Clinical laboratories and pathology groups can benefit from knowing how genetic testing is being used for other than medical testing purposes
It is useful for pathologists and clinical laboratory managers to be aware of the different ways genetic testing and DNA sequencing is being conducted. That’s because a genetic test for one purpose—such as identifying an individual’s relatives and connection to a region or a cultural group—might generate data that could become part of that person’s medical care.
Thus, an ongoing genetic study in South Africa highlighting the issue of so-called “helicopter research” will be informative for Dark Daily’s readers.
Also known as “neo-colonial science,” helicopter research describes when scientists from wealthy countries perform research in lower-income countries in ways that may be deemed exploitative or disrespectful to local populations.
“Scientists conduct helicopter research when they collect data from developing countries and marginalized communities with little to no involvement from local researchers and community members,” wrote researchers Dana Al-Hindi, and Brenna Henn PhD, in an article for The Conversation. “Helicopter research also occurs when researchers take data out of the country they collected it from without either providing benefit to or sharing the results with the community.”
In an article for The Conversation, UC Davis researchers Brenna Henn, PhD (left), and Dana Al-Hindi (right), wrote, “While we have learned a great deal from these communities, we have been unable to fulfill a common request: providing them their individual genetic ancestry result. In our attempts to overcome the logistical challenges of providing this information, we’ve grappled with the common question of how to ensure an equitable balance of benefits between researchers and the community they study. What we’ve found is that there is no easy answer.” Clinical laboratories will want to remember the term “Helicopter Research” in relation to these types of studies. (Photos copyright: UC Davis/The Conversation.)
The South Africa study, conducted over the past 12 years, aims to use genetic data “to help unravel the history and prehistory of southern Africans and their relationship to populations around the world,” the authors wrote in The Conversation.
The researchers have been using the genetic data to trace the ancestry of indigenous Khoekhoe and San peoples in South Africa as well as other populations that self-identify as “Colored.”
“Early European colonizers initially used this term to refer to indigenous Khoekhoe and San groups long before it was codified by the apartheid government in 1948,” the researchers wrote. “It persists today as an ethnic category, broadly encompassing Khoe-San groups, various East African, Indian, and Southeast Asian populations brought by the slave trade, and people of mixed ancestry.”
Challenges Sharing Genetic Data with Study Participants
Participants in the study have asked to see their personal genetic ancestry results, but the researchers noted several challenges, including local restrictions and the difficulty of presenting complex data in “an accessible and digestible form.” So, the researchers partnered with consumer-focused genetic testing company 23andMe (NASDAQ:ME).
23andMe provided additional funding for the research, assisted the researchers in community outreach, and “expanded our ability to ‘capacity-build’—that is, to make sure that the knowledge and skills we gain are shared with local institutions,” Henn and Al-Hindi wrote in The Conversation. They added that they are still dealing with questions about whether their efforts to provide equitable benefits are sufficient.
“Our research team, local collaborators, and 23andMe are all concerned about how to best address the risk of helicopter research, coercion, and any unknown risks that may arise from disclosing personal ancestry results,” they wrote.
Cape Town Statement on Fostering Research Integrity
The issue of helicopter research was a major focus at the 7th World Conference on Research Integrity (WCRI), held May 29-June 1 in Cape Town, South Africa. It was the first WCRI to be held in Africa and adopted the theme “Fostering Research Integrity in an Unequal World.”
One outcome of the conference will be an effort to produce what is known as the Cape Town Statement on Fostering Research Integrity. The statement will “highlight the importance of fairness in international research partnerships,” noted Research Professional News.
The statement “compels institutions and researchers alike to act on their responsibilities to promote equity, diversity, and fairness in research partnerships,” conference speaker Retha Visagie, DCur, told the publication. She leads the Research Integrity Office at the University of South Africa.
Conference co-chair Lyn Horn, PhD, director the Office of Research Integrity at the University of Cape Town, told the publication that it could take up to a year before a draft of the statement is ready for comment.
One overarching goal will be to “demonstrate why inequity and unfair practices in research collaborations and contexts is a research integrity (RI) matter,” the authors wrote. “Second it must identify some key values or principles and action guides that will address the issue of equity and fairness in research within the context of the complete research life cycle from research agenda setting and call to proposal development, through grant application, allocation and management of funding, data production, analysis, management and sharing, to outputs, translation, and evaluation.”
Another conference speaker, Francis Kombe PhD, told attendees the statement will offer guidance specifically to institutions such as universities, journals, and funding organizations, the journal Science reported. That stands in contrast to earlier statements on helicopter research, which were geared more toward individuals and small groups.
How any of this will impact clinical laboratories and pathology groups remains unclear. Nevertheless, it is worthwhile knowing how gene sequencing is being used by researchers for purposes other than to guide diagnoses and treatment of patients.
MUSE microscope speeds up some anatomic pathology laboratory processes and removes exposure to toxic fixative chemicals
Because they handle tissue specimens, histotechnologists, anatomic pathologists, and hospital nurses are exposed to deadly chemicals such as formaldehyde, formalin, Xylene, and Toluene. The risks associated with these chemicals has been covered regularly by Dark Daily as recently as 2018 and as far back as 2011. (See, “Europe Implements New Anatomic Pathology Guidelines to Reduce Nurse Exposure to Formaldehyde and Other Toxic Histology Chemicals,” January 3, 2018; and, “Health of Pathology Laboratory Technicians at Risk from Common Solvents like Xylene and Toluene,” July 5, 2011.)
Now, scientists at the University of California at Davis (UC Davis) have developed a microscope that uses ultraviolet light (UV) to illuminate tissue samples. The UV microscope removes the need for traditional histology processes involved with preparation of tissue to produce conventional slides and makes it possible for anatomic pathologists to evaluate tissues without formalin fixation, according to a UC Davis news release.
“Here, we introduce a simple, non-destructive slide-free technique that, within minutes, provides high-resolution diagnostic histological images resembling those obtained from conventional hematoxylin and eosin histology,” the researchers wrote in their paper, published in Nature Biomedical Engineering.
High-resolution Biopsy Images in Minutes
The UV microscope relies on technology that UC Davis researchers dubbed MUSE, which stands for Microscopy with Ultraviolet Surface Excitation. According to the researchers, MUSE produces high-resolution images of biopsies and other fresh tissue samples that are ready for a pathologist’s review within minutes.
“MUSE eliminates any need for conventional tissue processing with formalin fixation, paraffin embedding, or thin-sectioning. It doesn’t require lasers, confocal, multiphoton, or optical coherence tomography instrumentation. And the simple technology makes it well-suited for deployment wherever biopsies are obtained and evaluated,” stated Richard Levenson, MD, MUSE Microscopy CEO, Professor, and Vice Chair for Strategic Technologies in the Department of Pathology and Laboratory Medicine at UC Davis, in the news release.
Ultraviolet microscopy is distinguished by its ability to magnify samples and enable views with greater resolution. This is due to the shorter wavelength of ultraviolet light, which improves image resolution beyond the diffraction limit of optical microscopes using normal white light, according to News Medical.
The unique ultraviolet light microscope tool may soon enable clinical laboratories and anatomic pathology groups to accurately report on biopsies to physicians and patients faster, for less money, and without exposure to deadly chemicals. This would be timely considering the pressure on the pathology industry to switch to value-based reimbursement from fee-for-service billing, and to embrace personalized medicine.
“It has become increasingly important to submit relevant portion of often tiny tissue samples for DNA and other molecular functional tests,” notes Richard Levenson, MD, MUSE Microscopy CEO, Professor, and Vice Chair for Strategic Technologies in the Department of Pathology and Laboratory Medicine at UC Davis, shown above with MUSE. “Making sure that the submitted material actually contains tumor in sufficient quantity is not always easy and sometimes just preparing conventional microscope slices can consume most of or even all of small specimens. MUSE is important because it quickly provides images from fresh tissue without exhausting the sample.” (Photo and caption copyright: UC Davis.)
Traditional Microscopy is Time-Consuming, Hazardous, Expensive
Light microscopy, a time-honored technology, has been available to pathologists for more than 200 years. It is the cornerstone for cancer diagnostics and pathology, the UC Davis researchers acknowledged. But it requires time-consuming and expensive processes, which are especially glaring in a resource-challenged healthcare industry, they pointed out.
“Histological examination of tissues is central to the diagnosis and management of neoplasms and many other diseases. However, commonly used bright-field microscopy requires prior preparation of micrometer-thick tissue sections mounted on glass slides—a process that can require hours or days, contributes to cost, and delays access to critical information,” they wrote in their paper.
“MUSE promises to improve the speed and efficiency of patient care in both state-of-the art and low-resource settings, and to provide opportunities for rapid histology in research,” they continued.
No Histology Slide Preparation Needed
MUSE developers also called attention to the use of hazardous chemicals, such as formalin, in lab processes, which has been linked to cancers including myeloid leukemia, nasopharyngeal cancer, and sinonasal cancer, according to a National Academy of Sciences report. Still, more than 300 million slides are prepared in the US each year at a cost of several billion dollars to the healthcare industry, according to the MUSE Website.
MUSE, however, penetrates tissue samples by using ultraviolet light at short wavelengths—below the 300-nanometer range. The MUSE ultraviolet microscope can reach several microns-deep into tissues.
That’s enough, the researchers claim, to be comparable with the thickness of tissue slices anatomic pathologists use with traditional microscope slides. However, MUSE requires no conventional tissue processing associated with histology slides.
How Does it Work?
MUSE is comprised of an optical system with UV light-emitting diodes (LEDs), a UV compatible stage, and a conventional microscope. That’s according to Photonics Online, which described the process:
“UV light at 280 nanometer spectral range illuminates about one square millimeter of specimen;
“Surface is limited to a few nanometers deep to make high-contrast images possible;
“Excitation light, at sub-300 nanometer spectral region, elicits bright emission from tissue specimens;
“Specimens, which were stained with conventional florescent dyes, emit photons;
“Photons are captured using glass-based microscope optics;
“Images are comparable to the hematoxylin and eosin versions histologists and pathologists are accustomed to.”
The result, according the MUSE website, “is stunning detailed images conveying a degree of resolution, structure, and depth unachievable until now by any single technology.”
Other Alternative Histology Processes Under the Microscope
MUSE is not the only approach being studied that could create cellular images without sectioning tissue samples. Anatomic and histopathology laboratory leaders looking to differentiate their labs should keep watch on the development of MUSE and other alternatives to current histology methods, especially once these new devices become green-lighted by the Food and Drug Administration (FDA) for use in patient care.
Studies at the two universities produced intriguing insights into the ability of pigeons to discriminate between benign and malignant breast cancer slides at all magnifications
Researchers at the University of Iowa and the University of California Davis (UC Davis) are reporting intriguing results from a study indicating that pigeons have the potential to be “proficient pathologists” when it comes to telling the difference between healthy and cancerous cells in human breast tissue.
With minimal training and food reinforcement, the common pigeon or rock dove, performed as well as humans at identifying and classifying (AKA, pigeonholing) digitized slides and mammograms of benign and malignant human breast tissue, stated the researchers. (more…)
American Gut is using test results to create a microbiome database for use by researchers to better understand how microbes impact human health
Have you ever wondered what lurks in the dark corridors of your bowels? Now you can find out. Two entrepreneurial organizations—one a not-for-profit and the other a new clinical lab company—are charting new medical laboratory territory with the offer of an inexpensive poop test that reveals the type of microbes residing in your gut.
Where to Get Your Gut Microbes Analyzed
The not-for-profit organization American Gut, or British Gut in the United Kingdom (UK), which launched as crowd-funding projects on FundRazr, involve a private research project called the Human Food Project (HFP), which was initiated to compare the microbiomes of populations around the world. The Human Food Project is seeking a better understanding of modern disease by studying the coevolution of humans and their microbes.
People who pay American Gut’s $99 test fee (£75 for the UK project) receive a test kit to collect a stool sample to mail back for DNA sequencing. The test results will be provided to participants, but also benefit microbiome research. (more…)
Developed to detect pathogens missed in wounds of soldiers, this technology was licensed to a company for development into a test for use by clinical laboratories
Diagnostic technology developed for rapid detection of pathogens in the wounds of soldiers has been licensed to a private company that intends to use it to create new medical laboratory tests. This new technology is capable of identifying thousands of bacteria and viruses in a single test.
