Combining consumers’ health data, including clinical laboratory test results, to genetic data for predispositions to chronic diseases could be key to developing targeted drugs and precision medicine treatments
Genetic testing company 23andMe is beta testing a method for combining customers’ private health data—including clinical laboratory test results and prescription drug usage—with their genetic data to create the largest database of its kind.
Such information—stored securely but accessible to 23andMe for sale to pharmaceutical companies for drug research and to diagnostics developers—would place 23andMe in a market position even Apple Health cannot claim.
Additionally, given the importance of clinical lab test data—which makes up more than 70% of a patient’s medical records—it’s reasonable to assume that innovative medical laboratories might consider 23andMe’s move a competitive threat to their own efforts to capitalize on combining lab test results with patients’ medical histories, drug profiles, and demographic data.
23andMe plans to use third-party medical network Human API to collect and manage the data. Involvement in the beta test is voluntary and currently only some of the genetic company’s customers are being invited to participate, CNBC reported.
Apple Healthcare, 23andMe, and Predicting Disease
The announcement did not go unnoticed by Apple, which has its own stake in the health data market. Apple Healthcare’s product line includes:
Mobile device apps for using at point-of-care in hospitals;
iPhone apps that let customers store and share their medical and pharmaceutical histories and be in contact with providers;
ResearchKit, which lets researchers build specialized apps for their medical research;
CareKit, which lets developers build specialized monitoring apps for patients with chronic conditions; and
Apple Watch, which doubles as a medical device for heart monitoring.
What Apple does not have is genetic data, which is an issue.
An Apple Insider post notes, “As structured, 23andMe’s system has advantages over Apple’s system including not just genetic data, but insights into risks for chronic disease.”
This is significant. The ability to predict a person’s predisposition to specific chronic diseases, such as cancer, is at the heart of Precision Medicine. Should this capability become not only viable and reliable but affordable as well, 23andMe could have a sizeable advantage in that aspect of the health data market.
Anne Wojcicki (above) is CEO and co-founder of 23andMe. The genetic company is inviting some of its customers to combine their medical information—including clinical laboratory test results and medication histories—with their stored genetic data. Customers would have access to the combined data and be able to share it with providers. In exchange, 23andMe gets to sell it to pharmaceutical companies and diagnostics developers. If successful and popular with the eight to 10-million peoplewho have reportedly purchased its test kits, 23andMe could produce a significant source of revenue. (Photo copyright: Inc.)
Genetic Test Results Combined with Clinical Laboratory
Test Results
23andMe is hopeful that after people receive their genetic test
results, they will then elect to add their clinical laboratory results, medical
histories, and prescription drug information to their accounts as well. 23andMe
claims its goal is to provide customers with easy, integrated access to health
data that is typically scattered across multiple systems, and to assist with
medical research.
“It’s a clever move,” Ruby Gadelrab, former Vice President of Commercial Marketing at 23andMe who now provides consulting services to health tech companies, told CNBC. “For consumers, health data is fragmented, and this is a step towards helping them aggregate more of it.”
CNBC also reported that Gadelrab said such a database
“might help 23andMe provide people with information about their risks for complex,
chronic ailments like diabetes, where it’s helpful for scientists to access a
data-set that incorporates information about individual health habits,
medications, family history and more.”
Of course, it bears saying that the revenue generated from cornering
the market on combined medical, pharmaceutical, and genetic data from upwards
of 10-million customers would be a sizable boon to the genetic test company.
CNBC reported that “the company confirmed that it’s a
beta program that will be gradually rolled out to all users but declined to
comment further on its plans. The service is still being piloted, said a person
familiar with the matter, and the product could change depending on how it’s
received.”
Will 23andMe Have to Take on Apple?
23andMe already earns a large portion of its revenue through
research collaborations with pharmaceutical companies, and it hopes to leverage
those collaborations to produce new drug therapies, CNBC reported.
This new venture, however, brings 23andMe into competition
with Apple on providing a centralized location from where consumers can access
and share their health data. But it also adds something that Apple does not
have—genetic data that can provide insight into consumers’ predispositions to
certain diseases, which also can aid in the development of precision medicine
treatments for those diseases.
Whether Apple Healthcare perceives 23andMe’s encroachment on
the health data market as a threat remains to be seen.
Nevertheless, this is another example of a prominent company
attempting to capitalize on marketable customer information. Adding medical information
to its collected genetic data could position 23andMe to generate significant
revenue by selling the merged data to pharmaceutical companies and diagnostics
developers, while also helping patients easily access and share their data with
healthcare providers.
It’s a smart move, and those clinical laboratory executives
developing ways to produce revenue from their lab organization’s patient lab test
data will want to watch closely as 23andMe navigates this new market.
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.
For blood brothers Quest and LabCorp this is good news, since the two medical laboratory companies perform most of the testing for the biggest DTC genetic test developers
Should clinical laboratories be concerned about direct-to-consumer (DTC) genetic tests? Despite alerts from healthcare organizations about the accuracy of DTC genetic testing—as well as calls from privacy organizations to give DTC customers more control over the use of their genetic data—millions of people have already taken DTC tests to learn about their genetic ancestry. And millions more are expected to send samples of their saliva to commercial DTC companies in the near future.
This growing demand for at-home DTC tests does not appear to be subsiding. And since most of the genetic testing is completed by the two largest lab companies—Quest Diagnostics (NYSE:DGX) and Laboratory Corporation of America (NYSE:LH)—other medical laboratories have yet to find their niche in the DTC industry.
Another factor is the recent FDA authorization allowing DTC company 23andme to report the results of its pharmacogenetic (PGx) test directly to customers without requiring a doctor’s order. For these reasons, this trend looks to be gaining momentum and support from federal governing organizations.
Dark Daily has
reported on DTC genetic
testing for many years. According to MIT’s Technology Review, 26 million people—roughly
8% of the US population—have already taken at-home DNA tests. And that number
is expected to balloon to more than 100 million in the next 24 months!
“The genetic genie is out of the bottle. And it’s not going
back,” Technology Review reports.
The vast majority of the genetic information gathered goes into the databases of just four companies, with the top two—Ancestry and 23andMe—leading by a wide margin. The other two major players are FamilyTreeDNA and MyHeritage, however, Ancestry and 23andMe have heavily invested in online and television advertising, which is paying off.
In an op-ed response to a NYT editorial that warned readers to avoid 23andMe’s DTC genetic testing, 23andMe CEO and co-founder Anne Wojcicki (above) wrote, “We believe that consumers can learn about genetic information without the help of a medical professional, and we have the data to support that claim.” The FDA agreed and in February approved 23andMe to report pharmacogenetic test results directly to its customers. How this will play out for clinical laboratories remains to be seen. (Photo copyright: Inc.com.)
As more people add their data to a given database, the likelihood they will find connections within that database increases. This is called the Network Effect (aka, demand-side economies of scale) and social media platforms grow in a similar manner. Because Ancestry and 23andMe have massive databases, they have more information and can make more connections for their customers. This has made it increasingly difficult for other companies to compete.
Quest Diagnostics and LabCorp do the actual gene sequencing
for the top players in the DTC genetic testing sector. The expected wave of new
DTC genetic test costumers (74 million in the next 24 months) will certainly
have a beneficial revenue impact on those two lab companies.
Why the Explosion in Genetic
Testing by Consumers?
In 2013, just over 100,000 people took tests to have their
DNA analyzed, mostly using Ancestry’s test, as Dark Daily reported. By 2017, that
number had risen to around 12 million, and though Ancestry still had the
majority market share, 23andMe was clearly becoming a force in the industry,
noted Technology Review.
And now there are several health-related reasons as well. For
example, the study of pharmacogenetics has led clinicians to understand that
certain genes reveal how our bodies process some medications. The FDA’s clearance
allows 23andMe to directly inform customers about “genetic variants that may be
associated with a patient’s ability to metabolize some medications to help
inform discussions with a healthcare provider. The FDA is authorizing the test
to detect 33 variants for multiple genes,” the FDA’s press
release noted.
Controversy Over DTC
Genetic Tests
The use of DTC genetic tests for healthcare purposes is not without scrutiny by regulatory agencies. The FDA removed 23andMe’s original health test from the market in 2013. According to Technology Review, the FDA’s letter was “one of the angriest ever sent to a private company” and said “that the company’s gene predictions were inaccurate and dangerous for those who might not fully understand the results.”
23andMe continues to refine its DTC tests. However, the debate continues. In February of this year, the New York Times (NYT) editorial board published an op-ed warning consumers to be wary of health tests offered by 23andMe, saying the tests “look for only a handful of [genetic] errors that may or may not elevate your risk of developing the disease in question. And they don’t factor into their final analysis other information, like family history.”
Anne Wojcicki, CEO and co-founder of 23andMe, responded with her own op-ed to the NYT, titled, “23andMe Responds: Empowering Consumers.” In her letter, Wojcicki contends that people should be empowered to take control of their own health, and that 23andMe allows them to do just that. “While 23andMe is not a diagnostic test for individuals with a strong family history of disease, it is a powerful and accurate screening tool that allows people to learn about themselves and some for the most common clinically useful genetic conditions,” she wrote.
Nevertheless, privacy concerns remain:
Who owns the results, the company or the
consumer?
Who can access them?
What happens to them a year or five years after
the test is taken?
When they are sold or used, are consumers
informed?
Even as experts question the accuracy of DTC genetic testing
in a healthcare context, and privacy concerns continue to grow, more people
each year are ordering the tests. With predictions of 74 million more tests
expected in the next 24 months, it’s certain that the medical laboratories that
process those tests will benefit.
Studies show consumer genealogy databases are much broader than is generally known. If your cousins are in such a database, it’s likely you are too
Recent news stories highlighted crime investigators who used the DNA data in consumer genetic genealogy databases to solve cold cases. Though not widely known, such uses of direct-to-consumer DNA databases is becoming more commonplace, which might eventually lead to requests for clinical laboratories to assist in criminal investigations involving DNA data.
Case in point: investigators found the Golden State Killer, a serial killer/rapist/burglar who terrorized multiple California counties over a dozen years in the 1970s to 1980s, after uploading a DNA sample from the crime scene to GEDmatch, an open-data genomics database that features tools for genealogy research. They made the arrest after discovering a distant relative’s DNA in the genealogy database and matching it to the suspect, CBS News revealed in a 60 Minutes Overtime online report.
These and other investigators are using a technique called familial DNA testing (AKA, DNA Profiling), which enables them to use genetic material from relatives to solve crimes.
Clinical laboratories oversee DNA databases. Could DNA databases—developed and managed over years by medical laboratories for patient care—be subpoenaed by law enforcement investigating crimes?
The question raises many issues for society and for labs, including privacy responsibilities and appropriate use of genetic information. On the other hand, the genetic genie is already out of the bottle.
Leveraging Familia DNA to Solve Crimes a New Trend
“The solving of the Golden State Killer case opened this method up as a possibility, and other crime labs are taking advantage of it. Clearly, a trend has started,” Ruth Dickover, PhD, Director of Forensic Science, University of California, Davis, told the Los Angeles Times.
Indeed, the use of familial DNA testing is moving forward. The Verge reported 19 cold case samples have been identified in recent familial DNA testing and public database searches. It also said two new published studies may propel the technique further.
One study, published in the journal Science, suggests nearly every American of European ancestry may soon be identified through familial DNA testing.
The other study, published in Cell, shows that a person’s relatives can be detected when forensic DNA data are compared with consumer genetic databases.
Noah Rosenberg, PhD (above left), Professor of Population Genetics and Society Biology at Stanford University, is shown above working with Jaehee Kim, PhD (right), a Postdoctoral Research Fellow in Biology, on math that could be used to track down relatives in genealogy databases based on forensic DNA. “This could be a way of expanding the reach of forensic genetics, potentially for solving even more cold cases. But at the same time, it could be exposing participants in those databases to forensic searches they might not have anticipated,” he told Wired. (Photo copyright: Stanford University/L.A. Cicero.)
15 Million People Already in Genealogy Databases
Researchers at Columbia University in New York and Hebrew University of Jerusalem told Science they were motivated by the recent trend of investigations leveraging third-party consumer genomics services to find criminals. But they perceived a gap.
“The big limitation is coverage. And even if you find an individual it requires complex analysis from that point,” Yaniv Erlich, PhD, Associate Professor at Columbia and Chief Science Officer at MyHeritage, told The Verge. MyHeritage is an online genealogy platform.
Others offering consumer genetic testing and family history exploration include 23andMe and Ancestry. As of April 2018, more than 15 million people have participated in direct-to-consumer genetic testing, the researchers noted.
The study aimed to find the likelihood that a person can be identified using a long-range familial search. It included these steps and findings:
Statistical analysis of 1.28 million people in the MyHeritage database;
Pairs of people with “identity-by-descent” were removed to avoid bias, such as first cousins and closer relationships;
Researchers aimed at finding a third cousin or closer relatives for each person in the database;
60% of the 1.28 million people were matched with a third cousin or closer relative.
“We project that about 60% of the searches for individuals of European-descent will result in a third cousin or closer match, which can allow their identification using demographic identifiers. Moreover, the technique could implicate nearly any US individual of European descent in the near future,” the researchers wrote.
In an interview with Wired, Erlich added, “The takeaway is it doesn’t matter if you’ve been tested or not tested. You can be identified because the databases already cover such large fractions of the US—at least for European ancestry.”
Matching Forensic and Consumer Genetic Data
Meanwhile, the study published in Cell by researchers at Stanford University, University of California, Davis, and the University of Michigan also suggests investigators could compare forensic DNA samples with consumer genetic databases to find people related to criminals.
That study found:
30% to 32% of people in a forensic database could be related to a child or parent in a consumer database;
35% to 36% could be tied to a sibling.
These studies reveal that genetic data and familial DNA testing can help law enforcement find suspects, which is a good thing for society. But people who uploaded DNA data to some direct-to-consumer databases may find themselves caught up in searches they do not know about. So may their cousins.
Dark Daily recently covered other similar studies that showed it takes just one person’s DNA to reveal genetic information on an entire family. (See, “The Problems with Ancestry DNA Analyses,” October 18, 2018.) These developments in the use of DNA databases to identify criminals should be an early warning to clinical laboratories building databases of genetic information that, at some future point, law enforcement agencies might want access to those databases as part of ongoing criminal investigations.
Diagnostic medical laboratories may sequence DNA genetic tests correctly, but there are issues with how companies analyze the information
In 2017, some 12 million people paid to spit in a tube and have their genetic data analyzed, according to Technology Review. Many companies offer this type of DNA testing, and each of them works with one or more clinical laboratories to get the actual sequencing performed. For example, Ancestry.com, one of the largest direct-to-consumer genetic data testing companies, works with both Quest Diagnostics and Illumina.
In the case of Quest Diagnostics, the clinical laboratory company does the actual sequencing for Ancestry. But the analysis of the genetic data for an individual and its interpretation is performed by Ancestry’s team.
There are critics of the booming direct-to-consumer genetic testing business, but it’s not due to the quality of the sequencing. Rather, critics cite other issues, such as:
Privacy concerns;
How the physical samples are stored and used;
Who owns the data; and,
That this branch of genetics is an area of emerging study and not clearly understood.
What Does All That Genetic Data Mean?
The consumer DNA testing market was worth $359 million dollars in 2017 and is projected to grow to $928 million by 2023, according to a report from Research and Markets. Those numbers represent a lot of spit, and an enormous amount of personal health information. As of now, some one in every 25 adults in the US has access to their genetic data. But, what does all that data mean?
The answer depends, in large part, on who you ask. Many reporters, scientists, and others have taken multiple DNA tests from different companies and received entirely different results. In some cases, the sequencing from one sample submitted to different companies for analysis have rendered dramatically different results.
“There is a wild-west aspect to all of this,” Erin Murphy, a New York University law professor and genetics specialist who focuses on privacy implications, told McClatchy. “It just takes one person in a family to reveal the genetic information of everyone in the family,” she notes. (Photo copyright: New York University.)
It’s All About the Database
Although some people purchase kits from multiple companies, the majority of people take just one test. Each person who buys genetic analysis from Ancestry, for example, consents to having his/her data become part of Ancestry’s enormous database, which is used to perform the analyses that people pay for. There are some interesting implications to how these databases are built.
First, they are primarily made up of paying customers, which means that the vast majority of genetic datasets in Ancestry’s database come from people who have enough disposable income to purchase the kit and analysis. It may not seem like an important detail, but it shows that the comparison population is not the same as the general population.
Second, because the analyses compare the sample DNA to DNA already in the database, it matters how many people from any given area have taken the test and are in the database. An article in Gizmodo describes one family’s experience with DNA testing and some of the pitfalls. The author quotes a representative from the company 23andMe as saying, “Different companies have different reference data sets and different algorithms, hence the variance in results. Middle Eastern reference populations [for example] are not as well represented as European, an industry-wide challenge.”
The same is true for any population where not many members have taken the test for a particular company. In an interview with NPR about trying to find information about her ancestry, journalist Alex Wagner described a similar problem, saying, “There are not a lot of Burmese people taking DNA tests … and so, the results that were returned were kind of nebulous.”
Wagner’s mother and grandmother both immigrated to the US from Burma in 1965, and when Wagner began investigating her ancestry, she, both of her parents, and her grandmother, all took tests from three different direct-to-consumer DNA testing companies. To Wagner’s surprise, her mother and grandmother both had results that showed they were Mongolian, but none of the results indicated Burmese heritage. In the interview she says that one of the biggest things she learned through doing all these tests was that “a lot of these DNA test companies [are] commercial enterprises. So, they basically purchase or acquire DNA samples on market-demand.”
As it turns out, there aren’t many Burmese people taking DNA tests, so there’s not much reason for the testing companies to pursue having a robust Burmese or even Southeast Asian database of DNA.
Who Owns Your Genetic Data?
As is often the case when it comes to technological advances, existing law hasn’t quite caught up with the market for ancestry DNA testing. There are some important unanswered questions, such as who owns the data that results from a DNA analysis?
An investigation conducted by the news organization McClatchy found that Ancestry does allow customers to request their DNA information be deleted from the company’s database, and that they can request their physical sample be destroyed as well. The author writes, “But it is a two-step process, and customers must read deep into the company’s privacy statement to learn how to do it. Requests for DNA data elimination can be made online, but the company asks customers to call its support center to request destruction of their biological sample.”
Another concern is hacking or theft. Ancestry and similar companies take steps to protect customers’ information, such as using barcodes rather than names and encryption when samples are sent to labs. Nevertheless, there was an incident in 2017 in which hackers infiltrated a website owned by Ancestry called RootsWeb. “The RootsWeb situation was certainly unfortunate,” Eric Heath, Ancestry’s Chief Privacy Officer, told McClatchy. He added that RootsWeb was a “completely separate system” from the Ancestry database that includes DNA information.
What We Don’t Know
The biggest pitfall for consumers may be that geneticists don’t know very much about DNA analysis. Adam Rutherford, PhD, is a British geneticist who interviewed for the Gizmodo story. He said that the real problem with companies like Ancestry is that people have a basic, fundamental misunderstanding of what can be learned from a DNA test.
“They’re not telling you where your DNA comes from in the past. They’re telling you where on Earth your DNA is from today,” Rutherford told Gizmodo.
Science evolves, of course, and genetic testing has much evolving to do. The author of the Gizmodo piece writes, “It’s not that the science is bad. It’s that it’s inherently imperfect.” There aren’t any best-practices for analyzing DNA data yet, and companies like Ancestry aren’t doing much to make sure their customers understand that fact.
Nevertheless, issues surrounding genetic testing, the resulting data, and its storage, interpretation, and protection, continue to impact clinical laboratories and anatomic pathology groups.
