This is not the first time genetic-testing company Orig3n has been scrutinized by state and federal investigators over its business practices
It’s not often that multiple employees of a clinical laboratory company go public with criticism about the quality of their lab company’s tests. But that is what is happening at Orig3n. Problems at the Boston-based genetic testing company were the subject of an investigative report published by Bloomberg Businessweek (Bloomberg).
In September, Bloomberg reported that 17 former Orig3n employees said the company’s Deoxyribonucleic acid (DNA) tests sometimes failed to deliver the intended results or were often contaminated or inaccurate. The individuals had been employed by the company as managers, lab technicians, software engineers, marketers, and salespeople between 2015 and 2018.
The former employees claimed that Orig3n “habitually cut
corners, tampered with or fabricated results, and failed to meet basic
scientific standards,” Bloomberg reported. The individuals also stated
that advice intended to be personalized to individual consumers’ genetic
profiles was often just generic information or advice that had no scientific
basis.
According to Bloomberg, the individuals also alleged
that Orig3n’s lab was careless in its handling of genetic samples in several
ways, including:
Multiple samples being labeled with the same
barcode;
DNA and blood samples for stem cell bank
misplaced or mixed up;
No controls to ensure accuracy;
Handling methods that could lead to
contamination; and
Fabricating results when a test outcome was
unclear.
The former employees also stated that “Orig3n ran tests without proper authorization in its lab at the 49ers’ stadium, and that managers regularly compelled them to write positive reviews of Orig3n’s tests on Amazon.com and Google to offset waves of negative feedback,” Bloomberg reported.
“Accurate science didn’t seem to be a priority. Marketing
was the priority,” said a former lab technician who spoke with Bloomberg
on the condition of anonymity. Orig3n denied the accusations in a statement,
describing them as “grossly inaccurate,” and claimed the former employees were
simply disgruntled.
“In some cases, former employees are former employees for a reason,” Orig3n Chief Executive Officer Robin Smith told Bloomberg. “We’ve found after employees are gone that they have not done things appropriately.”
Is it Dog or Human DNA?
In 2018, NBC Chicago(NBC) conducted an investigation into various consumer DNA testing kits. NBC sent DNA samples to several different testing companies. This included non-human samples, which NBC’s investigators had obtained from a female Labrador Retriever.
With the exception of Orig3n, all of companies identified
the DNA as non-human and did not process the kits. Orig3n did, however, process
the canine DNA. It then returned a seven-page analysis that suggested the
subject of the sample “would probably be great for quick movements like boxing
and basketball, and that she has the cardiac output for long endurance bike
rides or runs,” NBC reported.
This would be funny if it weren’t so concerning.
Following reports that it had processed dog DNA, Orig3n stated
it had made changes and improvements to the company’s testing methodologies. Smith
also stated Orig3n’s lab protocols had been improved as well.
“Sometimes we look at the accuracy of things and go, ‘Man,
that’s not working,’” Smith told Bloomberg. “Our approach and our
philosophy is [sic] to constantly improve the products.”
Serious Accusations of Clinical Laboratory Malfeasance
Founded in 2014 with the intent of creating the world’s largest stem cell bank, by 2016, Boston-based Orig3n had refocused its attention on the burgeoning field of direct-to-consumer DNA testing. On its website, Orig3n sells several DNA-testing kits with varying costs.
Orig3n’s attempt to offer free genetic tests to large numbers of people at a professional sporting event in the fall of 2017 may be what caught the attention of federal investigators and led to a deeper investigation. Dark Daily previously covered this controversy, which centered around Orig3n’s plan to distribute free genetic testing kits to fans at a Baltimore Ravens football game.
In that situation, state and federal healthcare regulators blocked the giveaway over concerns about protected health information (PHI). Now, Orig3n is being accused of questionable business practices by 17 of its former employees.
The former employees’ statements that the company’s genetic
testing lab did not follow appropriate test protocols—and that it allegedly
mishandled specimens and even reported false test results—are serious
allegation of malfeasance and warrants an investigation.
Pathologists and clinical laboratory managers know that patient
harm can potentially result from inaccurate genetic test results if used for
clinical purposes. Dark Daily will continue to follow the investigation
into Orig3n.
Sale of respected laboratory information system company may be an early sign that investors believe clinical laboratories and pathology groups are ready to upgrade their LISs and add needed capabilities
In the past 10 years there has been little disruption to the
laboratory
information systems (LIS) market that clinical
laboratories and anatomic
pathology groups use. Yet, over that same 10-year period, almost every
hospital and physician group practice adopted an electronic
health system (EHR), primarily because of federal financial incentives that
encouraged such adoption.
For medical
laboratories and pathology groups, this widespread—nearly
universal—adoption of EHRs by the nation’s hospitals and physicians was
disruptive. Labs were required to expend resources building digital interfaces
to the EHRs of their parent hospitals and client physicians to support
electronic test ordering and test reporting.
However, because that wave of EHR adoption is now over,
clinical labs and pathology groups have an opportunity to assess the current
state of the health
information technology (HIT) that they use daily, primarily in the form of
the classic laboratory information system that handles nearly all the primary
functions needed to support testing and other operational needs.
This opportunity to help medical laboratories enhance and/or
upgrade the capabilities of their laboratory information systems may be one
motivation behind the recent sale of a well-known LIS company.
Private Equity Firm Buys Orchard Software
On Oct. 7, 2019, Orchard Software Corporation of Carmel,
Ind., announced its acquisition by Franciscan Partners, a private equity firm
based in San Francisco.
Orchard Software, founded in 1993, has grown steadily over
the past 20 years, primarily by serving physician office laboratories,
community hospital labs, and independent clinical laboratory companies. With each
stage of growth, Orchard added functionality to its LIS and related software
offerings and moved up-market to serve larger hospitals and larger labs.
The purchase price and the terms of the sale were not
announced. Orchard’s Founder, President and CEO, Rob Bush, will retire. The new
CEO is Billie Whitehurst, who came to Orchard from Netsmart Technologies, where she was Senior
Vice President. The remainder of Orchard’s management team will be kept in
place.
Is the LIS Market Heating Up?
What makes the purchase of Orchard by a multi-billion-dollar
private equity company noteworthy is the fact that it is the first significant
transaction in the LIS sector probably since the mid-2000s, which saw several
significant mergers and acquisitions.
Other acquisitions or investments involving LIS companies
need to happen before it would be appropriate to say that investor interest in
the LIS sector is heating up. However, it is accurate to say that many
professional investors will be watching to see whether Franciscan Partners
succeeds with its investment in Orchard Software. If Orchard’s revenue and
operating profits increase substantially in the next few years, that may
encourage other investors to look for LIS companies and products that they can
buy.
If this were to happen, that would be a positive development
for both clinical laboratories and anatomic pathology groups, because these
investors would have a motive to add new functions and capabilities to their
LIS products. It would also wake up a sector of lab information technology that
has been relatively quiet for several years.
Researchers believe new findings about genetic changes in C. difficile are a sign that it is becoming more difficult to eradicate
Hospital infection control teams, microbiologists, and clinical laboratory professionals soon may be battling a strain of Clostridium difficile (C. difficile) that is even more resistant to disinfectants and other forms of infection control.
A WSI news release states the researchers “identified genetic changes in the newly-emerging species that allow it to thrive on the Western sugar-rich diet, evade common hospital disinfectants, and spread easily.”
Microbiologists and infectious disease doctors know full well that this means the battle to control HAIs is far from won.
Genomic Study Finds New Species of Bacteria Thrive in
Western Hospitals
In the published paper, Nitin Kumar, PhD, Senior Bioinformatician at the Wellcome Sanger Institute and Joint First Author of the study, described a need to better understand the formation of the new bacterial species. To do so, the researchers first collected and cultured 906 strains of C. difficile from humans, animals, and the environment. Next, they sequenced each DNA strain. Then, they compared and analyzed all genomes.
The researchers found that “about 70% of the strain collected specifically from hospital patients shared many notable characteristics,” the New York Post (NYPost) reported.
Hospital medical laboratory leaders will be intrigued by the
researchers’ conclusion that C. difficile is dividing into two separate
species. The new type—dubbed C. difficile clade A—seems to be targeting
sugar-laden foods common in Western diets and easily spreads in hospital
environments, the study notes.
“It’s not uncommon for bacteria to evolve, but this time we actually see what factors are responsible for the evolution,” Kumar told Live Science.
New C. Difficile Loves Sugar, Spreads
Researchers found changes in the DNA and ability of the C.
difficile clade A to metabolize
simple sugars. Common hospital fare, such as “the pudding cups and instant
mashed potatoes that define hospital dining are prime targets for these strains”,
the NYPost explained.
Indeed, C. difficile clade A does have a sweet tooth. It was associated with infection in mice that were put on a sugary “Western” diet, according to the Daily Mail, which reported the researchers found that “tougher” spores enabled the bacteria to fight disinfectants and were, therefore, likely to spread in healthcare environments and among patients.
“The new C. difficile produces spores that are more
resistant and have increased sporulation
and host colonization capacity when glucose or fructose is available for
metabolism. Thus, we report the formation of an emerging C. difficile
species, selected for metabolizing simple dietary sugars and producing high
levels or resistant spores, that is adapted for healthcare-mediated
transmission,” the researchers wrote in Nature Genetics.
Bacteria Pose Risk to Patients
The findings about the new strains of C. difficile bacteria
now taking hold in provider settings are important because hospitalized
patients are among those likely to develop life-threatening diarrhea due to
infection. In particular, people being treated with antibiotics are vulnerable
to hospital-acquired infections, because the drugs eliminate normal gut
bacteria that control the spread of C. difficile bacteria, the
researchers explained.
According to the Centers for Disease Control and Prevention (CDC), C. difficile causes about a half-million infections in patients annually and 15,000 of those infections lead to deaths in the US each year.
New Hospital Foods and Disinfectants Needed
The WSI/LSHTM study suggests hospital representatives should
serve low-sugar diets to patients and purchase stronger disinfectants.
“We show that strains of C. difficile bacteria have continued to evolve in response to modern diets and healthcare systems and reveal that focusing on diet and looking for new disinfectants could help in the fight against this bacteria,” said Trevor Lawley, PhD, Senior Author and Group Leader of the Lawley Lab at the Wellcome Sanger Institute, in the news release.
Microbiologists, infectious disease physicians, and their
associates in nutrition and environmental services can help by understanding
and watching development of the new C. difficile species and offering
possible therapies and approaches toward prevention.
Meanwhile, clinical laboratories and microbiology labs will
want to keep up with research into these new forms of C. difficile, so
that they can identify the strains of this bacteria that are more resistant to
disinfectants and other infection control methods.
Metabolic panels of 14 blood-based biomarkers that can predict when a patient is likely to die may be coming to a medical laboratory near you
Clinical pathologists soon may be able to predict when patients will die, thanks to a recent study that reveals new insights into how the human body works. Researchers at the Max Planck Institute for Biology of Ageing in Germany and the Leiden University Medical Center (LUMC) in the Netherlands revealed a metabolic panel of biomarkers that can more accurately predict death within five to 10 years than standard measures.
The researchers’ original goal was to find blood-based
biomarkers that could show whether a person was vulnerable to death,
particularly if that vulnerability was related to modifiable lifestyle factors.
The researchers published their study, titled, “A Metabolic Profile of All-Cause Mortality Risk Identified in an Observational Study of 44,168 Individuals,” in the journal Nature Communications last August.
Metabolic Biomarkers More Accurate than Current Health
Measures
During their investigation, the researchers looked at 12
cohorts from previous studies and examined the results of 44,168 individuals
between the ages of 18 and 109. In the follow-up to the study, 5,512 of the
participants died.
In the introduction to their published study the researchers
wrote, “We first determine which metabolic biomarkers independently associate
with prospective mortality in all individuals. Subsequently, we test the
association of the biomarkers with mortality in different age strata.”
The researchers then used the 14 biomarkers they identified to
create a score that predicts mortality within five to 10 years.
The measures that most providers currently use to determine an elderly person’s overall health generally include blood pressure, heart rate, and functionality measures such as grip strength and gait. However, P. Eline Slagboom, PhD, LUMC Professor of Molecular Epidemiology and the study’s director, told The Scientist that those metrics are not always accurate methods for measuring health.
“For example, a somewhat higher weight, blood pressure, or
cholesterol level is not as bad for individuals over 80 years of age as
compared to younger individuals,” she said.
As it turned out, the traditional measures were
significantly less accurate than the score Slagboom and her team developed.
Traditional measures were accurate about 78% of the time, while the metabolic
panel was accurate about 83% of the time, reported The Scientist.
Additionally, the score based on metabolic biomarkers was accurate for people
of all ages, rather than only among the young.
Study Yields Strong but Surprising Results
Researchers have studied biomarkers as predictive tools for quite some time, with only narrow success. The positive results of the Max Planck Institute/LUMC study even surprised those who worked on it. “We were surprised that the association of our biomarker score with mortality was so strong, given that it is only based on 14 metabolic markers in the blood measured at a single point in the life of individuals,” the study’s lead author Joris Deelen, PhD, a postdoctoral researcher at the Max Planck Institute for Biology of Ageing, said in The Scientist.
But though the results of the study are intriguing, some
experts remain skeptical that a new biomarker for death has been found.
In reactions published by the Science Media Centre, an independent organization in the UK that promotes “the reporting of evidence-based science,” Kevin McConway, PhD, Emeritus Professor of Applied Statistics at The Open University wrote, “This is a solid and interesting piece of research. But it doesn’t go beyond investigating the plausibility of setting up a system for predicting risk of death, based on this type of data. It doesn’t claim to do more than that, and makes clear that there’s some way to go, in terms of research and analysis, until a risk prediction tool that’s useable in clinical work with patients might emerge.”
And in the same article, Amanda Heslegrave, PhD, a post-doctoral research associate and researcher at the UK Dementia Research Institute at the University College London wrote, “Whilst this study shows that this type of profiling can be useful, [the researchers] do point out importantly that it would need further work to develop a score at the individual level that would be useful in real life situations. We’d need to see: validation to ensure repeatability in different labs, production of reference samples to test this on an ongoing basis, work to make the individual score possible, validation in other cohorts and validation of all components of the panel. So, it’s an exciting step, but it’s not ready yet.”
Past Mortality Biomarker Studies
Other investigations into the use of biomarkers as a predictive tool have focused more narrowly on specific causes of death. For example, in 2008, the New England Journal of Medicine (NEJM) published a study titled, “Use of Multiple Biomarkers to Improve the Prediction of Death from Cardiovascular Causes.” The study concluded that using biomarkers and risk factors together “substantially improves the risk stratification for death from cardiovascular causes.”
Another study, from 2017, examined stress biomarkers, hospital readmission, and death. Published in the Journal of Hospital Medicine titled, “Association of Stress Biomarkers with 30-Day Unplanned Readmission and Death,” the researchers found that “stress biomarkers improved the performance of prediction models and therefore could help better identify high-risk patients.”
Other studies have examined the predictive possibilities of
biomarkers in:
Even with all of the research into biomarkers, scientists are still a long way from having a clinical tool to predict death. However, according to Leo Cheng, PhD, Associate Biophysicist, Pathology and Radiology at Massachusetts General Hospital, and Associate Professor of Radiology at Harvard Medical School, the Max Planck study is on the right path.
The Scientist states that though Cheng believes the
study doesn’t “prove anything,” he also notes that “using a score that combines
the information from all 14 biomarkers is ‘the correct thing [to do]’ to
provide a holistic look at metabolic pathways that may represent a person’s
health.”
So, it might be awhile before clinical laboratories will be
processing metabolic panels that return test results predicting a patient’s
mortality within 10-15 years. Nevertheless, how medical labs would be involved
in such testing is certainly something to think about.
Use of synthetic genetics to replicate an infectious disease agent is a scientific accomplishment that many microbiologists and clinical laboratory managers expected would happen
Microbiologists and infectious disease doctors are quite familiar with Escherichia coli (E. coli). The bacterium has caused much human sickness and even death around the globe, and its antibiotic resistant strains are becoming increasingly difficult to eradicate.
Now, scientists in England have created a synthetic “recoded” version of E. coli bacteria that is being used in a positive way—to fight disease. Their discovery is being heralded as an important breakthrough in the quest to custom-alter DNA to create synthetic forms of life that one day could be designed to fight specific infections, create new drugs, or produce tools to diagnose or treat disease.
Scientists worldwide working in the field of synthetic genomics are looking for ways to modify genomes in order to produce new weapons against infection and disease. This research could eventually produce methods for doctors—after diagnosing a patient’s specific strain of bacteria—to then use custom-altered DNA as an effective weapon against that patient’s specific bacterial infection.
This latest milestone is the result of a five-year quest by researchers at the Medical Research Council Laboratory of Molecular Biology (MRC-LMB) in Cambridge, England, to create a man-made version of the intestinal bacteria by redesigning its four-million-base-pair genetic code.
The MRC-LMB lab’s success marks the first time a living
organism has been created with a compressed genetic code.
The researchers published their findings in the journal Nature.
“This is a landmark in the emerging field of synthetic
genomics and finally applies the technology to the laboratory’s workhorse
bacterium,” they wrote. “Synthetic genomics offers a new way of life, while at
the same time moving synthetic biology towards a future in which genomes can be
written to design.”
All known forms of life on Earth contain 64 codons—a specific sequence of three consecutive nucleotides that corresponds with a specific amino acid or stop signal during protein synthesis. Jason Chin, PhD, Program Lead at MRC-LMB, said biologists long have questioned why there are 20 amino acids encoded by 64 codons.
“Is there any function to having more than one codon to encode each amino acid?” Chin asked during an interview with the Cambridge Independent. “What would happen if you made an organism that used a reduced set of codons?”
The MRC-LMB research team took an important step toward
answering that question. Their synthetic E. coli strain, dubbed Syn61,
was recoded through “genome-wide substitution of target codons by defined
synonyms.” To do so, researchers mastered a new piece-by-piece technique that
enabled them to recode 18,214 codons to create an organism with a 61-codon
genome that functions without a previously essential transfer RNA.
“Our synthetic genome implements a defined recoding and refactoring scheme–with simple corrections at just seven positions–to replace every known occurrence of two sense codons and a stop codon in the genome,” lead author Julius Fredens, PhD, a post-doctoral research associate at MRC, and colleagues, wrote in their paper.
Joshua Atkinson, PhD, a postdoctoral research associate at Rice University in Houston, labeled the breakthrough a “tour de force” in the field of synthetic genomics. “This achievement sets a new world record in synthetic genomics by yielding a genome that is four times larger than the pioneering synthesis of the one-million-base-pair Mycoplasma mycoides genome,” he stated in Synthetic Biology.
“Synthetic genomics is enabling the simplification of
recoded organisms; the previous study minimized the total number of genes and
this new study simplified the way those genes are encoded.”
Manmade Bacteria That are Immune to Infections
Researchers from the J.
Craig Venter Institute in Rockville, Maryland, created the first synthetic
genome in 2010. According to an article in Nature,
the Venter Institute successfully synthesized the Mycoplasma mycoides genome
and used it “reboot” a cell from a different species of bacterium.
The MRC-LMB team’s success may prove more significant.
“This new synthetic E. coli should not be able to decode DNA from any other organism and therefore it should not be possible to infect it with a virus,” the MRC-LMB stated in a news release heralding the lab’s breakthrough. “With E. coli already being an important workhorse of biotechnology and biological research, this study is the first time any commonly used model organism has had its genome designed and fully synthesized and this synthetic version could become an important resource for future development of new types of molecules.”
Because the MRC-LMB team was able to remove transfer RNA and
release factors that decode three codons from the E. coli bacteria,
their achievement may be the springboard to designing manmade bacteria that are
immune to infections or could be turned into new drugs.
“This may enable these codons to be cleanly reassigned and
facilitate the incorporation of multiple non-canonical amino acids. This
greatly expands the scope of using non-canonical amino acids as unique tools
for biological research,” the MRC-LMB news release added.
Though synthetic genomics impact on clinical laboratory diagnostics is yet to be known, medical laboratory leaders should be mindful of the potential for rapid innovation in this field as proof-of-concept laboratory innovations are translated into real-world applications.
How medical laboratories can show value through process improvement methods and analytics will be among many key topics presented at the upcoming Lab Quality Confab conference
Quality management is the clinical laboratory’s best strategy for surviving and thriving in this era of shrinking lab budgets, PAMA price cuts, and value-based payment. In fact, the actions laboratories take in the next few months will set the course for their path to clinical success and financial sustainability in 2020 and beyond.
But how do medical laboratory managers and pathologists address these challenges while demonstrating their lab’s value? One way is through process improvement methods and another is through the use of analytics.
Clinical pathologists, hospital lab leaders, and independent lab executives have told Dark Daily that the trends demanding their focus include:
Ensuring needed resources and appropriate tests,
while the lab is scrutinized by insurance companies and internally by hospital
administration;
“Our impact on patient care, in many cases, is very
indirect. So, it is difficult to point to outcomes that occur. We know things
we do matter and change patient care, but objectively showing that is a real
struggle. And we are being asked to do more than we ever had before, and those
are the two big things that keep me up at night these days,” he added.
This is where process improvement methods and analytics are
helping clinical laboratories understand critical issues and find opportunities
for positive change.
“You need to have a strategy that you can adapt to a changing landscape in healthcare. You have to use analytics to guide your progress and measure your success,” Patricia Nortmann, System Director of Laboratory Services at St. Elizabeth Healthcare, Erlanger, Ky., told Dark Daily.
Clinical Laboratories Can Collaborate Instead of Compete
Prior to a joint venture with TriHealth in Cincinnati, St. Elizabeth lab leaders used data to inform their decision-making. Over about 12 years preceding the consolidation of labs they:
Implemented front-end automation outside the core area and in the microbiology lab.
“We are now considered a regional reference lab in the state
of Kentucky for two healthcare organizations—St. Elizabeth and TriHealth,”
Nortmann said.
Thanks to these changes, the lab more than doubled its
workload, growing from 2.1 million to 4.3 million outreach tests in the core
laboratory, she added.
Using Analytics to Test the Tests
Clinical laboratories also are using analytics and information technology (IT) to improve test utilization.
At VCH Health, Doern said an analytics solution interfaces
with their LIS, providing insights into test orders and informing decisions
about workflow. “I use this analytics system in different ways to answer
different questions, such as:
How are clinicians using our tests?
When do things come to the lab?
When should we be working on them?
“This is important for microbiology, which is a very delayed
discipline because of the incubation and growth required for the tests we do,”
he said.
Using analytics, the lab solved an issue with Clostridium
difficile (C diff) testing turnaround-time (TAT) after associating it with
specimen transportation.
Inappropriate or duplicate testing also
can be revealed through analytics. A physician may reconsider a test after discovering
another doctor recently ordered the same test. And the technology can guide
doctors in choosing tests in areas where the related diseases are obscure, such
as serology.
Avoiding Duplicate Records While
Improving Payment
Another example of process
improvement is Health Network Laboratories (HNL) in Allentown, Pa. A team there established an enterprise master patient index (EMPI) and implemented digital tools to find and eliminate
duplicate patient information and improve lab financial indicators.
“The system uses trusted sources of data to make sure data is clean and the lab has what it needs to send out a proper bill. That is necessary on the reimbursement side—from private insurance companies especially—to prevent denials,” Joseph Cugini, HNL’s Manager Client Solutions, told Dark Daily.
HNL reduced duplicate records in its database from 23% to
under one percent. “When you are talking about several million records, that is
quite a significant improvement,” he said.
Processes have improved not only on the billing side, but in
HNL’s patient service centers as well, he added. Staff there easily find
patients’ electronic test orders, and the flow of consumers through their
visits is enhanced.
Learn More at Lab Quality Confab Conference
Cugini, Doern, and Nortmann will speak on these topics and more during the 13th Annual Lab Quality Confab (LQC), October 15-16, 2019, at the Hyatt Regency in Atlanta, Ga. They will offer insights, practical knowledge, and case studies involving Lean, Six Sigma, and other process improvement methods during this important 2-day conference, a Dark Dailynews release notes.
Register for LQC, which is produced by Dark Daily’s sister publication The Dark Report, online at https://www.labqualityconfab.com/register, or by calling 512-264-7103.