Expanded ‘Cancer Gene Census’ is expected to accelerate development of new therapeutics and biomarker-based personalized medicine diagnostic tests for disease; could be useful for anatomic pathologists
Oncology is one of the fastest-developing fields in precision medicine and use of DNA-based diagnostics. Surgical pathologists are helping many cancer patients benefit from the use of a companion genetic test that shows their tumors are likely to respond to a specific drug or therapy. Consistent with that work, researchers in the United Kingdom (UK) have now produced the first comprehensive summary of all genes known to be strongly associated with cancer in humans.
The expansion of the “Cancer Gene Census” is noteworthy for anatomic pathologists who should expect to see the information increase the understanding of cancer causes and accelerate the development of new therapeutics and biomarker-based molecular diagnostics.
In this latest Cancer Gene Census, researchers from the Wellcome Sanger Institute (WSI) used CRISPR gene editing systems to produce an expanded catalog of 719 cancer-driving genes in humans.
According to a review article on the project published in Nature Reviews Cancer, “The recent expansion includes functional and mechanistic descriptions of how each gene contributes to disease generation in terms of the key cancer hallmarks and the impact of mutations on gene and protein function.”
The 2018 Cancer Gene Census from the Wellcome Sanger Institute in the United Kingdom summarizes 719 genes suspected of causing cancer in humans and describes how they function across all forms of the disease. (Photo copyright: Wellcome Sanger Institute.)
The Catalogue of Somatic Mutations in Cancer (COSMIC) provided the foundation for the WSI’s research. It involved manually condensing almost 2,000 research papers to develop evidence for a gene’s role in cancer.
While the COSMIC database characterizes more than 1,500
forms of human cancer and types of mutations, the U.K.’s Cancer Gene Census
goes further and “describes which genes are fundamentally involved and
describes how these genes cause disease,” a Wellcome Sanger Institute news
release states.
“For the first time ever, functional changes to these genes
are summarized in terms of the 10 cancer hallmarks—biological processes that
drive cancer,” the statement explains. “Mutations in some genes lead to errors
in repairing DNA, whereas mutations in other genes can suppress the immune
system or promote tumor invasion or spreading. Across the 700 genes in the
Cancer Gene Census, many have two or more different ways of causing cancer.”
Zbyslaw Sondka,
PhD, lead author on the WSI project, believes their study has provided
scientists with much needed new insights. “Scientific literature is very compartmentalized.
With the Cancer Gene Census, we’re breaking down all those compartments and
putting everything together to reveal the full complexity of cancer genetics,” he
noted in a WSI
article.
“This is the broadest and most detailed review of human
cancer genes and their functions ever created and will be continually updated
and expanded to keep it at the forefront of cancer genetics research,” Sondka
added.
Making Precision
Medicine More Precise
An understanding of the roles played by different genes in
various cancers is key to enabling researchers to develop drugs that will be
effective against individual cancers.
“The combination of the Cancer Gene Census with COSMIC will
enable researchers to investigate individual mutations and try to find good
targets for anti-cancer drugs based on the actual processes involved,” Simon Forbes, PhD,
Senior Author of the Cancer Gene Census paper and Director of COSMIC at the
Wellcome Sanger Institute, stated in the WSI news release.
Simon Forbes, PhD (above), Director of COSMIC at the Wellcome Sanger Institute and Senior Author of the Cancer Gene Census paper, believes the institute’s latest Cancer Gene Census, which catalogs 719 cancer-causing genes, will “help make precision medicine even more precise” by allowing “biologists and pharmaceutical scientists to see patterns and target particular pathways with anti-cancer drugs, not solely single genes.” (Photo copyright: Wellcome Sanger Institute.)
The path to precision medicine cancer treatments was further boosted this month when Wellcome Sanger Institute researchers, in partnership with the Open Targets Platform, announced a new system to prioritize and rank 600 drug targets that show the most promise for development into cancer treatments, noted a WSI statement.
The WSI/Open Targets team published its research in the international science journal Nature.
CRISPR-Cas9 and
Personalized Medicine
This latest research springboards off one of the largest CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats)-Cas9 screens of cancer genes to date. Researchers used CRISPR gene-editing systems to disrupt every gene within 30 different types of cancers and locate several thousand key genes essential for cancer’s survival. They then identified 600 genes that potentially could be used in personalized medicine treatments.
“The results bring researchers one step closer to producing
the Cancer
Dependency Map, a detailed rulebook of precision cancer treatments to help
more patients receive effective therapies,” the Wellcome Sanger Institute statement
notes.
Anatomic pathologists and clinical laboratories should note
the speed at which development of useful biomarkers for diagnosing cancer is
progressing. All labs will want to be prepared to capitalize on those
advancements through the lab testing services they offer in their medical laboratories.
As a
result of the drive toward consumer-driven healthcare, and because of rising
health insurance deductibles,patients are increasingly becoming
the new payers. Efficient patient access management is now viewed as critical
to reversing the resulting trend of uncompensated care, and to meeting the
lab’s revenue cycle objectives.
As patients take on more risk and assume more
of their own healthcare costs, and as registration errors, authorization, and
medical necessity continue to contribute to a large percentage of claim
denials—laboratory leaders need to examine new patient access technologies and
modernize their collection practices. In order to
continue to profitably provide quality care and to meet revenue cycle
objectives, it is crucial for labs to get a handle on plummeting accounts
receivable.
DarkDaily.com is
pleased to offer a recently published free White Paper that covers common trends having an impact on
revenue cycle management and best patient access practices, as well as recommended
strategies that labs and pathology groups can employ to take a proactive
approach to their collection practices—and why it’s so important for the
process to begin upfront.
“Patient
Access Antidote: Retaining More Revenue with Front-End Solutions” shares useful insights regarding front-end patient access
management, and equips clinical laboratories and pathology groups with the expert tools and solutions they need to optimize their cash flow and
successfully meet key revenue cycle objectives.
Just a few examples of the best practices covered in this complimentary White Paper: determining patient responsibility and factoring in prior-authorization and medical necessity, identifying patients’ financial clearance or propensity to pay, and providing consumers a clear explanation of their financial policies—along with a detailed, reliable estimate of their out-of-pocket expenses—as early in the revenue cycle as possible.
At DarkDaily.com, readers can access free resources on a variety of topics tailored specifically to the needs of laboratory administrators, lab managers, pathologists, and lab industry consultants.
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.
Customer relationship
management (CRM) plays a critical role in helping providers care for patients
with chronic diseases and clinical laboratories are part of those solutions
Home healthcare continues to boom in the US and more
technology companies each year—including Salesforce—strive to expand their
presence within the industry. This represents a significant shift in site of
service for a substantial and growing number of Americans. Equally true is that
home healthcare is an opportunity for clinical laboratories to serve this
increasing proportion of the American population.
Statistics tell the tale behind the boom in home healthcare.
The Centers
for Disease Control and Prevention (CDC) estimates that six in 10 adults in
the United States suffer from chronic diseases, such as cancer, and four in 10
adults live with two or more chronic illnesses.
This means that among medical laboratories and other
providers servicing the home healthcare industry demand for clinical laboratory
testing will increase.
Last year, approximately $103 billion was spent on home
healthcare services and that number is expected to reach $173 billion by 2026,
according to the Centers for Medicare and
Medicaid Services (CMS). Approximately 7.6 million people in the US now
require some level of in-home medical care. The overall employment of in-home
healthcare providers is projected to grow 41% between 2016 and 2026.
Efficient tools that assist home healthcare organizations and
their providers are critical. Customer
Relationship Management (CRM) platforms that combine data gathered during
office visits with patients’ living and economic situations are proving to be powerful
allies for treating chronic disease populations.
Social Determinants
of Health
One such CRM developer, Salesforce,
is rising to the demand by adding new features to its existing Health
Cloud platform. Originally introduced in 2016 as a way to improve how
healthcare and life sciences organizations connect with patients, this product
is one example of how Silicon Valley companies are attempting to make inroads
within the healthcare sector. Health Cloud’s newest functional upgrades include:
These social determinants of health are typically not
included in health records. But they can be vital information for healthcare
providers. Clinical laboratory managers should pay attention to “social
determinants of health” because this term describes a new dimension in medical
care and how patients with chronic diseases are managed.
“A lot of people in healthcare know about the importance of social determinants of health, but the volume of information is so great that being able to display things clearly and concisely in front of the [providers who] are using it—when they need it—makes it more operant and more prominent in the care of that patient,” Joshua Newman, MD, Chief Medical Officer at Salesforce, told MedCity News. (Photo copyright: San Francisco Business Times/Biz Journals.)
This is a critical factor. Healthcare providers who use Salesforce’s
Health Cloud can now record a patient’s social determinant information—such as,
transportation issues, housing status, and care network—directly into that
patient’s profile. Access to this type of information can give healthcare
professionals a more complete understanding of each patient’s unique situation.
Here are some examples from a Salesforce press
release that illustrate how social-determinants-of-health data can help
patients and care providers:
“A care provider that wants to limit a patient’s
risk for readmission can know if the patient has access to transportation or
the ability to purchase healthy meals.
“A life science organization that wants to help
patients adhere to their therapies, or properly use their medical devices, can
see a patient’s employment status and living arrangements, and thus offer the
necessary level of financial and in-home support.
“A payer organization can deliver personalized
preventative or wellness material to members based on the member’s education or
reading level.”
“Our industry continues to centralize and integrate patient
data, but it is critical that we stay focused on improving the patient
experience,” noted Ashwini
Zenooz, MD, in the press release. Zenooz is Salesforce’s Senior Vice
President and General Manager, Global Healthcare and Life Sciences. “By surfacing
critical factors of a patient’s life in a single view, we empower care
providers to personalize patient care experiences and improve outcomes.”
Many
existing CRM products cannot collect data from a variety of sources and then
sort and analyze that information to provide users with actionable
intelligence. Salesforce is attempting to fill that void among health and
medical software products with Health Cloud.
“Healthcare has been slower culturally, politically, and
socially to share their data. But what we’re seeing now is even those
organizations that have historically not shared their data are realizing they
can do a better job if they do,” Newman told MedCity News.
Outside Hospital Care
Increasing
Salesforce has also added a service it calls the Connected
Patient Journey to its Health Cloud platform. This service is an
integration between Health Cloud and Salesforce marketing, which can
personalize information given to patients based on their unique health needs.
Using this feature allows providers to build patient lists and use marketing techniques
to reach patients who would most benefit from specific campaigns and
information.
“The general overarching theme that unites all of these
innovations is that care is gravitating increasingly toward the home or outside
of the hospital and the doctor’s office,” said Newman.
Whether in-hospital or in-home, clinical laboratory tests play
a critical role in healthcare services. The ability for clinical laboratories
to enter patients’ test results data directly into CRM systems like Health
Cloud could help providers utilizing those systems better assist patients with
chronic diseases.
Starting in July 2019,
to comply with PAMA, medical laboratories are expected to analyze their private
payer price data to help ensure clean, complete, and accurate reporting by
March 31, 2020
The Centers for Medicare and Medicaid Services (CMS) did not implement fines with the first round of reporting, but that could change this round, noted Lâle White, Executive Chairman and CEO of XIFIN Inc., a healthcare IT company. White offered perspectives on PAMA’s impact to medical labs during EWC earlier this week.
“In this second period of data collection, it’s becoming
even more important for us to collect data accurately, precisely, and provide
nearly perfect information on this because we can see the impact is fairly
significant to our industry, and with payers ratcheting down their pricing,
it’s becoming even more significant,” White said.
The daylong workshop dedicated to PAMA compliance featured
legal and informatics
experts, consultants, and also laboratory healthcare executives who shared
lessons learned from the previous reporting cycle.
Sarah Simonson, Director of Client Management at Change Healthcare, advised labs to test their data extraction process now; produce a small sample of full data; then collaborate to filter out the exclusions, such as Medicaid and self-pay, among others. Simonson also recommends that labs designate a project champion.
Diana Voorhees (above), Principal/CEO for DV and Associates Inc., notes that “One benefit of the PAMA price reporting process is it can help labs identify coding errors that may not have been detected.” Voorhees was a presenter at the PAMA private payer price reporting workshop. (Photo copyright: DARK Daily.)
Things Clinical Labs
Should Watch for During the Validation Process
Looking forward, July 1, 2019, marks the start of the data
validation period. Here are some things labs should focus on and look out for.
Payments that are not applicable: These would include test codes paid under Medicare’s Physician Fee Schedule; denied ($0.00) payments; unresolved appeals; capitated payments; and payments where the associated test volume cannot be determined.
For example, when a private payer denies payment for a laboratory test, payments of $0.00 or “zero dollars” are not considered a private payer rate for purposes of determining applicable information under the new Clinical Laboratory Fee Schedule (CLFS), according to CMS. Laboratories should not report “zero dollars” for a laboratory test code where a private payer has denied payment within a data collection period.
Very low payments: Data reporters may be tempted to exclude very low payments. However, Joyce Gresko, JD, a Partner in the firm Alston and Bird LLP, based in Washington, DC, cautions that this choice may trigger civil monetary penalties. PAMA gives CMS the authority to issue civil monetary penalties if labs fail to report data, or if they misrepresent or omit reported data, according to CMS’ website.
Look outside the data
collection window: While CMS specifies that labs report payments received
between Jan. 1, 2019, and June 30, 2019, there may be important and related
test data points prior to and after those dates, says Craig Young, Senior
Financial Analyst for XIFIN. The adjudication date is key to helping report
correctly, he said.
When in doubt, leave
it out: Young emphasized double checking that payers have stated the unit correctly
to help ensure the correct volume will be reported per test, per price. And he
adds, when in doubt, leave it out, but be prepared to defend yourself if you do.
CMS Administrator
Seema Verma Hints at the Possibility of Audits
CMS requires independent laboratories, physician office laboratories, and hospital outreach laboratories that meet the current definition of “applicable laboratory” under PAMA regulations to report specific information. This includes laboratory test HCPCS (Healthcare Common Procedure Coding System) codes, associated private payer rates, and volume data that corresponds to each private payer rate. The data reporting period starts Jan. 1, 2020, and continues through March 31, 2020.
PAMA is particular in that it regularly resets the rates that Medicare pays for clinical diagnostic laboratory tests under the CLFS based on the data that labs submit. For the initial implementation of PAMA price reporting, CMS did not independently verify the accuracy of labs’ self-determination, but CMS Administrator Seema Verma recently made some provocative statements concerning analyzing claims data.
The CMS is “working to automatically detect claims that have
inappropriately unbundled the panel tests,” Verma wrote in a
letter to Senate Finance Chair Chuck Grassley (R-Iowa). As Modern Healthcare reported, “[CMS]
is scrutinizing lab test bills submitted to Medicare to make sure the
government hasn’t been overpaying laboratories because of inappropriate coding.”
Mining private payer price datasets out of billing systems
can be tedious, difficult, and the data may be overwhelming, said Trish Hankila, Vice President
of Finance for South Bend Medical Foundation
in South Bend, Ind., one of the EWC PAMA presenters. Hankila advises running a
global report to determine the scope of the project. Ultimately, diligence is
required, and labs will benefit from developing their PAMA team as soon as
possible.
Sonic’s data-driven
approach to population health management, based on helping clinicians intervene
with patients to control healthcare costs, increases the lab’s revenue
Using integrated financial and clinical analytics, Sonic is
developing technologies to build clinical
decision support tools for its provider and health plan clients. The
providers and health plans use those tools to engage patients and help them
manage their health.
“We are getting paid for contracting strategies beyond fee-for-service,” Sonic’s Chief Strategy Officer Phil Chen, MD, PhD, told the 875 attendees at the 24th Annual Executive War College (EWC) in New Orleans, one of the largest crowds in the history of the event. In his presentation, Chen outlined value-based contracting strategies that Sonic uses to share savings with its healthcare provider clients.
Identifying Low-Cost
Patients Who May Become High-Cost Patients
“Follow the people, follow the money,” Chen said. During his
presentation, he explained how Sonic uses lab test results and financial data
to show providers how some low-cost patients over time can become high-cost
patients. And how Sonic uses lab test data to help physicians identify low-cost
patients who may need certain interventions before they become high-cost
patients.
Providers have opportunities to intervene with patients who have renal failure, congestive heart failure, ischemic heart disease, diabetes, and other conditions, Chen said.
“Why do some people in the low-cost categories jump into the
high-cost category?” he asked. Lab test data offer clues, he suggested.
In his presentation at the 24th Annual Executive War College (EWC) in New Orleans, Sonic Healthcare’s Chief Strategy Officer Phil Chen, MD, PhD (above), explained how his lab has a data-driven approach to population health management. The strategy, he says, allows clinicians to intervene as needed with patients to improve their health and to control healthcare costs. (Photo copyright: DARK Daily.)
Over several years, Sonic has worked with one client
provider group to identify patients who would benefit the most from
interventions to prevent their healthcare costs from rising sharply. For a
health plan with 75,000 lives, Chen showed how Sonic tracked the cost of
patients from one to the next. “The goal is to find out who are the patients
who consume high healthcare cost, but may benefit from early intervention,” he
said.
Sonic found that about two-thirds of high-cost patients were
in the low-cost group just one year earlier. “We then focused on this subset
trying to determine the reasons they transitioned from low to high cost,” he
explained. “We found that the reason they were low cost the year before was not
because they were healthy. Instead, it was because they did not engage with the
healthcare system for their chronic disease management.”
Therefore, their treatment costs were low. But when they entered the healthcare system in the following year, their costs rose sharply, he said. Sonic used its iMorpheus data analytics system to show that 26.5% of the low-cost patients had diabetes, but that they had not seen their physician in the previous 12 months.
Partnering with
Health Plans Increases Patients’ Visits
When Sonic explained to its health plan client that the
health plan needed to contact those patients to ensure they would get the care
they needed, the health plan administrator told Sonic the health plan didn’t
have the resources to do the work. Instead, the health plan expected Sonic to
contact the patients. The administrator told Sonic, “You need to do it because
I need a healthcare partner,” Chen said.
Sonic did not have the staff to call those patients either. So,
the company developed an automated interactive voice response system to call the
patients. Sonic recorded the patients’ physicians and then had the system place
the calls. Of the patients who received the calls, 44% responded and visited
their physicians.
For this ACO, Sonic used its pathology and laboratory
informatics system to integrate clinical and claims-based financial risk
assessment data. As a result of Sonic’s work, the ACO’s payments from Medicare
rose from $12.8 million one year to $26 million the next. As a result, Chen
said, “We got a nice check for the work we did for this ACO.”
