The resulting genomic dataset may provide useful diagnostic insights that can be used by clinical laboratory and pathology professionals to learn how and why some people age with good health
Why do some seniors age in good health and other seniors
suffer with multiple chronic conditions? A new genetic database is using whole-genomic
sequencing (WGS) to answer that question in ways that may benefit medical
laboratories.
Because of the rapid aging of populations in the United
States and other developed nations throughout the world, there is keen interest
in how to keep seniors healthy. In fact, developing effective lab testing
services in support of improved senior health is one of the big opportunities
for both clinical laboratories and anatomic
pathology groups.
Until recent years, most clinical
pathologists dealt primarily with lab tests that used specimens such as blood
and urine. However, genetics researchers are using WGS to discover new causes
for many chronic illnesses. And the tools these researchers are developing offer
pathologists and clinical
laboratories powerful new ways to help doctors diagnose disease.
Through the use of WGS, the MGRB now features a huge
database of thousands of healthy elderly people. The data it contains may enable
pathology scientists to learn, from a genetic standpoint, why some people age
healthfully while others do not.
The researchers published their work titled, “The Medical
Genome Reference Bank: A Whole-Genome Data Resource of 4,000 Healthy Elderly
Individuals. Rationale and Cohort Design,” in the European Journal of
Human Genetics.
Finding New Applications for Genetic Data
According to the UNSW published study, “The MGRB is comprised
of individuals consented through the biobank programs of two contributing
studies … Each sample is from an individual who has lived to [greater than or
equal to] 70 years with no reported history or current diagnosis of
cardiovascular disease, dementia, or cancer, as confirmed by the participating
studies at recent follow-up study visits.”
The researchers noted in their paper, “Aged and healthy
populations are more likely to be selectively depleted of pathogenic alleles, and therefore
particularly suitable as a reference population for the major diseases of
clinical and public health importance.”
The MGRB plans to make its database openly accessible to the
international research community through its website once all 4,000 samples
have been sequenced. Currently, about 3,000 of the samples have been analyzed,
as noted on the Garvan website,
which is tracking the MGRB’s progress.
“The Medical Genome Reference Bank can tell us much about what it means to grow old but remain well, and is a powerful tool to help us deconstruct the genetics of common diseases,” said David Thomas, PhD (above), an NHMRC Principal Research Fellow, Director of The Kinghorn Cancer Center, and Head of the Cancer Division of the Garvan Institute in New South Wales, AU, in a statement reported by GenomeWeb. (Photo copyright: South West Sydney Research.)
Personal Genetic Data in Precision Medicine
“The integration of genomic knowledge and technologies into
healthcare is revolutionizing the way we approach clinical and public health
practice,” Caron
M. Molster, et al, noted in, “The Evolution of Public Health
Genomics: Exploring Its Past, Present, and Future,” published in Frontiers
in Public Health. Molster is Manager at the Health Department Western
Australia in Perth, and lead author of the paper.
“Public health genomics has evolved to responsibly integrate
advancements in genomics into the fields of personalized
medicine and public health,” the researchers wrote.
The 100,000
Genomes Project in the United Kingdom is sequencing the genomes of people
who have rare diseases and their families. Researchers all over the world are collecting
genomic data with plans to use it in different ways, and on various chronic
disease populations, in pursuit of precision medicine
goals.
Molster and her co-authors noted the comparable development
of genetic sequencing and precision medicine in their paper.
“Parallel to the developments in precision medicine has been
the advancement of technologies that enable the production, aggregation,
analysis, and dissemination of extremely large volumes of individual- and
population-level data on genes, environment, behavior, and other social and
economic determinants of health. These data have proven useful in finding new
correlations, patterns and trends, particularly those involving complex
interactions, in relation to diseases, pathogens, exposures, behaviors,
susceptibility (risk), and health outcomes in populations,” they wrote.
According to Paul Lacaze, PhD,
Head of the Public Health Genomics Program at Monash University, one of the
challenges in interpreting whole-genome data in order to diagnose disease is
“discriminating rare candidate disease-causing variants from the large numbers
of benign variants unique to each individual. Reference populations are
powerful filters,” he noted in the MGRB paper.
The MGRB database provides just such a powerful reference
population, giving researchers who are studying specific diseases a tool for
comparison.
Other Studies into Heathy Aging
Other initiatives to create datasets of genome information
for specific populations also are underway. The Scripps
Translational Science Institute (STSI) in La Jolla, Calif., has been
studying healthy aging since 2007. That’s when STSI launched the Wellderly Study,
according to a news
release. As of 2016, they had sequenced the genomes of 600 study
participants, as well as 511 samples for comparison from a study being conducted
separately by the Inova Translational Medicine Institute, a paper in Nature noted.
Another effort being conducted in China involves a database
called PGG.Population.
These researchers seek to “create a comprehensive depository of geographic and
ethnic variation of human genome, as well as a platform bringing influence on
future practitioners of medicine and clinical investigators,” according to
their 2018 paper published in Nucleic Acids
Research.
In this case, rather than identifying common genomic
variants among a specific population, such as the healthy elderly, the
researchers are working to understand how genetic variations are distributed
among specific populations. “The PGG.Population database documents 7,122
genomes representing 356 global populations from 107 countries and provides
essential information for researchers to understand human genomic diversity and
genetic ancestry,” wrote the researchers.
Each of these disparate datasets represents paths of
investigation that could lead to a better understanding of personal and public health.
As technologies continue to develop that enable scientists to sift through the
massive amount of WGS data being generated, a clearer picture of what healthy
aging at the genetic level looks like will likely emerge.
Precision medicine is leading to precision public health,
and clinical pathology laboratories are important parts of the public health
puzzle.
AUSTIN, Texas (August 14, 2018)—Precision Medicine is happening now at first-mover hospitals and health systems! September 12-13 in Nashville, experts from the nation’s most successful precision medicine clinical programs will gather to share their strategies and lessons learned. The goal of this conference is to provide hospital CEOs with the insights needed to initiate effective precision medicine programs in their own institutions.
Keynote speaker is Jeffrey Balser, MD, the CEO of Vanderbilt University Medical Center. VUMC is internationally recognized for its pioneering efforts to bring precision medicine into daily clinical care. Attendees will gain essential insights into the early successes of precision medicine at VUMC, and will also learn about how the healthcare big database at Vanderbilt is being used to inform population health initiatives while also guiding the care that clinicians deliver daily to individual patients.
Among the twenty expert speakers sharing their respective experiences at bringing precision medicine, genetic medicine, and genetic testing into the daily care provided to their patients, will be:
Howard L. McLeod, PharmD, Medical Director, Personalized Medicine Institute, Moffitt Cancer Center, on Precision Medicine in Oncology/Cancer Care
Mark Van Oene, Chief Commercial Officer, Illumina, Inc., on Genetic Testing and Gene Sequencing’s Role in Precision Medicine
Julie A Johnson, PharmD, Dean, College of Pharmacy, University of Florida, on Precision Medicine in Pharmacogenomics
Josh Denny, MD, Vice President of Personalized Medicine at Vanderbilt University Medical Center, on Genetic and Molecular Data in Population Health
For more information and to register to attend “Precision Medicine for Health Network CEOs: What You Need to Know about Genetic Testing, Precision Medicine, and Population Health Management,” click here. You may also contact Chris Garcia at 512-264-7103.
About Precision Medicine Institute, LLC
The Precision Medicine Institute has the unique mission of bringing together the executive leaders and physician leaders of the nation’s leading healthcare organizations, health networks, and corporations to understand the successes of first-movers and early-adopters as they bring precision medicine into clinical settings. The emphasis is on high-level knowledge of business strategies, clinical initiatives, and operational requirements needed to implement and sustain a clinically-effective and financially-sustainable precision medicine service that measurably improves patient care while helping hospitals avoid costs and generating ample reimbursement.
In what could be a major boon to clinical laboratories and healthcare providers, researchers found that fears of rampant testing and ballooning spending due to results of whole-genome sequencing may be less of a concern than opponents claim
Clinical laboratory testing and personalized medicine (AKA, precision medicine) continue to reshape how the healthcare industry approaches treating disease. And, whole-genome sequencing (WGS) has shown promise in helping in vitro diagnostic (IVD) companies develop specific treatments for specific patients’ needs based on their existing conditions and physiology.
Nevertheless, WGS development and the ensuing controversy continues. This has motivated researchers at Brigham and Women’s Hospital (BWH) in Boston to engage in a study that compares the upfront costs of WGS to the downstream costs of healthcare, in an attempt to determine if and how whole-genome sequencing does actually impact the cost of care.
Are Doctors Acting Responsibly?
The MedSeq Project study, published in Genetics in Medicine, a journal of the American College of Medical Genetics and Genomics, involved 200 people—100 of them healthy, the other 100 diagnosed with cardiomyopathy. Roughly half of each group underwent whole-genome sequencing, while the other half used family history to guide treatments and procedures. The project then collected data on downstream care costs for the next six months for each group to compare how whole-genome sequencing might impact the final totals.
“Whole genome sequencing is coming of age, but there’s fear that with these advancements will come rocketing healthcare costs,” lead author Kurt Christensen, PhD, Instructor of Medicine in the Division of Genetics at BWH, stated in a press release.
“Our pilot study is the first to provide insights into the cost of integrating whole-genome sequencing into the everyday practice of medicine,” noted Kurt Christensen, PhD, lead author of the Brigham and Women’s Hospital study. “Our data [provides] reassurance that physicians seem to be responding responsibly and that we’re not seeing evidence of dramatically increased downstream spending.” (Photo copyright: ResearchGate.)
Clinical Laboratory Testing Largest Difference in Cost/Services Rendered
Within the healthy volunteer group, patients who based treatment decisions solely on their family medical history averaged $2,989 in medical costs over the next six months. Those who received WGS incurred $3,670 in costs.
Services also remained relatively consistent between both groups. The WGS group averaging 5.5 outpatient lab tests and 8.4 doctor visits across the period, while the family history group averaged 4.4 outpatient lab tests and 6.9 doctor visits.
Within the cardiology patient group, however, the dynamic flipped. WGS recipients averaged $8,109 in spending, while the family history group averaged $9,670. Study authors attribute this to the possibility of treatments while being hospitalized for concerns unrelated to the study.
When removing hospitalizations from the data set, the WGS group averaged $5,392, while the family history group averaged $4,962—a result similar to that of the healthy group.
Utilization of services was also similar. The WGS group averaged 7.8 doctor visits, while the family history group averaged 7.2 visits. However, the outpatient lab testing spread was wider than any other group in the study. WGS patients averaged 9.5 tests compared to the 6.5 of the family history group.
Unanswered Questions
In their report, the study’s authors acknowledged a range of questions still unanswered by their initial research.
First, the project took place at a facility in which physicians were educated in genetics, had contacts familiar with genetics, and had the support of a genome resource center. The level of experience with genetics may also have prevented additional spending by tempering responses to results.
Although the whole-genome sequencing that took place during the project uncovered genetic variants known to or likely to cause disease within the healthy population, this did not trigger the wave of testing or panic many opponents of genetic sequencing predicted.
Authors also acknowledge that a longer, larger study would offer more conclusive results. Researchers are planning for a longer 5-year study to verify their initial findings. However, study co-author Robert Green, MD, Director of the Genomes2People Research Program at BWH told STAT, “… downstream medical costs of sequencing may be far more modest than the common narrative suggests.”
Further Research Needed
The BWH researchers acknowledged that monetary cost is only one facet of the impact of genetic sequencing results. “Patient time costs were not assessed,” the study authors pointed out. “Nor were the effects of disclosure on participants’ family members, precluding a complete analysis from a societal perspective.”
Lastly, they noted that while the sample size sufficed to verify their results, diversity was lacking. In particular, they mentioned that the participant pool was “more educated and less ethnically diverse than the general population.”
The cost of genetic sequencing and similar technologies continue to drop as automation and innovation make the process more accessible to clinicians and healthcare providers. This could further impact longer studies of the overall cost of sequencing and other genetics-based tools.
For medical laboratories, these results offer proof to both payers and physicians on the value of services in relation to the overall cost of care—a critical concern, as margins continue to shrink and regulations focus on efficiency across a broad spectrum of healthcare-related service industries.
Genetic counselors struggle to explain direct-to-consumer genetic test data—or correct provider misinterpretations of results—while often encountering resistance and anger from patients who don’t accept their counseling
Healthcare consumers who want to know more about their family’s genealogy are purchasing direct-to-consumer (DTC) home genetic tests in record numbers. It is a trend that worries some medical laboratory professionals and certain federal government agencies.
MITTechnology Review (MIT) dubbed 2017, “The year consumer DNA testing blew up.” As a result of record-breaking sales of DTC genetic testing last year, about 12-million people have now been tested, MIT reported. “The inflection pointed started in the summer of 2016, and from there it’s gone into the stratosphere,” David Mittelman, PhD, Molecular Biophysics, told MIT.
Clearly, consumers are becoming comfortable with the concept of genetic testing on themselves and their family members. However, major issues—such as who owns genetic information and how patient privacy is protected—have yet to be resolved.
Dark Daily recently reported that more than 1.5 million kits were sold by Ancestry.com during the four-day Black Friday/Cyber Monday weekend prior to Christmas 2017. That e-briefing also explored related privacy issues and informed readers about efforts by federal lawmakers to explore genetic testing companies’ privacy and disclosure practices.
According to a news release, by the end of November, sales of AncestryDNA kits exceeded the total number of subscribers the Utah-based company had when it started the year. Now, more than seven million people are in Ancestry’s database.
Meanwhile, 23andMe, a personal genomics company established in 2006, has genotyped more than three million people worldwide. In addition to an ancestry test, it offers a health and ancestry service providing information on genetic health risks, carrier status, traits, wellness, and ancestry, according to the company’s website.
Experts Concerned About Privacy and Use of ‘Raw’ DNA Data
“2018 will bring a regular drumbeat of new experiences and enhancements across both DNA and family history,” Howard Hochhauser, Ancestry’s Interim Chief Executive Officer, predicted in the news release.
However, a recent study published in Translational Behavioral Medicine (TBM) which noted the robust sales of DTC genetic tests in 2017, also called attention to a new concern surrounding the impact of “raw” DNA interpretation results.
“People often enter the direct-to-consumer market for recreational purposes, such as learning about their ancestry. Yet, what we started seeing was that these same individuals subsequently come across third-party interpretation services where they proceeded to learn more about their ‘raw’ DNA made available by the ancestry testing companies,” stated Catharine Wang, PhD, Boston University (BU) Associate Professor of Community Health Sciences, and the study’s lead author, in a BU statement.
The study cited sales of DTC genetic tests at $99 million in 2017 and explored potential negative implications of consumers’ access to “raw” DNA data.
“We were especially interested in the downstream implications of receiving unexpected disease risk information from these newer services that subsequently lead consumers to seek out a genetic counselor’s consult,” Wang noted.
Catharine Wang, PhD (above), Associate Professor of Community Health Sciences at Boston University and lead author of the study, notes, “There are a lot of people saying, ‘I’m smart enough to make decisions; give me the information and get the doctors out of the way. But they’re making some serious decisions about their health after seeing only part of the picture.” (Photo copyright: Boston University Research.)
After Getting DNA Data, Consumers Turn to Interpretation Services, Genetic Counselors
The research team surveyed 85 genetic counselors. Fifty-three percent of them reported meeting with DTC test costumers who had accessed ‘raw’ DNA data and used genetic interpretation companies, which are not regulated by the US Food and Drug Administration (FDA), to get more information about themselves. However, results of the sessions were not always positive for either patients or counselors.
According to the study, counselors reported their biggest challenge as “undoing misinterpretations and correcting patient beliefs about their raw DNA results.”
The study noted, “When genetic counselors tried to clarify misunderstandings, patients were not only resistant but sometimes appeared hurt and frustrated that counselors were not taking their results seriously.”
Other negative experiences counselors reported while interpreting “raw” DNA test results for patients include:
“Time required to review and understand interpretation reports;
“Feeling ill equipped and uncomfortable providing the service;
“A lack of supportive organizational structure; and,
“[Having to] correct a patient’s misunderstanding, following a primary care physician’s misinterpretation of her raw DNA results.”
“Counselors expressed concern about the quality of the raw data and the clarity and usefulness of interpretation reports. Efforts to better support both consumers and genetic service providers are needed to maximize the effective translation of genome-based knowledge for population health,” the study authors concluded.
Providers Should Improve Ability to Help Patients with DTC Genetic Data
In a MedCity News blog post, Peter Hulick, MD, Director of Personalized Medicine, NorthShore University HealthSystem, called for healthcare providers to assist patients who are dealing with new DTC genetic services and possible data overload.
“Findings show having widespread access to personal genetic information—without the knowledge of how to interpret results—can lead to problems ranging from misinterpretation to emotional distress,” he noted. “The medical community must work harder and smarter to incorporate this information into practice and empower patients as consumers and partners in healthcare decision-making.”
Anatomic pathologists and clinical laboratory leaders also should acknowledge and monitor consumers’ growing interest in these tests. Once patients’ have their DNA sequenced, the likelihood they will seek to know their predisposition to diseases is high and increasing. Thus, opportunities exist for medical laboratories to help physicians and consumers interpret DTC test results.
Operations ended last week after reports suggested the end came as a result of misalignment of goals among investors in a lab company many considered to be successful
One contributing factor the surprise announcement that the owners of Claritas Genomics were closing the clinical laboratory company may have been the struggle to get payers to reimburse its genetics test claims. If true, it is the latest market sign of how health insurers are making it difficult for labs to get paid for proprietary molecular diagnostic assays and genetic tests.
With no official announcement, Claritas Genomics quietly ended operations effective on Friday, Jan. 19. That evening, a spokeswoman for Claritas Genomics’ majority owner, Boston Children’s Hospital (BCH), confirmed for Dark Daily that the lab was closed and said no reason was given for the closing. More details may be forthcoming this week, she added.
As of the close of business on Tuesday, there was still no word from the genetics testing company founded in 2013. GenomeWeb was the first to report that Claritas Genomic’s diagnostic laboratories no longer do any testing. According to GenomeWeb, Brian Quirbach, former Clinical Testing Coordinator at Claritas Genomics, and part of the lab’s client services team, confirmed that the last day of business was Friday, Jan. 19. The BCH spokeswoman said the GenomeWeb article was accurate.
Asked if there had been a precipitating event at Claritas, if the company had experienced any serious business trouble, if it had struggled to get paid, or if payers were slow in paying, the spokeswoman declined to comment. Instead, she referred to the GenomeWeb article, saying it was mostly accurate.
Claritas Genomics a Casualty of Clinical Laboratory Price Wars
According GenomeWeb, Claritas was like other genetic testing laboratories that have long struggled to get health insurers to pay for rare disease tests. Also, Claritas and other genetic and molecular testing labs suffer financially as a direct result of the ongoing price wars among competing genetic testing lab companies.
“As a small company, it also wasn’t able to offer testing that did not come with potential patient payment obligations, which larger laboratories with better resources or payer contracts can do,” the GenomeWeb article noted.
According to GenomeWeb’s sources, Claritas had a reputation for delivering highly-accurate test results. The reason for this level of performance, the article noted, was Claritas’ use of two sequencing platforms, which lowered false-positive rates. The testing lab combined low false-positive rates with interpretations from WuXi NextCode. The clinical expertise available at BCH gave Claritas the best diagnostic exome in the industry in terms of technical quality and diagnostic power, one source told GenomeWeb.
The decision to close the company, the source noted, was a result of misalignment between investors at WuXi NextCode and BCH. Other sources speculated that Claritas and WuXi NextCode were considering a merger, which did not happen, GenomeWeb reported.
Ultimately, the source stated, BCH held the controlling interest and made the business decision to close the clinical laboratory company. And that the decision was unrelated to the lab’s quality.
Claritas’ clients were told, according to GenomeWeb, to download all test results and data by Thursday, Jan. 18, and that the lab’s operations manager would be available for a few weeks to answer customers’ questions.
Genetic Tests Developer for Pediatrics and Hereditary Disorders
Claritas, which was headquartered in Cambridge, Mass., had about 30 employees. When it was founded as a partnership between BCH and Life Technologies, its goal was to develop genetic and genomics-based diagnostic tests, primarily for pediatric patients with hereditary disorders.
In 2014, Dark Daily’s sister print publication The Dark Report (TDR) reported on the development of Claritas Genomics as an in-hospital lab that became independent. For 15 years, the lab operated as the genetic diagnostic laboratory at 396-bed BCH, we reported. (See The Dark Report, “Claritas Is Example of New Lab Business Model,” June 13, 2014.)
“As one of the hospital’s CLIA-certified laboratories, it provided the advanced molecular diagnostic testing services used by the hospital,” said Patrice M. Milos, PhD, who was Claritas Genomic’s CEO at the time.
At the 2014 Executive War College in New Orleans, Patrice Milos, PhD, then President and CEO, Claritas Genomics, spoke with Adam Slone, CEO, Slone Partners, about her path to becoming CEO of Claritas Genomics, how to foster a strong company culture, and what traits she looks for in a leadership team. Click on the photo above to watch the video interview. (Video copyright: Sloan Partners.)
In the early days of Claritas Genomics, BCH was challenged to provide the capital and resources needed for the molecular lab to grow, Milos said. “This was due to the rapid pace of genetic discovery, ongoing advances in gene sequencing technologies, and the difficult financial environment in healthcare,” she recalled. “Thus, to make it easier for the lab to grow, the hospital spun out the lab and created Claritas Genomics in February 2013.”
Informatics Tools to Support Clinical Use of Genetic Data
As an independent lab, Claritas had early success winning a role to do testing for the Million Veteran Program (MVP), a $9-million project of the US Department of Veterans Affairs. In October 2013, the lab company reported that it would do exome sequencing of samples from veterans. At the time, it was one of the largest sequencing initiatives in the nation. (The VA has since reported in 2016 that the program was the largest genomic database in the world.)
Further, this MVP was significant because Claritas benefited by generating cash flow, which it could use to acquire the gene sequencing system and staff expertise in next-generation sequencing (NGS) technologies. And, it developed the informatics infrastructure needed to collect, store, and analyze large volumes of genetic data, TDR reported.
Two months later, in December 2013, Claritas entered into a partnership with Cerner Corp. of Kansas City, Mo., to build the tools and connectivity systems needed to integrate NGS-based diagnostic testing into healthcare data systems. Specifically, the companies said they would develop a system “for molecular diagnostics that is tailored to NGS workflows, which are more complex and generate much more data than traditional molecular diagnostic tests.”
At the time, Milos explained the role that Claritas would play in this partnership. “In terms of this collaboration, one barrier to the use of genomics in medicine is the challenge of integrating the complex information derived from large-scale genomic measurements into a patient’s medical record and clinical practice,” he said. “Our mutual goal is to develop the informatics tools that support clinical use of genetic data.”
Claritas also was working with other pediatric institutions, such as Cincinnati Children’s Hospital, to advance clinical knowledge in a number of ways. “For example, we are facilitating a research network by connecting patients with experts who can provide care and by licensing assays from the hospitals where the discoveries that lead to diagnostic tests are made,” Milos said. “Also, in this business model, we can receive investment from outside sources, such as we have from two of our Series A investors, Life Technologies and Cerner.”
The abrupt closure of Claritas Genomics makes this clinical laboratory company the latest to disappear from the marketplace. The mystery factor in this case is why a company viewed by many as establishing a credible reputation for itself came to such a sudden end.
