Center, told MedPage Today. “This is another indicator of how all hospitals need to implement stewardship programs to have a good handle on decreasing antibiotic use.” [Photo copyright: University of Nebraska.]
Don’t Waste the Wastewater
Antibiotic resistance occurs when bacteria change in response to medications to prevent and treat bacterial infections, according to a World Health Organization (WHO) fact sheet. The CDC estimates that more than 23,000 people die annually from two million antibiotic-resistance infections.
Wastewater, the UE scientists suggest, should not go to
waste. It could be leveraged to improve hospitals’ detection of patients with antimicrobial
resistance, as well as to boost environment antimicrobial-resistance polices.
They used metagenomics (the study of genetic material
relative to environmental samples) to compare the antimicrobial-resistance
genes in hospital wastewater against wastewater from community sewage
points.
The UE researchers:
First collected samples over a 24-hour period from various areas in a tertiary hospital;
They then obtained community sewage samples from various locations around Seafield, Scotland;
Antimicrobial-resistance genes increased with longer length of patient stays, which “likely reflects transmission amongst hospital inpatients,” researchers noted.
Fey suggests that further research into using sequencing
technology to monitor patients is warranted.
“I think that monitoring each patient and sequencing their
bowel flora is more likely where we’ll be able to see if there’s a significant
carriage of antibiotic-resistant organisms,” Fey told MedPage Today. “In
five years or so, sequencing could become so cheap that we could monitor every
patient like that.”
Fey was not involved in the University of Edinburgh
research.
Given the rate at which AMR bacteria spreads, finding antibiotic-resistance
genes in hospital wastewater may not be all that surprising. Still, the University
of Edinburgh study could lead to cost-effective ways to test the genes of
bacteria, which then could enable researchers to explore different sources of
infection and determine how bacteria move through the environment.
And, perhaps most important, the study suggests clinical
laboratories have many opportunities to help eliminate infections and slow
antibiotic resistance. Microbiologists can help move their organizations forward
too, along with infection control colleagues.
