The focus of the ongoing GenoVA study is to “determine the clinical effectiveness of polygenic risk score testing among patients at high genetic risk for at least one of six diseases measured by time-to-diagnosis of prevalent or incident disease over 24 months,” according to the National Institutes of Health.
The scientists used data obtained from 36,423 patients enrolled in the Mass General Brigham Biobank. The six diseases they researched were:
The polygenic scores were then tested among 227 healthy adult patients to determine their risk for the six diseases. The researchers found that:
11% of the patients had a high-risk score for atrial fibrillation,
7% for coronary artery disease,
8% for diabetes, and
6% for colorectal cancer.
Among the subjects used for the study:
15% of the men in the study had a high-risk score for prostate cancer, and
13% of the women in the study had a high score for breast cancer.
The researchers concluded that the implementation of PRS may help improve disease prevention and management and give doctor’s a way to assess a patient’s risk for these conditions. They published their findings in the journal Nature Medicine, titled, “Development of a Clinical Polygenic Risk Score Assay and Reporting Workflow.”
“We have shown that [medical] laboratory assay development and PRS reporting to patients and physicians are feasible … As the performance of PRS continues to improve—particularly for individuals of underrepresented ancestry groups—the implementation processes we describe can serve as generalizable models for laboratories and health systems looking to realize the potential of PRS for improved patient health,” the researchers wrote.
Using PRS in Clinical Decision Support
Polygenetic risk scores examine multiple genetic markers for risk of certain diseases. A calculation based on hundreds or thousands of these genetic markers could help doctors and patients make personalized treatment decisions, a core tenet of precision medicine.
“As a primary care physician myself, I knew that busy physicians were not going to have time to take an entire course on polygenic risk scores. Instead, we wanted to design a lab report and informational resources that succinctly told the doctor and patient what they need to know to make a decision about using a polygenic risk score result in their healthcare,” epidemiologist Jason Vassy, MD, told The Harvard Gazette. Vassy is Associate Professor, Harvard Medical School at VA Boston Healthcare System and one of the authors of the research.
“This is another great example of precision medicine,” Jason Vassy, MD (above), Adjunct Assistant Professor, General Internal Medicine at Boston University School of Medicine, told WebMD. “There’s always been a tantalizing idea that someone’s genetic makeup might help tailor preventative medicine and treatment.” Personalized clinical laboratory testing is increasingly becoming based on an individual’s genetics. (Photo copyright: Harvard Medical School.)
Increasing Diversity of Patients in Genomic Research
The team did encounter some challenges during their analysis. Because most existing genomic research was performed on persons of European descent, the risk scores are less accurate among non-European populations. The researchers for this study addressed this limitation by applying additional statistical methods to qualify accurate PRS calculations across multiple racial groups.
“Researchers must continue working to increase the diversity of patients participating in genomics research,” said Matthew Lebo, PhD, Chief Laboratory Director, Laboratory Molecular Medicine, at Mass General Brigham and one of the authors of the study. “In the meantime, we were heartened to see that we could generate and implement valid genetic scores for patients of diverse backgrounds,” he told The Harvard Gazette.
The team hopes the scores may be utilized in the future to help doctors and patients make better decisions regarding preventative care and screenings.
“It’s easy to say that everyone needs a colonoscopy at age 45,” Vassy told WebMD. “But what if you’re such a low risk that you could put it off for longer? We may get to the point where we understand risk so much that someone may not need one at all.”
Future of PRS in Clinical Decision Making
The scientists plan to enroll more than 1,000 patients in a new program and track them for two years to assess how medical professionals use PRS in clinical care. It is feasible that patients who are at high risk for certain diseases may opt for more frequent screenings or take preventative medicines to mitigate their risk.
“Getting to that point will take time,” Vassy added. “But I can see this type of information playing a role in shared decision making between doctor and patient in the near future.”
The team also established resources and educational materials to assist both doctors and patients in using the scores.
“It’s still very early days for precision prevention,” Vassy noted, “but we have shown it is feasible to overcome some of the first barriers to bringing polygenic risk scores into the clinic.”
More research and studies are needed to prove the effectiveness of using PRS tests in clinical care and determine its role in customized treatment plans based on personal genetics. Nevertheless, pathologists and medical scientists will want to follow the GenoVA study.
“It is probably most helpful to think of polygenic risk scores as a risk factor for disease, not a diagnostic test or an indication that an individual will certainly develop the disease,” Vassy said. “Most diseases have complex, multifactorial etiologies, and a high polygenic risk score is just one piece of the puzzle.”
Pathologists and clinical laboratory managers may want to stay informed as researchers in the GenoVA study tease new useful diagnostic insights from their ongoing study of the whole human genome. Meanwhile, the GenoVA team is moving forward with the 1,000-patient study with the expectation that this new knowledge may enable earlier and more accurate diagnoses of the health conditions that were the focus of the GenoVA study.
The new method employs a pH sensitive dye and AI algorithms to ‘distinguish between cells originating from normal and cancerous tissue, as well as among different types of cancer’ the researchers said
Might a pH-sensitive dye in tandem with an image analysis solution soon be used to identify cancerous cells within blood samples as well within tissue? Recent research indicates that could be a possibility. If further studies and clinical trials confirm this capability, then anatomic pathologists could gain another valuable tool to use in diagnosing cancers and other types of disease.
Currently, surgical pathologists use a variety of hematoxylin and eosin stains (H/E) to bring out useful features in cells and cell structures. So, staining tissue on glass slides is a common practice. Now, thanks to machine learning and artificial intelligence, anatomic pathologists may soon have a similar tool for spotting cancer cells within both tissue and blood samples.
Researchers at the National University of Singapore (NUS) have developed a method for identifying cancer that uses a pH sensitive dye called bromothymol blue. The dye reacts to various levels of acidity in cancer cells by turning colors. “The pH inside cancer cells tends to be higher than that of healthy cells. This phenomenon occurs at the very early phases of cancer development and becomes amplified as it progresses,” Labroots reported.
In “Machine Learning Based Approach to pH Imaging and Classification of Single Cancer Cells,” published in the journal APL Bioengineering, the NUS researchers wrote, “Here, we leverage a recently developed pH imaging modality and machine learning-based single-cell segmentation and classification to identify different cancer cell lines based on their characteristic intracellular pH. This simple method opens up the potential to perform rapid noninvasive identification of living cancer cells for early cancer diagnosis and further downstream analyses.”
According to an NUS news release, the bromothymol blue dye is “applied onto patients’ cells” being held ex vivo in cell culture dishes. The dye’s color changes depending on the acidity level of the cancer cells it encounters. Microscopic images of the now-visible cancers cells are taken, and a machine-learning algorithm analyzes the images before generating a report for the anatomic pathologist.
The NUS researchers claim the test can provide answers in about half an hour with 95% accuracy, Labroots reported.
“The ability to analyze single cells is one of the holy grails of health innovation for precision medicine or personalized therapy. Our proof-of-concept study demonstrates the potential of our technique to be used as a fast, inexpensive and accurate tool for cancer diagnosis,” said Lim Chwee Teck, PhD, NUS Society Professor and Director of NUS’ Institute for Health Innovation and Technology, in the NUS news release.
The novel technique for differentiating cancer cells from non-cancerous cells being developed at the National University of Singapore (NUS) could eventually become useful in detecting cancer cells in tissue samples, either obtained from tumor biopsies or blood samples. “As the number of cells in these samples can be in millions or even billions, the ability to detect the very few cancer cells among the others will be useful for clinicians,” NUS Society Professor and Director of NUS’ Institute for Health Innovation and Technology, Lim Chwee Teck, PhD (above) told The Straits Times. (Photo copyright: The Straits Times.)
AI Cell Analysis versus Laborious Medical Laboratory Steps
By developing an AI-driven method, Professor Lim and the NUS team sought to improve upon time-consuming techniques for identifying cells that traditionally involve using florescent probes, nanoparticles, and labeling steps, or for cells to be fixed or terminated.
“Unlike other cell analysis techniques, our approach uses simple, inexpensive equipment, and does not require lengthy preparation and sophisticated devices. Using AI, we are able to screen cells faster and accurately,” Professor Lim told Labroots. “Furthermore, we can monitor and analyze living cells without causing any toxicity to the cells or the need to kill them.”
The new technique may have implications for cancer detection in tumor tissue as well as in liquid biopsies.
“We are also exploring the possibility of performing the real-time analysis on circulating cancer cells suspended in blood,” Professor Lim said in the NUS news release. “One potential application for this would be in liquid biopsy where tumor cells that escaped from a primary tumor can be isolated in a minimally-invasive fashion from bodily fluids such as blood.”
Diagnosing Cancer in Real Time
The NUS’ method requires more research and clinical studies before it could become an actual tool for anatomic pathologists and other cancer diagnosticians. Additionally, the NUS researchers acknowledged that the focus on only four cell lines (normal cells, benign breast tumor cells, breast cancer cells, and pancreatic cancer cells) limited their study, as did lack of comparison with conventional florescent pH indicators.
Still, the NUS scientists are already planning more studies to advance their concept to different stages of cell malignancy. They envision a “real-time” version of the technique to enable recognition of cells and fast separation of those that need to be referred to clinical laboratories for molecular testing and/or genetic sequencing.
Medical laboratory leaders may want to follow the NUS study. An inexpensive AI-driven method that can accurately detect and classify cancer cells based on pH within the cells is provocative and may be eventually become integrated with other cancer diagnostics.
Hello primary diagnosis of digital pathology images via artificial intelligence! Goodbye light microscopes!
Digital pathology is poised to take a great leap forward. Within as few as 12 months, image analysis algorithms may gain regulatory clearance in the United States for use in primary diagnosis of whole-slide images (WSIs) for certain types of cancer. Such a development will be a true revolution in surgical pathology and would signal the beginning of the end of the light microscope era.
A harbinger of this new age of digital pathology and automated image analysis is a press release issued last week by Ibex Medical Analytics of Tel Aviv, Israel. The company announced that its Galen artificial intelligence (AI)-powered platform for use in the primary diagnosis of specific cancers will undergo an accelerated review by the Food and Drug Administration (FDA).
FDA’s ‘Breakthrough Device Designation’ for Pathology AI Platform
Ibex stated that “The FDA’s Breakthrough Device Designation is granted to technologies that have the potential to provide more effective treatment or diagnosis of life-threatening diseases, such as cancer. The designation enables close collaboration with, and expedited review by, the FDA, and provides formal acknowledgement of the Galen platform’s utility and potential benefit as well as the robustness of Ibex’s clinical program.”
“All surgical pathologists should recognize that, once the FDA begins to review and clear algorithms capable of using digital pathology images to make an accurate primary diagnosis of cancer, their daily work routines will be forever changed,” stated Robert L. Michel, Editor-in-Chief of Dark Daily and its sister publication The Dark Report. “Essentially, as FDA clearance is for use in clinical care, pathology image analysis algorithms powered by AI will put anatomic pathology on the road to total automation.
“Clinical laboratories have seen the same dynamic, with CBCs (complete blood counts) being a prime example. Through the 1970s, clinical laboratories employed substantial numbers of hematechnologists [hematechs],” he continued. “Hematechs used a light microscope to look at a smear of whole blood that was on a glass slide with a grid. The hematechs would manually count and record the number of red and white blood cells.
“That changed when in vitro diagnostics (IVD) manufacturers used the Coulter Principle and the Coulter Counter to automate counting the red and white blood cells in a sample, along with automatically calculating the differentials,” Michel explained. “Today, only clinical lab old-timers remember hematechs. Yet, the automation of CBCs eventually created more employment for medical technologists (MTs). That’s because the automated instruments needed to be operated by someone trained to understand the science and medicine involved in performing the assay.”
Primary Diagnosis of Cancer with an AI-Powered Algorithm
Surgical pathology is poised to go down a similar path. Use of a light microscope to conduct a manual review of glass slides will be supplanted by use of digital pathology images and the coming next generation of image analysis algorithms. Whether these algorithms are called machine learning, computational pathology, or artificial intelligence, the outcome is the same—eventually these algorithms will make an accurate primary diagnosis from a digital image, with comparable quality to a trained anatomic pathologist.
How much of a threat is automated analysis of digital pathology images? Computer scientist/engineer Ajit Singh, PhD, a partner at Artiman Ventures and an authority on digital pathology, believes that artificial intelligence is at the stage where it can be used for primary diagnosis for two types of common cancer: One is prostate cancer, and the other is dermatology.
On June 17, Ajit Singh, PhD (above), Partner at Artiman Ventures, will lead a special webinar and roundtable discussion for all surgical pathologists and their practice administrators on the coming arrival of artificial intelligence-powered algorithms to aid in the primary diagnosis of certain cancers. Regulatory approval for such solutions may happen by the end of this year. Such a development would accelerate the transition from light microscopes to a fully digital pathology workflow. Singh is shown above addressing the 2018 Executive War College. (Photo copyright: The Dark Report.)
“It is now possible to do a secondary read, and even a first read, in prostate cancer with an AI system alone. In cases where there may be uncertainty, a pathologist can review the images. Now, this is specifically for prostate cancer, and I think this is a tremendous positive development for diagnostic pathways,” he added.
Use of Digital Pathology with AI-Algorithms Changes Diagnostics
Pathologists who are wedded to their light microscopes will want to pay attention to the impending arrival of a fully digital pathology system, where glass slides are converted to whole-slide images and then digitized. From that point, the surgical pathologist becomes the coach and quarterback of an individual patient’s case. The pathologist guides the AI-powered image analysis algorithms. Based on the results, the pathologist then orders supplementary tests appropriate to developing a robust diagnosis and guiding therapeutic decisions for that patient’s cancer.
In his interview with The Dark Report, Singh explained that the first effective AI-powered algorithms in digital pathology will be developed for prostate cancer and skin cancer. Both types of cancer are much less complex than, say, breast cancer. Moreover, the AI developers have decades of prostate cancer and melanoma cases where the biopsies, diagnoses, and downstream patient outcomes create a rich data base from which the algorithms can be trained and tuned.
This webinar is organized as a roundtable discussion so participants can interact with the expert panelists. The Chair and Moderator is Ajit Singh, PhD, Adjunct Professor at the Stanford School of Medicine and Partner at Artiman Ventures.
The panelists (above) represent academic pathology, community hospital pathology, and the commercial sector. They are:
Because the arrival of automated analysis of digital pathology images will transform the daily routine of every surgical pathologist, it would be beneficial for all pathology groups to have one or more of their pathologists register and participate in this critical webinar.
The roundtable discussion will help them understand how quickly AI-powered image analysis is expected be cleared for use by the FDA in such diseases as prostate cancer and melanomas. Both types of cancers generate high volumes of case referrals to the nation’s pathologists, so potential for disruption to long-standing client relationships, and the possible loss of revenue for pathology groups that delay their adoption of digital pathology, can be significant.
On the flip side, community pathology groups that jump on the digital pathology bandwagon early and with the right preparation will be positioned to build stronger client relationships, increase subspecialty case referrals, and generate additional streams of revenue that boost partner compensation within their group.
Also, because so many pathologists are working remotely, Dark Daily has arranged special group rates for pathology practices that would like their surgical pathologists to participate in this important webinar and roundtable discussion on AI-powered primary diagnosis of pathology images. Inquire at info@darkreport.com or call 512-264-7103.
Many other healthcare systems also are partnering with private genetic testing companies to pursue research that drive precision medicine goals
It is certainly unusual when a major health network announces that it will give away free genetic tests to 10,000 of its patients as a way to lay the foundation to expand clinical services involving precision medicine. However, pathologists and clinical laboratory managers should consider this free genetic testing program to be the latest marketplace sign that acceptance of genetic medicine continues to move ahead.
Notably, it is community hospitals that are launching this
new program linked to clinical laboratory research that uses genetic tests for
specific, treatable conditions. The purpose of such genetic research is to
identify patients who would benefit from test results that identify the best
therapies for their specific conditions, a core goal of precision medicine.
Clinical laboratory leaders will be interested in this
initiative, as well other partnerships between healthcare systems and private
genetic testing companies aimed at identifying and enrolling patients in
research studies for disease treatment protocols and therapies.
The Future of Precision Medicine
Modern Healthcare reported that data from the WholeMe DNA study, which was funded through donations to the AdventHealth Foundation, also will be used by the healthcare network for research beyond FH, as AdventHealth develops its genomics services. The project’s cost is estimated to reach $2 million.
“Genomics is the future of medicine, and the field is rapidly evolving. As we began our internal discussions about genomics and how to best incorporate it at AdventHealth, we knew research would play a strong role,” Wes Walker MD, Director, Genomics and Personalized Health, and Associate CMIO at AdventHealth, told Becker’s Hospital Review.
“We decided to focus on familial hypercholesterolemia
screening initially because it’s a condition that is associated with
life-threatening cardiovascular events,” he continued. “FH is treatable once
identified and finding those who have the condition can lead to identifying
other family members who are subsequently identified who never knew they had
the disease.”
The AdventHealth Orlando website states that participants in the WholeMe study receive information stored in a confidential data repository that meets HIPAA security standards. The data covers ancestry and 22 other genetic traits, such as:
Asparagus Odor Detection
Bitter Taste
Caffeine Metabolism
Cilantro Taste Aversion
Circadian Rhythm
Coffee Consumption
Delayed Sleep
Earwax Type
Endurance vs Power
Exercise Impact on Weight
Eye Color
Freckling
Hair Curl and Texture
Hand Grip Strength
Height
Lactose Tolerance
Sleep Duration
Sleep Movement
Sleeplessness
Sweet Tooth
Tan vs. Sunburn
Waist Size
Those who test positive for a disease-causing FH variant will be referred by AdventHealth for medical laboratory blood testing, genetic counseling, and a cardiologist visit, reported the Ormond Beach Observer.
One in 250 people have FH, and 90% of them are undiagnosed,
according to the FH Foundation,
which also noted that children have a 50% chance of inheriting FH from parents
with the condition.
AdventHealth plans to expand the free testing beyond central
Florida to its 46 other hospitals located in nine states, Modern Healthcare
noted.
Other Genetics Data Company/Healthcare Provider Partnerships
Helix (above) is one of the world’s largest CLIA-certified, CAP-accredited next-generation sequencing labs. The partnership with AdventHealth offered study participants Exome+: a panel-grade medical exome enhanced by more than 300,000 informative non-coding regions; a co-branded ancestry + traits DNA product for all participants; secure storage of genomic data for the lifetime of the participant; infrastructure and data to facilitate research; and in-house clinical and scientific expertise, according to Helix’s website. (Photo copyright: Orlando Sentinel.)
Business Insider noted that Helix has focused on clinical partnerships for about a year and seems to be filling a niche in the genetic testing market.
“Helix is able to sidestep the costs of direct-to-consumer
marketing and clinical test development, while still expanding its customer
base through predefined hospital networks. And the company is in a prime
position to capitalize on providers’ interest in population health management,”
Business Insider reported.
Ochsner’s program is the first “fully digital population
health program” aimed at including clinical genomics data in primary care in an
effort to affect patients’ health, FierceHealthcare
reported.
Hereditary breast and ovarian cancer due to
mutations in BRCA1 and BRCA2 genes;
Lynch
syndrome, associated with colorectal and other cancers; and
FH.
Color also offers genetic testing and whole genome sequencing services to NorthShore’s DNA10K program, which plans to test 10,000 patients for risk for hereditary cancers and heart diseases, according to news release.
And, Jefferson Health offered Color’s genetic testing to the healthcare system’s 33,000 employees, 10,000 of which signed up to learn their health risks as well as ancestry, a Color blog post states.
“Understanding the genome warning signals of every patient will be an essential part of wellness planning and health management,” said Geisinger Chief Executive Officer David Feinberg, MD, when he announced the new initiative at the HLTH (Health) Conference in Las Vegas. “Geisinger patients will be able to work with their family physician to modify their lifestyle and minimize risks that may be revealed,” he explained. “This forecasting will allow us to provide truly anticipatory healthcare instead of the responsive sick care that has long been the industry default across the nation.”
It will be interesting to see how and if genetic tests—free
or otherwise—will advance precision medicine goals and population health
treatments. It’s important for medical laboratory leaders to be involved in health
network agreements with genetic testing companies. And clinical laboratories should
be informed whenever private companies share their test results data with
patients and primary care providers.
This research could lead to a useful liquid biopsy test that would be a powerful new tool for clinical laboratories and anatomic pathologists
Cancer researchers have long sought the Holy Grail of
diagnostics—a single biomarker that can quickly detect cancer from blood or
biopsied tissue. Now, researchers in Australia may have found that treasure. And
the preliminary diagnostic test they have developed reportedly can return
results in just 10 minutes with 90% accuracy.
In a news release, University of Queensland researchers discussed identifying a “simple signature” that was common to all forms of cancer, but which would stand out among healthy cells. This development will be of interest to both surgical pathologists and clinical laboratory managers. Many researchers looking for cancer markers in blood are using the term “liquid biopsies” to describe assays they hope to develop which would be less invasive than a tissue biopsy.
“This unique nano-scaled DNA signature appeared in every type of breast cancer we examined, and in other forms of cancer including prostate, colorectal, and lymphoma,” said Abu Sina, PhD, Postdoctoral Research Fellow at the Australian Institute for Bioengineering and Nanotechnology (AIBN), University of Queensland (UQ), in the news release.
“We designed a simple test using gold nanoparticles that
instantly change color to determine if the three-dimensional nanostructures of cancer
DNA are present,’ said Matt
Trau, PhD, Professor of Chemistry at the University of Queensland, and
Deputy Director and Co-Founder of UQ’s AIBN, in the news release.
The team’s test is preliminary, and more research is needed before
it will be ready for Australia’s histopathology laboratories (anatomic
pathology labs in the US). Still, UQ’s research is the latest example of how
increased knowledge of DNA is making it possible for researchers to identify
new biomarkers for cancer and other diseases.
“We certainly don’t know yet whether it’s the holy grail for
all cancer diagnostics, but it looks really interesting as an incredibly simple
universal marker of cancer, and as an accessible and inexpensive technology
that doesn’t require complicated lab-based equipment like DNA sequencing,” Trau
added.
The UQ researchers published their study in the journal Nature Communications. In it, they noted that “Epigenetic reprogramming in cancer genomes creates a distinct methylation landscape encompassing clustered methylation at regulatory regions separated by large intergenic tracks of hypomethylated regions. This methylation landscape that we referred to as ‘Methylscape’ is displayed by most cancer types, thus may serve as a universal cancer biomarker.”
While methyl patterning is not new, the UQ researchers say they were the first to note the effects of methyl pattern in a particular solution—water. With the aid of transmission electron microscopy, the scientists saw DNA fragments in three-dimensional structures in the water. But they did not observe the signature in normal tissues in water.
“To date, most research has focused on the biological consequences of DNA Methylscape changes, whereas its impact on DNA physicochemical properties remains unexplored,” UQ scientists Matt Trau, PhD (left), Abu Sina, PhD (center), and Laura Carrascosa (right), wrote in their study. “We exploit these Methylscape differences to develop simple, highly sensitive, and selective electrochemical or colorimetric one-step assays for the detection of cancer.” (Photo copyright: University of Queensland.)
Their test averaged 90% accuracy during the testing of 200
human cancer samples. Furthermore, the researchers found the DNA structure to
be the same in breast, prostate, and bowel cancers, as well as lymphomas, noted
The Conversation.
“We find that DNA polymeric
behavior is strongly affected by differential patterning of methylcytosine
leading to fundamental differences in DNA solvation and DNA-gold affinity
between cancerous and normal genomes,” the researchers wrote in NatureCommunications.“We exploit
these methylscape differences to develop simple, highly sensitive, and
selective electrochemical or one-step assays for detection of cancer.”
Next Steps for the
“Gold Test”
“This approach represents an exciting step forward in
detecting tumor DNA in blood samples and opens up the possibility of a generalized
blood-based test to detect cancer, Ged Brady, PhD, Cancer Research UK
Manchester Institute, told The
Oxford Scientist. “Further clinical studies are required to evaluate
the full clinic potential of the method.”
Researchers said the next step is a larger clinical study to
explore just how fast cancer can be detected. They expressed interest in
finding different cancers in body fluids and at various stages. Another opportunity
they envision is to use the cancer assay with a mobile device.
DiCarlo told USA Today
that such a mobile test could be helpful to clinicians needing fast answers for
people in rural areas. However, he’s also concerned about false positives. “You
don’t expect all tumors to have the same methylation pattern because there’s so
many different ways that cancer can develop,” he told USA Today. “There
are some pieces that don’t exactly align logically.”
The UQ researchers have produced an intriguing study that differs
from other liquid biopsy papers covered by Dark Daily. While their test may need to be used in combination with other
diagnostic tests—MRI, mammography, etc.—it has the potential to one day be used
by clinical laboratories to quickly reveal diverse types of cancers.
