The Office of Management and Budget (OMB) concluded its review of the final rule on April 22. Former FDA commissioner Scott Gottlieb, MD, and other regulatory experts expect the White House to send the final rule to Congress as early as late April and no later than May 22.
On Tuesday morning, Lâle White, executive chair and CEO of San Diego’s XiFin, Inc., will present a keynote on new regulations and diagnostics players that are “poised to reshape lab testing.” Her presentation is followed by a general session on Clinical Laboratory Improvement Amendments (CLIA) regulations featuring Salerno Reynolds, PhD., acting director at the U.S. Centers for Disease Control and Prevention (CDC) Center for Laboratory Systems and Response.
Robert Michel, Editor-in-Chief of The Dark Report will wrap day one with a general session on the regulatory trifecta coming soon to all labs, from LDT to CLIA to private payers’ policies for genetic claims.
Innovation in the spotlight
“It’s a rich mix of expert speakers, lab leaders who are doing innovative things in their own organizations, along with the consultants and the lab vendors who are pushing the front edge of laboratory management, operations, and clinical service delivery,” says Michel, who each year creates the agenda for EWC.
Several sessions, master classes, and speakers will look to the future with discussions about how healthcare data drives innovations in diagnostics and patient care, digital pathology adoption around the world, and hot topics such as artificial intelligence (AI), big data and precision medicine.
Panels offer a variety of viewpoints
“One valuable benefit of participating at the Executive War College is the various panel discussions,” Michel says. “Each panel brings together national experts in a specific area of the laboratory profession. As an example, our lab legal panel this year brings together four prominent and experienced attorneys who share opinions, insights, and commentary about relevant issues in compliance, regulations, and contractual issues with health plans and others.”
This allows attendees to experience a breadth of opinions from multiple respected experts in this area, he adds.
For example, a digital pathology panel will bring together representatives from labs, service providers, and the consultants that are helping labs implement digital pathology. The session will be especially helpful to labs that are deciding when to acquire digital pathology tools and how to deploy them effectively to improve diagnostic accuracy, Michel says.
And a managed care panel will feature executives from some of the nation’s biggest health plans—the ones that sit on the other side of the table from labs—to provide insights and guidance on how labs can work more effectively with them.
Networking opportunities abound
The event is about much more than politics and policy, however. There’s also a distinct social aspect.
“Everyone is welcome, and everyone appreciates the camaraderie, so don’t be shy about going up and introducing yourself to someone. The quality of the crowd is top-notch, yet I’ve always experienced a willingness for those of us who have been to this rodeo to always be welcoming,” she notes.
Michel agrees. “One of the special benefits of participation at the EWC is the superb networking interactions and collaboration that takes place,” he says.
“From the first moments that attendees walk into our opening reception on Monday night until the close of the optional workshops on Thursday, one can see a rich exchange happening amongst circles of attendees. Introductions are being made. Connections are developing into business opportunities. The sum of an attendee’s experience at the Executive War College is to gain as much knowledge from the networking and collaboration as they do from the sessions.”
In a follow-up story, investigative news team in Boston sends a reporter’s cheek swab sample to the same pet DNA testing lab: report states the reporter is part Malamute, Shar Pei, and Labrador Retriever
One pet DNA testing company returned results from human cheek swabs showing two different people were in fact part dog. The resulting local reporting calls into question the accuracy of DNA testing of our beloved furry friends and may impact the trust people have in clinical laboratory genetic testing as well.
Pet DNA analysis is nearly as popular as human DNA analysis. The market is expected to exceed $700 million by the end of the decade, according to Zion Market Research. But are customers getting their money’s worth? One CBS news station in Boston decided to find out.
Last year, the WBZ I-Team, the investigative part of a CBS News station in Boston, looked into the accuracy of pet DNA testing. They reported on a pet owner who questioned the DNA test results she received for her German Shepard. The report indicated that her dog had DNA from more than 10 breeds, besides German Shepard.
During their research, the WBZ investigative reporters learned that pet owners order these tests to reveal what one pet DNA testing company described as understanding “your dog’s unique appearance, behavior, and health.”
“So, the WBZ-TV I-Team came with more tests from different companies to compare. All came back with some German Shepherd, but the percentages ranged from 65% to just 29%. Aside from that, the three companies showed a puzzling hodgepodge of other breeds. One included Great Pyrenees, another came back with Siberian Husky, another listed Korean Jindo, and the list goes on,” WBZ News reported.
The owner of the German Shepard then sent two swab samples from her own cheeks to one of the pet DNA testing companies. The test results indicated that she was 40% Border Collie, 32% Cane Corso, and 28% Bulldog.
The company that performed that DNA testing—DNA My Dog—insisted to the WBZ I-Team that one of the pet owner’s cheek samples contained dog DNA, WBZ News reported.
“The second sample did in fact yield canine DNA. … The results provided would not be possible on a human sample,” Jessica Barnett, Director of Service Operations, DNA My Dog, told WBZ News.
This must have come as a shock to the pet owner, who is probably sure she is not part dog.
“I think that is a red flag for sure,” Lisa Moses, VMD (above), a veterinarian and bioethicist with Harvard Medical School, told WBZ News. “A company should know if they’ve in any basic way analyzed a dog’s DNA, that that is not a dog,” she said. One wonders what might happen if a dog’s DNA was secretly sent to a clinical laboratory performing human genetic testing. What might the results be? (Photo copyright: Harvard Medical School.)
Two Times is the Charm
To continue its investigation into this odd occurrence, the WBZ I-Team decided to repeat the test this year. They sent a cheek saliva sample from one of their own reporters to three different dog DNA testing companies.
According to the I-Team report, one company, Orivet, said the sample “failed to provide the data necessary to perform breed ID analysis. Another company, Wisdom Panel stated the sample “didn’t provide enough DNA to produce a reliable result.”
However, DNA My Dog once again reported that the human sample belonged to a canine. This time the company’s test reported that the DNA sample was 40% Alaskan Malamute, 35% Shar Pei, and 25% Labrador Retriever.
DNA My Dog did not respond to WBZ I-Team’s attempt to contact them for a comment, WBZ News reported.
Wild West of DNA Testing
“I personally do have concerns about the fact that, from a consumer standpoint, you don’t always know what you’re getting when you work with those companies,” said geneticist Elinor Karlsson, PhD, Director of the Vertebrate Genomics Group at the Broad Institute of MIT and Harvard, told WBZ News. “There’s not a lot of rules in this space.”
Karlsson is also founder and Chief Scientist at Darwin’s Ark, a nonprofit organization that combines dog genetics and behavior to advance the understanding of complex canine diseases. People participating in the initiative contribute data about their dogs to an open source database, which is then shared with researchers around the globe. To date, more than 44,000 dogs have been registered with the project.
She hopes that reports like the one from the WBZ I-Team will not dissuade interest in pet genetics, as the science does have significant value when performed correctly.
“We might be able to figure out which dogs are at risk of getting cancer, and screen them more often and be able to diagnose it earlier,” Karlsson said. “We might be able to develop new treatments for that cancer.”
“There isn’t necessarily a gold standard answer for what your dog is,” veterinarian and bioethicist Lisa Moses, VMD, co-director of the Capstone Program for the Master of Science in Bioethics Program at Harvard Medical School, told WBZ News. “A breed is something that we’ve decided, which is based upon essentially the way a dog looks. But that doesn’t necessarily mean that we’re going to know what their genes look like.”
DNA My Dog Awarded ‘Best Budget Dog DNA Test’
In February, US News and World Report published an article rating the best dog DNA tests of 2024. The magazine ranked the DNA My Dog Essential Breed ID Test as the “best budget dog DNA test on the market.” The test sells for $79.99. According to the company’s website, a simple cheek swab yields:
A complete breed breakdown,
Genetic health concerns,
Unique personality traits, and
Bonding tips for dogs and their owners.
“I worry about people making medical decisions … based on one of these tests,” Moses told WBZ News, which added that, “She and some of her colleagues have called on lawmakers to set standards and regulations for pet DNA labs, and to require them to share their databases with each other, for more consistent results.”
The investigation into pet DNA testing by the television news reporters in Boston is a reminder to clinical lab managers and pathologists that DNA testing can be problematic in many ways. Also, when consumers read news stories like this one about inaccurate canine DNA testing, it can cause them to question the accuracy of other types of DNA testing.
Speedy DNA sequencing and on-the-spot digital imaging may change the future of anatomic pathology procedures during surgery
Researchers at the Center for Molecular Medicine (CMM) at UMC Utrecht, a leading international university medical center in the Netherlands, have paired artificial intelligence (AI) and machine learning with DNA sequencing to develop a diagnostic tool cancer surgeons can use during surgeries to determine in minutes—while the patient is still on the operating table—whether they have fully removed all the cancerous tissue.
The method, “involves a computer scanning segments of a tumor’s DNA and alighting on certain chemical modifications that can yield a detailed diagnosis of the type and even subtype of the brain tumor,” according to The New York Times, which added, “That diagnosis, generated during the early stages of an hours-long surgery, can help surgeons decide how aggressively to operate, … In the future, the method may also help steer doctors toward treatments tailored for a specific subtype of tumor.”
This technology has the potential to reduce the need for frozen sections, should additional development and studies confirm that it accurately and reliably shows surgeons that all cancerous cells were fully removed. Many anatomic pathologists would welcome such a development because of the time pressure and stress associated with this procedure. Pathologists know that the patient is still in surgery and the surgeons are waiting for the results of the frozen section. Most pathologists would consider fewer frozen sections—with better patient outcomes—to be an improvement in patient care.
“It’s imperative that the tumor subtype is known at the time of surgery,” Jeroen de Ridder, PhD (above), associate professor in the Center for Molecular Medicine at UMC Utrecht and one of the study leaders, told The New York Times. “What we have now uniquely enabled is to allow this very fine-grained, robust, detailed diagnosis to be performed already during the surgery. It can figure out itself what it’s looking at and make a robust classification,” he added. How this discovery affects the role of anatomic pathologists and pathology laboratories during cancer surgeries remains to be seen. (Photo copyright: UMC Utrecht.)
Rapid DNA Sequencing Impacts Brain Tumor Surgeries
The UMC Utrecht scientists employed Oxford Nanopore’s “real-time DNA sequencing technology to address the challenges posed by central nervous system (CNS) tumors, one of the most lethal type of tumor, especially among children,” according to an Oxford Nanopore news release.
The researchers called their new machine learning AI application the “Sturgeon.”
According to The New York Times, “The new method uses a faster genetic sequencing technique and applies it only to a small slice of the cellular genome, allowing it to return results before a surgeon has started operating on the edges of a tumor.”
Jeroen de Ridder, PhD, an associate professor in the Center for Molecular Medicine at UMC Utrecht, told The New York Times that Sturgeon is “powerful enough to deliver a diagnosis with sparse genetic data, akin to someone recognizing an image based on only 1% of its pixels, and from an unknown portion of the image.” Ridder is also a principal investigator at the Oncode Institute, an independent research center in the Netherlands.
The researchers tested Sturgeon during 25 live brain surgeries and compared the results to an anatomic pathologist’s standard method of microscope tissue examination. “The new approach delivered 18 correct diagnoses and failed to reach the needed confidence threshold in the other seven cases. It turned around its diagnoses in less than 90 minutes, the study reported—short enough for it to inform decisions during an operation,” The New York Times reported.
But there were issues. Where the minute samples contain healthy brain tissue, identifying an adequate number of tumor markers could become problematic. Under those conditions, surgeons can ask an anatomic pathologist to “flag the [tissue samples] with the most tumor for sequencing, said PhD candidate Marc Pagès-Gallego, a bioinformatician at UMC Utrecht and a co-author of the study,” The New York Times noted.
“Implementation itself is less straightforward than often suggested,” Sebastian Brandner, MD, a professor of neuropathology at University College London, told The Times. “Sequencing and classifying tumor cells often still required significant expertise in bioinformatics as well as workers who are able to run, troubleshoot, and repair the technology,” he added.
“Brain tumors are also the most well-suited to being classified by the chemical modifications that the new method analyzes; not all cancers can be diagnosed that way,” The Times pointed out.
Thus, the research continues. The new method is being applied to other surgical samples as well. The study authors said other facilities are utilizing the method on their own surgical tissue samples, “suggesting that it can work in other people’s hands.” But more work is needed, The Times reported.
UMC Utrecht Researchers Receive Hanarth Grant
To expand their research into the Sturgeon’s capabilities, the UMC Utrecht research team recently received funds from the Hanarth Fonds, which was founded in 2018 to “promote and enhance the use of artificial intelligence and machine learning to improve the diagnosis, treatment, and outcome of patients with cancer,” according to the organization’s website.
The researchers will investigate ways the Sturgeon AI algorithm can be used to identify tumors of the central nervous system during surgery, a UMC Utrecht news release states. These type of tumors, according to the researchers, are difficult to examine without surgery.
“This poses a challenge for neurosurgeons. They have to operate on a tumor without knowing what type of tumor it is. As a result, there is a chance that the patient will need another operation,” said de Ridder in the news release.
The Sturgeon application solves this problem. It identifies the “exact type of tumor during surgery. This allows the appropriate surgical strategy to be applied immediately,” the news release notes.
The Hanarth funds will enable Jeroen and his team to develop a variant of the Sturgeon that uses “cerebrospinal fluid instead of (part of) the tumor. This will allow the type of tumor to be determined already before surgery. The main challenge is that cerebrospinal fluid contains a mixture of tumor and normal DNA. AI models will be trained to take this into account.”
The UMC Utrecht scientists’ breakthrough is another example of how organizations and research groups are working to shorten time to answer, compared to standard anatomic pathology methods. They are combining developing technologies in ways that achieve these goals.
Palmetto GBA’s Chief Medical Officer will cover how clinical laboratories billing for genetic testing should prepare for Z-Codes at the upcoming Executive War College in New Orleans
After multiple delays, UnitedHealthcare (UHC) commercial plans will soon require clinical laboratories to use Z-Codes when submitting claims for certain molecular diagnostic tests. Several private insurers, including UHC, already require use of Z-Codes in their Medicare Advantage plans, but beginning June 1, UHC will be the first to mandate use of the codes in its commercial plans as well. Molecular, anatomic, and clinical pathologist Gabriel Bien-Willner, MD, PhD, who oversees the coding system and is Chief Medical Officer at Palmetto GBA, expects that other private payers will follow.
“A Z-Code is a random string of characters that’s used, like a barcode, to identify a specific service by a specific lab,” Bien-Willner explained in an interview with Dark Daily. By themselves, he said, the codes don’t have much value. Their utility comes from the DEX Diagnostics Exchange registry, “where the code defines a specific genetic test and everything associated with it: The lab that is performing the test. The test’s intended use. The analytes that are being measured.”
The registry also contains qualitative information, such as, “Is this a good test? Is it reasonable and necessary?” he said.
Molecular, anatomic, and clinical pathologist Gabriel Bien-Willner, MD, PhD (above), Palmetto GBA’s Chief Medical Officer, will speak about Z-Codes and the MolDX program during several sessions at the upcoming Executive War College on Diagnostics, Clinical Laboratory, and Pathology Management taking place in New Orleans on April 30-May 1. Clinical laboratories involved in genetic testing will want to attend these critical sessions. (Photo copyright: Bien-Willner Physicians Association.)
Palmetto GBA Takes Control
Palmetto’s involvement with Z-Codes goes back to 2011, when the company established the MolDX program on behalf of the federal Centers for Medicare and Medicaid Services (CMS). The purpose was to handle processing of Medicare claims involving genetic tests. The coding system was originally developed by McKesson, and Palmetto adopted it as a more granular way to track use of the tests.
In 2017, McKesson merged its information technology business with Change Healthcare Holdings LLC to form Change Healthcare. Palmetto GBA acquired the Z-Codes and DEX registry from Change in 2020. Palmetto GBA had already been using the codes in MolDX and “we felt we needed better control of our own operations,” Bien-Willner explained.
In addition to administering MolDX, Palmetto is one of four regional Medicare contractors who require Z-Codes in claims for genetic tests. Collectively, the contractors handle Medicare claims submissions in 28 states.
Benefits of Z-Codes
Why require use of Z-Codes? Bien-Willner explained that the system addresses several fundamental issues with molecular diagnostic testing.
“Payers interact with labs through claims,” he said. “A claim will often have a CPT code [Current Procedural Technology code] that doesn’t really explain what was done or why.”
In addition, “molecular diagnostic testing is mostly done with laboratory developed tests (LDTs), not FDA-approved tests,” he said. “We don’t see LDTs as a problem, but there’s no standardization of the services. Two services could be described similarly, or with the same CPT codes. But they could have different intended uses with different levels of sophistication and different methodologies, quality, and content. So, how does the payer know what they’re paying for and whether it’s any good?”
When the CPT code is accompanied by a Z-Code, he said, “now we know exactly what test was done, who did it, who’s authorized to do it, what analytes are measured, and whether it meets coverage criteria under policy.”
The process to obtain a code begins when the lab registers for the DEX system, he explained. “Then they submit information about the test. They describe the intended use, the analytes that are being measured, and the methodologies. When they’ve submitted all the necessary information, we give the test a Z-Code.”
The assessment could be as simple as a spreadsheet that asks the lab which cancer types were tested in validation, he said. On the other end of the scale, “we might want to see the entire validation summary documentation,” he said.
Commercial Potential
Bien-Willner joined the Palmetto GBA in 2018 primarily to direct the MolDX program. But he soon saw the potential use of Z-Codes and the DEX registry for commercial plans. “It became instantly obvious that this is a problem for all payers, not just Medicare,” he said.
Over time, he said, “we’ve refined these processes to make them more reproducible, scalable, and efficient. Now commercial plans can license the DEX system, which Z-Codes are a part of, to better automate claims processing or pre-authorizations.”
In 2021, the company began offering the coding system for Medicare Advantage plans, with UHC the first to come aboard. “It was much easier to roll this out for Medicare Advantage, because those programs have to follow the same policies that Medicare does,” he explained.
As for UHC’s commercial plans, the insurer originally planned to require Z-Codes in claims beginning Aug. 1, 2023, then pushed that back to Oct. 1, according to Dark Daily’s sister publication The Dark Report.
Then it was pushed back again to April 1 of this year, and now to June 1.
“The implementation will be in a stepwise fashion,” Bien-Willner advised. “It’s difficult to take an entirely different approach to claims processing. There are something like 10 switches that have to be turned on for everything to work, and it’s going to be one switch at a time.”
For Palmetto GBA, the commercial plans represent “a whole different line of business that I think will have a huge impact in this industry,” he said. “They have the same issues that Medicare has. But for Medicare, we had to create automated solutions up front because it’s more of a pay and chase model,” where the claim is paid and CMS later goes after errors or fraudulent claims.
“Commercial plans in general just thought they could manually solve this issue on a claim-by-claim basis,” he said. “That worked well when there was just a handful of genetic tests. Now there are tens of thousands of tests and it’s impossible to keep up.
They instituted programs to try to control these things, but I don’t believe they work very well.”
Bien-Willner is scheduled to speak about Palmetto GBA’s MolDX program, Z-Codes, and related topics during three sessions at the upcoming 29th annual Executive War College conference. Clinical laboratory and pathology group managers would be wise to attend his presentations. Visit here (or paste this URL into your browser: https://www.executivewarcollege.com/registration) to learn more and to secure your seat in New Orleans.
New technology could enable genetic scientists to identify antibiotic resistant genes and help physicians choose better treatments for genetic diseases
Genomic scientists at the Icahn School of Medicine at Mount Sinai Medical Center in New York City have developed what they call a “smart tweezer” that enables researchers to isolate a single bacterium from a patient’s microbiome in preparation for genetic sequencing. Though primarily intended for research purposes, the new technology could someday be used by clinical laboratories and microbiologists to help physicians diagnose chronic disease and choose appropriate genetic therapies.
The researchers designed their new technology—called mEnrich-seq—to improve the effectiveness of research into the complex communities of microorganisms that reside in the microbiomes within the human body. The discovery “ushers in a new era of precision in microbiome research,” according to a Mount Sinai Hospital press release.
“Imagine you’re a scientist who needs to study one particular type of bacteria in a complex environment. It’s like trying to find a needle in a large haystack,” said the study’s senior author Gang Fang, PhD (above), Professor of Genetics and Genomic Sciences at Icahn School of Medicine at Mount Sinai Medical Center, in a press release. “mEnrich-seq essentially gives researchers a ‘smart tweezer’ to pick up the needle they’re interested in,” he added. Might smart tweezers one day be used to help physicians and clinical laboratories diagnose and treat genetic diseases? (Photo copyright: Icahn School of Medicine.)
Addressing a Technology Gap in Genetic Research
Any imbalance or decrease in the variety of the body’s microorganisms can lead to an increased risk of illness and disease.
In researching the microbiome, many scientists “focus on studying specific types of bacteria within a sample, rather than looking at each type of bacteria present,” the press release states. The limitation of this method is that a specific bacterium is just one part of a complicated environment that includes other bacteria, viruses, fungi and host cells, each with their own unique DNA.
“mEnrich-seq effectively distinguishes bacteria of interest from the vast background by exploiting the ‘secret codes’ written on bacterial DNA that bacteria use naturally to differentiate among each other as part of their native immune systems,” the press release notes. “This new strategy addresses a critical technology gap, as previously researchers would need to isolate specific bacterial strains from a given sample using culture media that selectively grow the specific bacterium—a time-consuming process that works for some bacteria, but not others. mEnrich-seq, in contrast, can directly recover the genome(s) of bacteria of interest from the microbiome sample without culturing.”
Isolating Hard to Culture Bacteria
To conduct their study, the Icahn researchers used mEnrich-seq to analyze urine samples taken from three patients with urinary tract infections (UTIs) to reconstruct Escherichia coli (E. Coli) genomes. They discovered their “smart tweezer” covered more than 99.97% of the genomes across all samples. This facilitated a comprehensive examination of antibiotic-resistant genes in each genome. They found mEnrich-seq had better sensitivity than standard study methods of the urine microbiome.
They also used mEnrich-seq to selectively examine the genomes of Akkermansia muciniphila (A. muciniphila), a bacterium that colonizes the intestinal tract and has been shown to have benefits for obesity and Type 2 diabetes as well as a response to cancer immunotherapies.
“Akkermansia is very hard to culture,” Fang told GenomeWeb. “It would take weeks for you to culture it, and you need special equipment, special expertise. It’s very tedious.”
mEnrich-seq was able to quickly segregate it from more than 99.7% of A. muciniphila genomes in the samples.
Combatting Antibiotic Resistance Worldwide
According to the press release, mEnrich-seq could potentially be beneficial to future microbiome research due to:
Cost-Effectiveness: It offers a more economical approach to microbiome research, particularly beneficial in large-scale studies where resources may be limited.
Broad Applicability: The method can focus on a wide range of bacteria, making it a versatile tool for both research and clinical applications.
Medical Breakthroughs: By enabling more targeted research, mEnrich-seq could accelerate the development of new diagnostic tools and treatments.
“One of the most exciting aspects of mEnrich-seq is its potential to uncover previously missed details, like antibiotic resistance genes that traditional sequencing methods couldn’t detect due to a lack of sensitivity,” Fang said in the news release. “This could be a significant step forward in combating the global issue of antibiotic resistance.”
More research and clinical trials are needed before mEnrich-seq can be used in the medical field. The Icahn researchers plan to refine their novel genetic tool to improve its efficiency and broaden its range of applications. They also intend to collaborate with physicians and other healthcare professionals to validate how it could be used in clinical environments.
Should all this come to pass, hospital infection control teams, clinical laboratories, and microbiology labs would welcome a technology that would improve their ability to detect details—such as antibiotic resistant genes—that enable a faster and more accurate diagnosis of a patient’s infection. In turn, that could contribute to better patient outcomes.
