Dec 3, 2018 | Digital Pathology, Instruments & Equipment, Laboratory Instruments & Laboratory Equipment, Laboratory Management and Operations, Laboratory Pathology, Laboratory Testing, Management & Operations
As personalized medicine becomes more popular, clinical laboratories, and anatomic pathologists are uniquely positioned to use next-generation sequencing to advance their scope among regulators, insurers, providers and patients, while adding clinical value and generating a new revenue source
By now, most clinical pathologists and medical laboratory scientists recognize that genetics, genetic testing, and gene sequencing will be a major transformative force in this country’s healthcare system. Genetics is the future of modern medicine.
At the same time, most independent labs and health network labs still lack the key resources needed for them to provide accurate and state-of-the-art genetic testing and gene sequencing services in support of clinical care.
The good news is that it is not yet prime time for genetic testing—meaning few genetic tests have become part of routine care, particularly in primary care settings. Today’s limited use of genetic tests creates the opportunity for any medical laboratory and anatomic pathology group to use this time to develop its genetic testing strategy. It also has time to incrementally put in place the resources it will need to offer genetic testing and gene sequencing services to its client physicians.
“Every clinical lab that wants to be a provider of genetic tests needs three basic resources,” stated Robert L. Michel, Editor-in-Chief of The Dark Report and Dark Daily. “First, the lab must have information technology in place that can handle genetic and molecular data. The second thing needed are pathologists, PhDs, and clinical laboratory scientists trained in genetic and molecular diagnostics. Of course, the third resource is to have the lab analyzers, instruments, and automation needed to extract, amplify, and sequence specimens.”
Experts agree that adoption of genetic testing will happen at a rapid pace. “Next-generation sequencing (NGS) is an incredibly powerful, positive force in medical care. We were in the Dark Ages before this. It is the tsunami on our shores, and it’s going to take over all of medicine. It’s not a trend. It’s the future of medicine. There’s no question about it,” predicts Maurie Markman, MD, an oncologist and President of Medicine and Science at Cancer Treatment Centers of America, in an article he penned for Health Connect South.
“As knowledge of genomic medicine has increased, its cost has plummeted,” notes Maurie Markman, MD (above), President of the Cancer Treatment Centers of America, in his Health Connect South article. “Sequencing a human genome [in 2015] costs less than $10,000, compared to more than $100 million in 2001. Not only are the tests more available to patients, but more oncologists are trying their hand at tumor testing and building on the base of knowledge.” (Photo copyright: Cancer Treatment Centers of America.)
“This can be done by either adding the needed functions to the existing laboratory information system (LIS) or supplementing that LIS with appropriate middleware solutions,” he continued. “This is true even if a lab plans to outsource both the gene sequencing and the annotation and interpretation of the resulting gene sequences. It will need in-house informatics capabilities to store and report that genetic information.”
NGS, Gene Sequencing, Precision Medicine, and Clinical Laboratories
Purchasing, implementing, and operating NGS technologies can be a costly venture, so it is critical that labs know and understand the needs of their referring clients.
“Knowing who your lab’s customers are and what you do for them today should guide you as a laboratory,” notes Brian Keefe, Vice President of Sales and Customer Innovation at Psyche Systems, a laboratory solutions developer for the medical industry based in Boston. “For example, your pathology group knows it should be offering NGS testing, and the justification for needing to go in this direction is because 90% of your clients are oncologists.”
Using NGS technology and marketing it to clients will be a valuable benefit for clinical laboratories. It will enable labs to participate in personalized medicine and allow them to become the “go to” facility for specific genetic tests.
“If you’re a laboratory that has figured out how to map the genome for nightmare bacteria, it doesn’t matter whether you’re three miles or 3,000 miles away, physicians will send their samples to your lab regardless of the distance,” Keefe notes. “If your lab is first to market, you establish powerful brand recognition and attract positive attention, which justifies your lab’s cost to set up and offer that testing in the first place.”
Learn More by Requesting the Dark Daily NGS White Paper
To help medical laboratories and anatomic pathology groups learn more about the growing role of NGS in clinical care, and how NGS can benefit clinical and molecular laboratories, Dark Daily and The Dark Report have produced a white paper titled, “How Next-Generation Sequencing Helps Molecular Laboratories Deliver Personalized Medicine Services to their Client Physicians.”
Medical laboratory leaders who want to learn how labs can establish NGS services and implement the IT/Informatics needed to be successful in using NGS should request a copy of this important white paper. It reviews how pathologists can help providers select targeted therapies and touches on marketing strategies to use NGS to procure new customers and retain existing customers.
The NGS white paper can be downloaded at no cost by clicking here or placing https://www.darkdaily.com/how-next-generation-sequencing-helps-molecular-laboratories-deliver-personalized-medicine-services-to-their-client-physicians-601/ into your browser.
—JP Schlingman
Related Information:
How Next-Generation Sequencing Helps Molecular Laboratories Deliver Personalized Medicine Services to their Client Physicians
Genomic Medicine: The Future of Cancer Treatment Is Now
Clinical Pathology Labs Are on Track to Get New Genetic Test That Screens for 448 Rare Childhood Diseases
Is Whole-genome Sequencing Reaching a Tipping Point for Clinical Pathology Laboratories?
Nov 26, 2018 | Coding, Billing, and Collections, Instruments & Equipment, Laboratory News, Laboratory Operations, Laboratory Pathology, Laboratory Testing, Management & Operations
Despite the widespread adoption of electronic health record (EHR) systems and billions in government incentives, lack of interoperability still blocks potential benefits of digital health records, causing frustration among physicians, medical labs, and patients
Clinical laboratories and anatomic pathology groups understand the complexity of today’s electronic health record (EHR) systems. The ability to easily and securely transmit pathology test results and other diagnostic information among multiple providers was the entire point of shifting the nation’s healthcare industry from paper-based to digital health records. However, despite recent advances, true interoperability between disparate health networks remains elusive.
One major reason for the current situation is that multi-hospital health systems and health networks still use EHR systems from different vendors. This fact is well-known to the nation’s medical laboratories because they must spend money and resources to maintain electronic lab test ordering and resulting interfaces with all of these different EHRs.
Healthcare IT News highlighted the scale of this problem in recent coverage. Citing data from the Healthcare Information and Management Systems Society (HIMSS) Logic database, they note that—when taking into account affiliated providers—the typical health network engages with as many as 18 different electronic medical record (EMR) vendors. Similarly, hospitals may be engaging with as many as 16 different EMR vendors.
The graphics above illustrates why interoperability is the most important hurdle facing healthcare today. Although the shift to digital is well underway, medical laboratories, physicians, and patients still struggle to communicate data between providers and access it in a universal or centralized manner. (Images copyright: Healthcare IT News.)
The lack of interoperability forces healthcare and diagnostics facilities to develop workarounds for locating, transmitting, receiving, and analyzing data. This simply compounds the problem.
According to a 2018 Physician’s Foundation survey, nearly 40% of respondents identified EHR design and interoperability as the primary source of physician dissatisfaction. It has also been found to be the cause of physician burnout, as Dark Daily reported last year in, “EHR Systems Continue to Cause Burnout, Physician Dissatisfaction, and Decreased Face-to-Face Patient Care.”
Pressure from Technology Giants Fuels Push for Interoperability
According to HITECH Answers, the Centers for Medicare and Medicaid Services (CMS) has paid out more than $38-billion in EHR Incentive Program payments since April 2018.
Experts, however, point out that government incentives are only one part of the pressure vendors are seeing to improve interoperability.
“There needs to be a regulatory push here to play referee and determine what standards will be necessary,” Blain Newton, Executive Vice President, HIMSS Analytics, told Healthcare IT News. “But the [EHR] vendors are going to have to do it because of consumer demand, as things like Apple Health Records gain traction.”
Dark Daily covered Apple’s progress into organizing protected health information (PHI) and personal health records (PHRs) earlier this year in, “Apple’s Update of Its Mobile Health App Consolidates Data from Multiple EHRs and Makes It Easier to Push Clinical Laboratory Data to Patients.” It is one of the latest examples of Silicon Valley tech companies attempting to jump into the health sector and providing patients and consumers access to the troves of medical data created in their lifetime.
Another solution, according to TechTarget, involves developing application programming interfaces (APIs) that allow tech companies and EHR vendors to achieve better interoperability by linking information in a structured manner, facilitating secure data transmission, and powering the next generation of apps that will bring interoperability ever closer to a reality.
TechTarget reported on how University of Utah Hospital’s five hospital/12 community clinic health network, and Intermountain Healthcare, also in Utah, successfully used APIs to develop customized interfaces and apps to improve accessibility and interoperability with their Epic and Cerner EHR systems.
Diagnostic Opportunities for Clinical Laboratories
As consumers gain increased access to their data and healthcare providers harness the current generation of third-party tools to streamline EHR use, vendors will continue to feel pressure to make interoperability a native feature of their EHR systems and reduce the need to rely on HIT teams for customization.
For pathology groups, medical laboratories, and other diagnosticians who interact with EHR systems daily, the impact of interoperability is clear. With the help of tech companies, and a shift in focus from government incentives programs, improved interoperability might soon offer innovative new uses for PHI in diagnosing and treating disease, while further improving the efficiency of clinical laboratories that face tightening budgets, reduced reimbursements, and greater competition.
—Jon Stone
Related Information:
Why EHR Data Interoperability Is Such a Mess in 3 Charts
EHR Incentive Program Status Report April 2018
New FDA App Streamlines EHR Patient Data Collection for Researchers
AAFP Nudges ONC toward EHR Interoperability
A New Breed of Interoperable EHR Apps Is Coming, but Slowly
Top Interoperability Questions to Consider during EHR Selection
EHR Design, Interoperability Top List of Physician Pain Points
2018 Survey of America’s Physicians: Practice Patterns & Perspectives
ONC: 93% of Hospitals Have Adopted Most Recent EHR Criteria, but Most Lag in Interoperability
Open Standards and Health Care Transformation: It’s Finally Delivering on the Value It Promised
Apple’s Update of Its Mobile Health App Consolidates Data from Multiple EHRs and Makes It Easier to Push Clinical Laboratory Data to Patients
EHR Systems Continue to Cause Burnout, Physician Dissatisfaction, and Decreased Face-to-Face Patient Care
Nov 23, 2018 | Laboratory Management and Operations, Laboratory News, Laboratory Operations, Laboratory Pathology, Laboratory Testing, Management & Operations
PwC report indicates deal-making may generate long-term savings, but adds to higher medical costs as hospital systems dominate markets and drive up prices
Consolidation of big hospital health networks combined with a loss of independent doctor practices has changed the healthcare landscape in recent years, and clinical laboratories and anatomic pathology groups have been directly impacted. Now, those trends, along with increased access to care, are expected to push employer medical cost up by as much as 6% in 2019.
That’s according to the PricewaterhouseCoopers (PwC) Health Research Institute (HRI) “Behind the Numbers” annual analysis of the employer-based market.
The continued deal-making is bad news for medical laboratories, since super-sized hospital systems typically trim the budgets of laboratory and other services to improve operating efficiencies.
At the same time, more doctors are practicing as employees of hospitals, health networks, and medical groups. This physician consolidation presents challenges for independent clinical laboratories, which often lose test orders to in-house hospital labs when physicians no longer practice independently.
Consumer Demand for Access to Healthcare Will Drive Costs Higher
Consolidation-related pressures are not the only forces pushing medical costs higher. HRI expects a third factor to inflate medical costs in 2019—consumer pressure for more ways to access care.
The growth of care options such as: retail clinics, telemedicine, urgent care, and on-site employer health clinics may bring prices down over time, however increased utilization often raises employers’ healthcare costs in the short-term as workers take advantage of easier ways to access care, the report states.
Less Flu and High-Performing Health Networks Expected to Lower Costs
Conversely, HRI believes a milder flu season in 2018-2019 may help keep spending increases in check. Additionally, the growing number of healthcare advocates in the workplace who educate employees on the use of their healthcare benefits, plus the creation of high-performing health networks—both of which emphasize high-quality care alongside cost savings—should serve to deflate healthcare spending.
In an interview with FierceHealthcare, Barbara Gniewek, a Health Services Principal at PwC, compared attempts to control healthcare spending to a balloon. “Every time you squeeze one area” another issue crops up, she said.
Employer healthcare costs have risen 5.5% to 7% annually for each of the past five years. HRI contends downward pressure on healthcare prices overall—not just drug prices—may be the only remaining way for employers and health plans to keep healthcare spending from outpacing inflation.
“Efforts by employers to cut utilization have mostly run their course,” the report states. “Employers and consumers are plagued by high prices that continue to grow because of new, expensive medical services and drugs, and other factors, such as consolidation.”
While the 2019 spending number pales in comparison to the annual double-digit growth in healthcare spending two decades ago, Gniewek told RevCycleIntelligence the inflation news should not be viewed as positive.
“While some people are relieved that it’s not the high rates of 15 or 20 years ago, costs going up at that rate still [are] unsustainable,” Barbara Gniewek, Health Services Principal at PwC, told RevCycleIntelligence. “We still haven’t figured out how to control healthcare costs and we still don’t have the type of healthcare that we need.” (Photo copyright: PricewaterhouseCoopers.)
In theory, healthcare consolidation should create economies of scale that result in efficiencies that drive costs lower. However, reality can be much different, since short-term prices often rise when one health system suddenly dominates a market.
“We need to start getting to the point where we pull out the excess redundancies in the system and be able to monetize that in terms of savings,” Gniewek told RevCycleIntelligence. “We just haven’t seen that happen yet. It’s been more, ‘I own the market, so I can drive up the prices.’ As the government and employers demand better price control and want to do some direct contracting or high-performing networks, then eventually consolidations will be more efficient.”
Knowledge@Wharton, an online business analysis journal from the Wharton School of the University of Pennsylvania, notes one of the consequences of the Affordable Care Act was the “giant wave of consolidation” it sparked.
“It’s both ‘horizontal’ and ‘vertical,’ meaning hospitals aren’t just buying other hospitals, they’re picking up physician practices, rehabilitation facilities, and other ancillary healthcare providers,” a Knowledge@Wharton article on hospital consolidation stated.
Of the 115 health-system and hospital mergers announced in 2017, 10 were mega-deals involving sellers with net annual revenues of at least $1 billion, PwC noted in its annual report. The largest is a $28.4 billion merger between San Francisco-based Dignity Health and Catholic Health Initiatives of Englewood, Colo., which is expected to close in the coming year, according to a press release.
And a July 2018 report from the National Council on Compensation Insurance (NCCI) notes that though hospital mergers can lead to operating cost reductions for acquired hospitals of 15% to 30%, those reductions usually do not translate into price decreases.
“Research to date shows that hospital mergers increase the average price of hospital services by 6% to 18%. For Medicare, hospital concentration increases costs by increasing the quantity of care, rather than the price of care,” NCCI stated.
Clinical Laboratories May Be Part of Cost Reductions
The impact of physician employment was underscored in the March 2018 update to the Physician Advocacy Institute’s “Physician Practice Acquisition Study: National and Regional Changes in Physician Employment 2012-2016.” Over a four-year period from July 2012 to July 2016, the percentage of hospital-employed physicians increased by more than 63%.
If the factors fueling today’s increases in healthcare spending—consolidation and convenience—continue pushing costs higher, clinical laboratories and anatomic pathology groups will most likely be impacted as employers, insurers, and consumers look for ways to cut medical costs.
In this environment, medical laboratories must continually work to deliver more value to providers, patients, and healthcare networks.
—Andrea Downing Peck
Related Information:
Medical Cost Trend: Behind the Numbers 2019
Report: Consolidation, Convenience Care Major Drivers Behind Increased Healthcare Costs in 2019
The Impact of Hospital Consolidation on Medical Costs
Dignity Health and Catholic Health Initiatives to Combine to Form New Catholic Health System Focused on Creating Healthier Communities
Updated Physician Practice Acquisition Study: National and Regional Changes in Physician Employment 2012-2016
Healthcare Mergers, Increased Access to Boost Medical Costs 6%
Nov 19, 2018 | Laboratory Management and Operations, Laboratory News, Laboratory Operations, Laboratory Pathology, Laboratory Testing, Management & Operations
New bioinformatic tool finds gut microbiota may be ‘potential reservoir of bloodstream pathogens’ suggesting patients’ own bodies can be source of infections
Clinical laboratories in hospitals and health networks throughout the nation are collaborating in the priority effort to reduce deaths from sepsis and related blood infections. Now comes news that researchers at Stanford have identified an unexpected source of bloodstream infections. This finding may help medical laboratories contribute to faster and more accurate diagnoses of blood infections, particularly for hospital inpatients.
Lax infection-control practices often are blamed for hospital-acquired infections (HAIs). And HAIs certainly have been responsible for many tragic avoidable deaths. However, new research from Stanford University School of Medicine shows that hospital staff, other patients, or unclean instruments may not be solely responsible for all infections that present during hospital stays. According to Stanford researchers, a patient’s own digestive tract can be the surprising culprit for many bloodstream infections. This finding confirms a common belief that the patient’s microbiome probably is involved in many blood infections.
Clinical pathologists have become vital players in infection prevention programs, as hospitals intensify their focus on reducing HAIs. That’s especially in light of the Centers for Medicare and Medicaid Services (CMS) implementation of the pay-for-performance Hospital-Acquired Condition (HAC) Reduction Program. Now, Stanford researchers have found that for many hospital patients their own bodies may be the source of infections.
The researchers published their findings in Nature Medicine.
Bacteria Causing Blood Infections Found in Patients’ Stool Samples After Bone Marrow Transplants
Using a new bioinformatic computational tool called StrainSifter, the Stanford University team rapidly and accurately identified a surprising infection source in a group of hospitalized patients—microbes already living in the patients’ large intestines—a Stanford University news release explained.
The researchers analyzed blood and stool samples from 30 patients who developed bloodstream infections after receiving bone marrow transplants between October 2015 and June 2017 at Stanford Hospital. The researchers sought to determine whether the bacteria isolated from the patients’ blood also was found in stool specimens that had been collected prior to the transplants. The process required sequencing not only the patients’ DNA, but also analyzing the genomes of all the individual microbial strains resident in each patient’s stool.
“Just finding E. coli in a patient’s blood and again in the patient’s stool doesn’t mean they’re the same strain,” Ami Bhatt, MD, PhD, Assistant Professor of Hematology and Genetics at Stanford, explained in the news release. Bhatt served as senior author of the study. (Photo copyright: Stanford University.)
Analysis found that more than one-third of the patients’ stool samples (11) contained detectable levels of the same bacterial strain that had caused those patients’ bloodstream infections.
“Because the gut normally harbors more than 1,000 different bacterial strains, it’s looked upon as a likely culprit of bloodstream infections, especially when the identified pathogen is one known to thrive inside the gut,” Ami Bhatt, MD, PhD, Assistant Professor of Hematology and Genetics at Stanford, said in the news release. “But while this culpability has been assumed—and it’s an entirely reasonable assumption—it’s never been proven. Our study demonstrates that it’s true.”
Clinical and DNA data confirmed the gastrointestinal presence of Escherichia coli and Klebsiella pneumonia, common causes of pneumonia, urinary tract infections, and other potentially serious conditions. In addition, they found other disease-causing pathogens in the gut that they would not have expected to be there.
“We also find cases where typically nonenteric [outside the intestine] pathogens, such as Pseudomonas aeruginosa and Staphylococcus epidermidis, are found in the gut microbiota, thereby challenging the existing informal dogma of these infections originating from environmental or skin sources,” Fiona Tamburini, a senior graduate student, and postdoctoral scholar Tessa Andermann, MD, MPH, Infectious Disease Medical Fellow, wrote in Nature Medicine.
New Tool for Precision Medicine
Bhatt believes being able to trace the source of bloodstream infections will help doctors provide more targeted treatments for HAIs and potentially lead to effective prevention methods. This will create a new opportunity for microbiology laboratories to provide the necessary diagnostic tests designed to guide therapeutic choices of attending physicians.
“Until now, we couldn’t pinpoint those sources with high confidence,” Bhatt said in the news release. “That’s a problem because when a patient has a bloodstream infection, it’s not enough simply to administer broad-spectrum antibiotics. You need to treat the source, or the infection will come back.”
Bhatt says the computational tool has the potential to allow medical practitioners to quickly identify whether a pathogen responsible for a patient’s bloodstream infection came from a break in the skin, leaked through the intestinal wall into the blood, or was passed on through an inserted catheter or other object.
Bhatt’s team focused on the intestines for their study because it’s the home of 1,000 to 2,000 different germs. Dark Daily has reported often on developments involving human gut bacteria (AKA, microbiome) in e-briefings going back to 2013. While these gut bacteria do not typically cause problems, Bhatt said, “It’s only when they show up in the wrong place—due, for example, to leaking through a disrupted intestinal barrier into the bloodstream—that they cause trouble.”
Because nearly 40% of immunocompromised patients who spend up to six weeks in a hospital develop bloodstream infections, the Stanford findings could signal a major breakthrough in preventing HAIs. However, larger studies are needed to validate the researchers’ contention that the gut is a “potential reservoir of bloodstreams pathogens.”
If true, microbiologists and clinical pathologists may in the future have a new method for helping hospitals identify, track, and treat blood-born infections as well as and preventing HAIs.
—Andrea Downing Peck
Related Information:
Study Traces Hospital-Acquired Bloodstream Infections to Patients’ Own Bodies
Hospital-Acquired Condition Reduction Program Fiscal Year 2019 Fact Sheet
Precision Identification of Diverse Bloodstream Pathogens in the Gut Microbiome
Multiple Dark Daily E-briefings on Human Gut Bacteria (Microbiome)
Nov 14, 2018 | Coding, Billing, and Collections, Laboratory Management and Operations, Laboratory News, Laboratory Operations, Laboratory Pathology, Laboratory Testing, Management & Operations
Physicians in Saskatchewan called for changes after wait times for anatomic pathology test results reached six weeks or more
Anatomic pathologist and histopathologist shortages have plagued the single-payer healthcare systems in Canada and the United Kingdom (UK) in recent years. The consequence is increased wait times for physicians in both countries to receive medical laboratory test results, which increases wait times across the entire healthcare continuum.
However, one Canadian province significantly reduced a backlog that had pushed wait times for surgical pathology test results to six weeks or more. It did this by having its pathologists perform first-stage examinations normally completed by pathology assistants or medical technologists.
The Saskatchewan Health Authority (SHA) announced in October it had cleared nearly half of the 2,600-plus biopsies that were waiting to be processed at hospital labs in Regina and Saskatoon, the Regina Leader-Post reported.
“I think we’ve been making amazing progress in the work,” Lenore Howey, Executive Director of Laboratory Services at SHA, told the newspaper. “It’s always good to take time to know and understand your process, so that we can put the right resources in the right places.”
Getting Anatomic Pathologists Involved
Howey stated the SHA cleared cases by having pathologists “assist with the work in the first phase”—or gross examination stage—of a biopsy. This is the part of the process during which pathology assistants or medical laboratory technologists typically record the size, weight, and description of a specimen and look for pathological changes.
In addition, the SHA hired an additional pathologist assistant and three histology/cytology technologists—one on a permanent basis and two on a temporary basis. Other improvements include:
- Working toward resolving problems with voice recognition transcription software being piloted in Regina for the gross examination phase of processing; and;
- Implementing an electronic specimen tracking system in Saskatoon, which eventually also may be used in Regina.
Physicians Express Dissatisfaction with Wait Times
Physicians attending the Saskatchewan Medical Association’s Spring Representative Assembly in May raised the backlog issue with Health Minister Jim Reiter, complaining about the impact on patient care. At that point, the backlog of pathology cases had hit 1,662 in Regina, while Saskatoon’s caseload totaled 1,005. Many of these biopsies involve cancer patients, thus delaying a diagnosis and the start of an appropriate treatment for these patients.
“I’m trying to get things done as expeditiously as possible,” urologist Francisco Garcia, MD, told the Leader-Post, “but for the first five or six weeks, I’m handcuffed in terms of what I’m able to do.”
Now, thanks to SHA’s efforts, as of Oct. 2 specimens in progress dropped to 785 in Regina and 748 in Saskatoon. Both numbers are within range of SHA’s target of 750.
“We do not have a backlog right now,” Lenore Howey, Executive Director of Laboratory Services at SHA, told the Leader-Post. “Our system is very stable, but we do have checks and balances to put in place so that we would never get there again, which we didn’t have prior.” (Photo copyright: Saskatchewan Health Authority.)
Wait Times Impacting Patient Care Worldwide
While Saskatchewan appears to have solved its most recent pathology reporting issue, this is not the first time the province has dealt with delays in lab testing reports. In 2011, Dark Daily reported on lengthy turnaround times for anatomic pathology test reports that averaged more than 12 days, which was blamed on shortage of pathologists dating back to 2001. (See, “Pathologist Shortage and Delays in Lab Test Reports Get Publicity in Saskatchewan,” August 15, 2011.)
And in October, Dark Daily reported that cancer patients in the UK are experiencing record waiting times for treatments, with more than 3,000 people waiting longer than two months to begin care, iNews reported. Delays there are being blamed in part on severe shortages of pathology staff. A 2017 workforce survey by the Royal College of Pathologists reported that only 3% of the National Health Service (NHS) histopathology departments responding to the survey had adequate staff. (See, “Shortage of Histopathologists in the United Kingdom Now Contributing to Record-Long Cancer-Treatment Waiting Times in England,” October 31, 2018.)
“Making sure pathology services can cope with current and future demand is essential if we are to ensure early diagnosis and improve outcomes for patients,” Jo Martin, PhD, President of the Royal College of Pathologists, told the BBC.
Increased workloads due to new NHS screening programs and an approaching retirement crisis—a quarter of all histopathologists in the UK are aged 55 or over—has caused the Royal College of Pathologists to call for more funded training places, better IT systems, and further investment in pathology services.
While the US healthcare system is not currently experiencing a shortage of clinical laboratory staff or anatomic pathologists, shortages in other countries illustrate the impact any delay in reporting results can have on patient care.
—Andrea Downing Peck
Related Information:
Backlog of Pathology Tests Cleared in Province
Technology and Staff Shortages Contribute to Biopsy Backlog
Pathology Staff Shortages Causing Delays to Cancer Diagnosis, Says Report
Cancer Waiting Times at their Worst Ever Level
Histopathology Workforce Survey 2018
Pathologists Shortage ‘Delaying Cancer Diagnosis’
Pathologists Shortage and Delays in Lab Test Reports Get Publicity in Saskatchewan
Shortage of Histopathologists in the United Kingdom Now Contributing to Record-Long Cancer-Treatment Waiting Times in England
Nov 7, 2018 | Instruments & Equipment, Laboratory Instruments & Laboratory Equipment, Laboratory News, Laboratory Pathology, Laboratory Testing, Management & Operations
CRISPR-Cas9 connection to cancer prompts research to investigate different approaches to gene editing
Dark Daily has covered CRISPR-Cas9 many times in previous e-briefings. Since its discovery, CRISPR, or Clustered Regularly Interspaced Short Palindromic Repeats, has been at the root of astonishing breakthroughs in genetic research. It appears to fulfill precision medicine goals for patients with conditions caused by genetic mutations and has anatomic pathologists, along with the entire scientific world, abuzz with the possibilities such a tool could bring to diagnostic medicine.
All of this research has contributed to a deeper understanding of how cells function. However, as is often the case with new technologies, unforeseen and problematic questions also have arisen.
CRISPR-Cas9 Connection to Cancer
Research conducted at the Wellcome Sanger Institute in the United Kingdom (UK) and published in Nature Biotechnology, examined potential damage caused by CRISPR-Cas9 editing.
“Here we report significant on-target mutagenesis, such as large deletions and more complex genomic rearrangements at the targeted sites in mouse embryonic stem cells, mouse hematopoietic progenitors, and a human differentiated cell line,” wrote the authors in their introduction.
Another study, this one conducted by biomedical researches at Cambridge, Mass., and published in Nature, describes possible toxicity caused by Cas9.
“Our results indicate that Cas9 toxicity creates an obstacle to the high-throughput use of CRISPR-Cas9 for genome engineering and screening in hPSCs [human pluripotent stem cells]. Moreover, as hPSCs can acquire P53 mutations, cell replacement therapies using CRISPR-Cas9-enginereed hPSCs should proceed with caution, and such engineered hPSCs should be monitored for P53 function.”
Essentially what both groups of researchers found is that CRISPR-Cas9 cuts through the double helix of DNA, which the cell responds to as it would any injury. A gene called p53 then directs a cellular “first-aid kit” to the “injury” site that either initiates self-destruction of the cell or repairs the DNA.
Therefore, in some instances, CRISPR-Cas9 is inefficient because the repaired cells continue to function. And, the repair process involves the p53 gene. P53 mutations have been implicated in ovarian, colorectal, lung, pancreatic, stomach, liver, and breast cancers.
Though important, some experts are downplaying the significance of the findings.
Erik Sontheimer, PhD (above), Professor, RNA Therapeutics Institute, at the University of Massachusetts Medical School, told Scientific American that the two studies are important, but not show-stoppers. “This is something that bears paying attention to, but I don’t think it’s a deal-breaker,” he said. (Photo copyright: University of Massachusetts.)
“It’s something we need to pay attention to, especially as CRISPR expands to more diseases. We need to do the work and make sure edited cells returned to patients don’t become cancerous,” Sam Kulkarni, PhD, CEO of CRISPR Therapeutics, told Scientific American.
Both studies are preliminary. The implications, however, is in how genes that have become corrupted are used.
“It is unclear if the findings translate into cells actually used in clinical studies,” Bernhard Schmierer, PhD, co-author of a paper titled, “CRISPR-Cas9 Genome Editing Induces a p53-mediated DNA Damage Response,” told Scientific American.
Nevertheless, the cancer-cat is out of the bag.
Targeting RNA Instead of DNA with CRISPR-Cas13d
A team from the Salk Institute may have found a solution. They are investigating a different enzyme—Cas13d—which, in conjunction with CRISPR would target RNA rather than DNA. “DNA is constant, but what’s always changing are the RNA messages that are copied from the DNA. Being able to modulate those messages by directly controlling the RNA has important implications for influencing a cell’s fate,” Silvana Konermann, PhD, a Howard Hughes Medical Institute (HHMI) Hanna Gray Fellow and member of the research team at Salk, said in a news release.
The Salk team published their findings in the journal Cell. The paper describes how “scientists from the Salk Institute are reporting for the first time the detailed molecular structure of CRISPR-Cas13d, a promising enzyme for emerging RNA-editing technology. They were able to visualize the enzyme thanks to cryo-electron microscopy (cryo-EM), a cutting-edge technology that enables researchers to capture the structure of complex molecules in unprecedented detail.”
The researchers think that CRISPR-Cas13d may be a way to make the process of gene editing more effective and allow for new strategies to emerge. Much like how CRISPR-Cas9 led to research into recording a cell’s history and to tools like SHERLOCK (Specific High-sensitivity Enzymatic Reporter unLOCKing), a new diagnostic tool that works with CRISPR and changed clinical laboratory diagnostics in a foundational way.
Dark Daily reported on this breakthrough last year. (See, “CRISPR-Related Tool Set to Fundamentally Change Clinical Laboratory Diagnostics, Especially in Rural and Remote Locations,” August 4, 2017.)
Each discovery will lead to more branches of inquiry and, hopefully, someday it will be possible to cure conditions like sickle cell anemia, dementia, and cystic fibrosis. Given the high expectations that CRISPR and related technologies can eventually be used to treat patients, pathologists and medical laboratory professionals will want to stay informed about future developments.
—Dava Stewart
Related Information:
Repair of Double-Strand Breaks Induced by CRISPR-Cas9 Leads to Large Deletions and Complex Rearrangements
P53 Inhibits CRISPR-Cas9 Engineering in Human Pluripotent Stem Cells
CRISPR-Edited Cells Linked to Cancer Risk in 2 Studies
CRISPR-Cas9 Genome Editing Induces a p53-Mediated DNA Damage Response
Decoding the Structure of an RNA-Based CRISPR System
Structural Basis for the RNA-Guided Ribonuclease Activity of CRISPR-Cas13d
CRISPR Timeline
What Are Genome Editing and CRISPR-Cas9?
Federal Court Sides with Broad in CRISPR Patent Dispute
Top Biologists Call for Moratorium on Use of CRISPR Gene Editing Tool for Clinical Purposes Because of Concerns about Unresolved Ethical Issues
CRISPR-Related Tool Set to Fundamentally Change Clinical Laboratory Diagnostics, Especially in Rural and Remote Locations
Researchers at Several Top Universities Unveil CRISPR-Based Diagnostics That Show Great Promise for Clinical Laboratories
