Clinical laboratories and pathology groups may soon have new assays for diagnosis, treatment identification, patient monitoring
It’s here at last! The human Y chromosome now has a full and complete sequence. This achievement by an international team of genetic researchers is expected to open the door to significant insights in how variants and mutations in the Y chromosome are involved in various diseases and health conditions. In turn, these insights could lead to new diagnostic assays for use by clinical laboratories and pathology groups.
Pathologists and clinical laboratories involved in genetic research will understand the significance of this accomplishment. The full Y chromosome sequence “fills in gaps across more than 50% of the Y chromosome’s length, [and] uncovers important genomic features with implications for fertility, such as factors in sperm production,” SciTechDaily noted.
This breakthrough will make it possible for other research teams to gain further understanding of the functions of the Y chromosome and how specific gene variants and mutations contribute to specific health conditions and diseases. In turn, knowledge of those genetic sequences and mutations would give clinical laboratories the assays that help diagnosis, identify relevant therapies, and monitor a patient’s progress.
“When you find variation that you haven’t seen before, the hope is always that those genomic variants will be important for understanding human health,” said Adam Phillippy, PhD, a senior investigator and head of the Genome Informatics Section at the National Human Genome Research Institute, in a press release. Clinical laboratories and anatomic pathology groups may soon have new assays based on the T2T study findings. (Photo copyright: National Human Genome Research Institute.)
Study Background and Recognition
Revolutionary thinking by the Telomere-to-Telomere (T2T) scientists led to the team’s breakthrough. The researchers “applied new DNA sequencing technologies and sequence assembly methods, as well as knowledge gained from generating the first gapless sequences for the other 23 human chromosomes,” SciTechDaily reported.
In 1977, the first complete genome of an organism was sequenced. Thus began the commencement of sequencing technology research. Twenty years ago the first human genome sequence was completed. The result was thanks to years of work through the preferred “chain termination” (aka, Sanger Sequencing) method developed by Fred Sanger and a $2.7 billion contribution from the Human Genome Project, according to a study published in the African Journal of Laboratory Medicine (AJLM).
By 2005, a new era in genomic sequencing emerged. Scientists now employed a technique called pyrosequencing and the change had great benefits. “Massively parallel or next-generation sequencing (NGS) technologies eliminated the need for multiple personnel working on a genome by automating DNA cleavage, amplification, and parallel short-read sequencing on a single instrument, thereby lowering costs and increasing throughput,” the AJLM paper noted.
The new technique brought great results. “Next-generation sequencing technologies have made sequencing much easier, faster and cheaper than Sanger sequencing,” the AJLM study authors noted.
The changes allowed more sequencing to be completed. Nevertheless, more than half of the Y chromosome sequence was still unknown until the new findings from the T2T study, SciTechDaily reported.
Why the TDT Breakthrough Is So Important
“The biggest surprise was how organized the repeats are,” said Adam Phillippy, PhD, a senior investigator and head of the NHGRI. “We didn’t know what exactly made up the missing sequence. It could have been very chaotic, but instead, nearly half of the chromosome is made of alternating blocks of two specific repeating sequences known as satellite DNA. It makes a beautiful, quilt-like pattern.”
Much can be gained in knowing more about the Y chromosome. Along with the X chromosome, it is significant in sexual development. Additionally, current research is showing that genes on the Y chromosome are linked to the risk and severity of cancer.
Might What Comes Next Give Clinical Labs New Diagnostic Tools?
The variety of new regions of the Y chromosome that the T2T team discovered bring into focus several areas of new genetic research. For instance, the “azoospermia factor region, a stretch of DNA containing several genes known to be involved in sperm production” was uncovered, and “with the newly completed sequence, the researchers studied the structure of a set of inverted repeats or palindromes in the azoospermia factor region,” SciTechDaily reported.
“This structure is very important because occasionally these palindromes can create loops of DNA. Sometimes, these loops accidentally get cut off and create deletions in the genome,” said Arang Rhie, PhD, a staff scientist at NHGRI and first author of the Nature study.
Missing regions would challenge the production of sperm, impacting fertility, so being able to finally see a complete sequence will help research in this area.
Scientists are only just beginning to recognize the value of this breakthrough to future genetic research and development. As genetic sequencing costs continue to drop, the T2T research findings could mean new treatment options for pathologists and diagnostic assays for clinical laboratories are just around the corner.
One of the world’s fastest growing medical laboratory companies in India is using digital pathology systems and AI to replace older diagnostic technologies
Artificial intelligence (AI) is gaining acceptance around the world and use of AI to analyze digital pathology images is expected to be a major disruptor to the profession of anatomic pathology. Internationally, several pathology companies already use AI-powered solutions to diagnose cancer.
One such example is Neuberg Diagnostics, a fast-growing clinical laboratory company in Chennai, India. Neuberg has been using AI to review digital pathology images for several years, according to Chairman and Managing Director GSK Velu, PhD, BPharm.
“We already use AI in our laboratories,” Velu said in an exclusive interview with Dark Daily. “Our main reference laboratories currently use digital pathology systems to support the pathologists and many of them are using AI with these digital pathology systems.
“AI and data analytics tools are being used in other departments too, such as in our wellness department where we use AI for predictive analytics,” he added. “We also use AI in our genomics division, and we are introducing AI into other divisions slowly and steadily.”
Neuberg operates 120 laboratories in an extensive network in India, South Africa, and the United Arab Emirates (UAE), and now in the US as well.
“Our idea is to enhance the access and affordability for next-generation techniques, meaning molecular diagnostics, genomics, pathology, digital pathology, proteomics, metabolomics, and all that. This is the spirit behind Neuberg Diagnostics,” said GSK Velu, PhD, BPharm (above), Chairman and Managing Director of Neuberg Diagnostics, in an exclusive interview with The Dark Report. Clinical laboratories that are considering investing in digital pathology technologies may want to follow its development at Neuberg’s Centre for Genomic Medicine in Raleigh, NC, which opened in May. (Photo copyright: Neuberg Diagnostics.)
Replacing Older Pathology Technologies
As has been happening at other anatomic pathology centers around the world, Neuberg has been using digital pathology systems to replace older technologies. “One of our largest labs is our Bangalore Reference Lab,” Velu said. “There, we do not use microscopes for histopathology, and that lab has used digital pathology for routine review of specimens for several years now.
“But because artificial intelligence is still emerging, we can’t rely on AI with all of our digital pathology systems,” he added. “Although, of course, AI is certainly an aid to everything we do with digital pathology.
“For a variety of reasons, the adaptation of artificial intelligence in anatomic pathology is not happening as effectively nor as fast as we would like,” he noted. “So, for now, we need to wait and watch a bit longer, either because adaptation by pathologists is slow, or because AI tools are still a bit of a worry for some pathologists.
Younger Pathologists Adapt Faster to Digital Pathology
One reason could be that conventional pathologists worry about relying completely on AI for any diagnosis, Velu noted. “I’m certain that the more recent generation of pathologists who are now in their 30s, and the new people coming into pathology, will start adapting more quickly to digital pathology and to AI faster than the older generation of pathologists have done.
“The younger pathologists have a greater appreciation for the potential of digital pathology, while the older pathologists don’t want to let go of conventional diagnosis methods,” he added.
“For example, we have not yet seen where pathologists are reviewing breast image scans,” he commented. “But, at the same time, AI has been well-accepted among radiologists who are reviewing breast mammography scans.”
In India and in other markets worldwide, radiologists have adapted AI tools for breast mammography scans to diagnose breast cancer, he noted. “But that’s not happening even among pathologists who are doing cancer screening,” he said.
Velu suggested that another reason for the slow adoption of AI tools in pathology is that these systems are relatively new to the market. “Maybe the AI tools that are used with digital pathology are not as reliable as we hoped they would be, or they are not fully robust at the moment,” he speculated. “That’s why I say it will take some time before the use of AI for diagnosis becomes more widespread among pathologists. So, for now, we must wait until digital pathology and AI tools work together more seamlessly.
Replacing Conventional Pathology Technologies and Methods
“When those two technologies—AI and digital pathology systems—are linked more closely, their use will take hold in a substantial way,” Velu predicted. “When that happens, they are likely to replace conventional pathology methods completely.
“Currently, we are in the early stages of a transformation,” he added. “In our labs, you can see that the transformation is ongoing. We are using digital pathology systems even in our smaller labs. Then, the staff in our smaller labs do the processing of slides to convert them to digital images and send them to our labs in the larger cities. There, the professional staff uses AI to review those digital images and issue reports based on those images.
“Using our digital pathology systems and AI in that way means that we can make that technology available even in smaller towns and villages that have access only to our smaller labs,” he commented.
Velu added that wider use of digital pathology systems could improve the quality of care that pathologists deliver to patients in a significant way, particularly in rural areas. “Here in India, we are not seeing a huge shortage of pathologists, except in rural areas and villages,” he explained. “In those places, we could run short of pathologists.
“That is the reason we are trying to adapt the use of telepathology more widely,” he noted. “To do that, we might have technicians and histologists who will do just processing of slides so that they can send the digital images to our pathologists located in larger cities. Then, those surgical pathologists will review the cases and send the reports out. That’s the model that we are trying to slowly follow here.”
As use of digital pathology images increased, many predicted that specimens would flow from the US to India. This would happen because of the belief that the lower cost of surgical pathology in India would successfully draw business away from pathology groups here in the United States.
However, Neuberg turned the tables on that belief when it announced the opening of its Neuberg Centre for Genomic Medicine (NCGM), a state-of-the-art esoteric and genetic testing laboratory in Raleigh, NC. The NCGM lab is CLIA-certified and Neuberg says it is ready to compete with labs in this country on their home turf.
These are reasons why pathologists and pathology practice administrators in the United States may want to watch how Neuberg Diagnostics continues to develop its use of digital pathology platforms and AI-powered digital image analysis tools throughout its international network of laboratories.
Using animal blood, the researchers hope to improve the accuracy of AI driven diagnostic technology
What does a cheetah, a tortoise, and a Humboldt penguin have
in common? They are zoo animals helping scientists at Saarland University in
Saarbrücken, Germany, find biomarkers that can help computer-assisted diagnoses
of diseases in humans at early stages. And they are not the only animals
lending a paw or claw.
In their initial research, the scientists used blood samples
that had been collected during routine examinations of 21 zoo animals between
2016 and 2018, said a news
release. The team of bioinformatics
and human genetics experts
worked with German zoos Saarbrücken and Neunkircher for the study. The project
progresses, and thus far, they’ve studied the blood of 40 zoo animals, the
release states.
This research work may eventually add useful biomarkers and
assays that clinical
laboratories can use to support physicians as they diagnose patients,
select appropriate therapies, and monitor the progress of their patients. As medical
laboratory scientists know, for many decades, the animal kingdom has been
the source of useful insights and biological materials that have been
incorporated into laboratory assays.
“Measuring the molecular blood profiles of animals has never
been done before this way,” said Andreas
Keller, PhD, Saarland University Bioinformatics Professor and Chair for
Clinical Bioinformatics, in the news release. The Saarland researchers published
their findings in Nucleic Acids
Research, an Oxford
Academic journal.
“Studies on sncRNAs [small non-coding RNAs] are often largely based on homology-based information, relying on genomic sequence similarity and excluding actual expression data. To obtain information on sncRNA expression (including miRNAs, snoRNAs, YRNAs and tRNAs), we performed low-input-volume next-generation sequencing of 500 pg of RNA from 21 animals at two German zoological gardens,” the article states.
Can Animals Improve the Accuracy of AI to Detect Disease
in Humans?
However, the researchers perceived an inability for AI and machine learning to
discern real biomarker patterns from those that just seemed to fit.
“The machine learning methods recognize the typical
patterns, for example for a lung tumor or Alzheimer’s disease. However, it is
difficult for artificial intelligence to learn which biomarker patterns are
real and which only seem to fit the respective clinical picture. This is where
the blood samples of the animals come into play,” Keller states in the news
release.
“If a biomarker is evolutionarily conserved, i.e. also
occurs in other species in similar form and function, it is much more likely
that it is a resilient biomarker,” Keller explained. “The new findings are now
being incorporated into our computer models and will help us to identify the
correct biomarkers even more precisely in the future.”
Andreas Keller, PhD (left), and zoo director Richard Francke (right), hold a pair of radiated tortoises that participated in the Saarland University study. (Photo copyright: Oliver Dietze/Saarland University.)
“Because blood can be obtained in a standardized manner and
miRNA expression patterns are technically very stable, it is easy to accurately
compare expression between different animal species. In particular, dried blood
spots or microsampling devices appear to be well suited as containers for
miRNAs,” the researchers wrote in Nucleic Acids Research.
Animal species that participated in the study include:
Additionally, human volunteers contributed blood specimens
for a total of 19 species studied. The scientists reported success in capturing
data from all of the species. They are integrating the information into their
computer models and have developed a public database of their
findings for future research.
“With our study, we provide a large collection of small RNA
NGS expression data of species that have not been analyzed before in great
detail. We created a comprehensive publicly available online resource for
researchers in the field to facilitate the assessment of evolutionarily
conserved small RNA sequences,” the researchers wrote in their paper.
Clinical Laboratory Research and Zoos: A Future
Partnership?
This novel involvement of zoo animals in research aimed at improving
the ability of AI driven diagnostics to isolate and identify human disease is
notable and worth watching. It is obviously pioneering work and needs much
additional research. At the same time, these findings give evidence that there
is useful information to be extracted from a wide range of unlikely sources—in
this case, zoo animals.
Also, the use of artificial intelligence to search for
useful patterns in the data is a notable part of what these researchers
discovered. It is also notable that this research is focused on sequencing DNA
and RNA of the animals involved with the goal of identifying sequences that are
common across several species, thus demonstrating the common, important
functions they serve.
In coming years, those clinical laboratories doing genetic
testing in support of patient care may be incorporating some of this research
group’s findings into their interpretation of certain gene sequences.
As personalized medicine becomes more popular, clinical laboratories, and anatomicpathologists are uniquely positioned to use next-generation sequencing to advance their scope among regulators, insurers, providers and patients, while adding clinical value and generating a new revenue source
By now, most clinical pathologists and medical laboratory scientists recognize that genetics, genetic testing, and gene sequencing will be a major transformative force in this country’s healthcare system. Genetics is the future of modern medicine.
At the same time, most independent labs and health network labs still lack the key resources needed for them to provide accurate and state-of-the-art genetic testing and gene sequencing services in support of clinical care.
The good news is that it is not yet prime time for genetic testing—meaning few genetic tests have become part of routine care, particularly in primary care settings. Today’s limited use of genetic tests creates the opportunity for any medical laboratory and anatomic pathology group to use this time to develop its genetic testing strategy. It also has time to incrementally put in place the resources it will need to offer genetic testing and gene sequencing services to its client physicians.
“Every clinical lab that wants to be a provider of genetic tests needs three basic resources,” stated Robert L. Michel, Editor-in-Chief of The Dark Report and Dark Daily. “First, the lab must have information technology in place that can handle genetic and molecular data. The second thing needed are pathologists, PhDs, and clinical laboratory scientists trained in genetic and molecular diagnostics. Of course, the third resource is to have the lab analyzers, instruments, and automation needed to extract, amplify, and sequence specimens.”
Experts agree that adoption of genetic testing will happen at a rapid pace. “Next-generation sequencing (NGS) is an incredibly powerful, positive force in medical care. We were in the Dark Ages before this. It is the tsunami on our shores, and it’s going to take over all of medicine. It’s not a trend. It’s the future of medicine. There’s no question about it,” predicts Maurie Markman, MD, an oncologist and President of Medicine and Science at Cancer Treatment Centers of America, in an article he penned for Health Connect South.
“As knowledge of genomic medicine has increased, its cost has plummeted,” notes Maurie Markman, MD (above), President of the Cancer Treatment Centers of America, in his Health Connect South article. “Sequencing a human genome [in 2015] costs less than $10,000, compared to more than $100 million in 2001. Not only are the tests more available to patients, but more oncologists are trying their hand at tumor testing and building on the base of knowledge.” (Photo copyright: Cancer Treatment Centers of America.)
“If you agree with Markman’s comments, then your medical lab should have a plan for how it will incorporate NGS technologies and genetic testing into its menu of lab tests,” observed Michel. “Because NGS is the engine powering much of this new genetic information and igniting the potential of personalized medicine, probably the single most important business step clinical labs and pathology groups can take at this point is to begin to create the informatics capabilities needed to support genetic testing.
“This can be done by either adding the needed functions to the existing laboratory information system (LIS) or supplementing that LIS with appropriate middleware solutions,” he continued. “This is true even if a lab plans to outsource both the gene sequencing and the annotation and interpretation of the resulting gene sequences. It will need in-house informatics capabilities to store and report that genetic information.”
NGS, Gene Sequencing, Precision Medicine, and Clinical Laboratories
Purchasing, implementing, and operating NGS technologies can be a costly venture, so it is critical that labs know and understand the needs of their referring clients.
“Knowing who your lab’s customers are and what you do for them today should guide you as a laboratory,” notes Brian Keefe, Vice President of Sales and Customer Innovation at Psyche Systems, a laboratory solutions developer for the medical industry based in Boston. “For example, your pathology group knows it should be offering NGS testing, and the justification for needing to go in this direction is because 90% of your clients are oncologists.”
Using NGS technology and marketing it to clients will be a valuable benefit for clinical laboratories. It will enable labs to participate in personalized medicine and allow them to become the “go to” facility for specific genetic tests.
“If you’re a laboratory that has figured out how to map the genome for nightmare bacteria, it doesn’t matter whether you’re three miles or 3,000 miles away, physicians will send their samples to your lab regardless of the distance,” Keefe notes. “If your lab is first to market, you establish powerful brand recognition and attract positive attention, which justifies your lab’s cost to set up and offer that testing in the first place.”
Learn More by Requesting the Dark Daily NGS White Paper
To help medical laboratories and anatomic pathology groups learn more about the growing role of NGS in clinical care, and how NGS can benefit clinical and molecular laboratories, Dark Daily and The Dark Report have produced a white paper titled, “How Next-Generation Sequencing Helps Molecular Laboratories Deliver Personalized Medicine Services to their Client Physicians.”
Medical laboratory leaders who want to learn how labs can establish NGS services and implement the IT/Informatics needed to be successful in using NGS should request a copy of this important white paper. It reviews how pathologists can help providers select targeted therapies and touches on marketing strategies to use NGS to procure new customers and retain existing customers.
The NGS white paper can be downloaded at no cost by clicking here or placing https://www.darkdaily.com/how-next-generation-sequencing-helps-molecular-laboratories-deliver-personalized-medicine-services-to-their-client-physicians-601/ into your browser.
Using precision genomics, Mayo researchers hope to develop improved medical laboratory tools for screening, diagnosing, and treating patients with inherited genetic disorders such as accelerated aging
Telomeres increasingly are on the radars of physicians and healthcare consumers alike, as researchers gain more knowledge about these critical nucleotides, and doctors continue to indicate their belief that telomeres could make useful diagnostic tools. If so, that would open up a new channel of precision medicine testing for clinical laboratories and anatomic pathology groups.
Telomeres are DNA strands that protect chromosome end points from degrading as people age. Their job is similar to the way plastic tips keep shoelaces from fraying, researchers at the Mayo Clinic explained in a news release. They have been using precision genomics in their assessment of 17 patients with short telomere syndrome (STS) to uncover the genetic causes of the condition.
Using Genetic Sequencing to Find Causes of Short Telomeres
People with STS could develop conditions including bone marrow failure, liver disease, and lung disease earlier in life than others, the news release pointed out.
However, according to the researchers’ paper, “Management of STSs is fraught with significant challenges such as delayed diagnoses, lack of routinely available diagnostics modalities, and standardized treatment guidelines.”
Nevertheless, some physicians are already leveraging information about telomeres in patient treatment. And many consumers have been turning to telomere diagnostic testing companies to learn the lengths of their own telomeres. They’ve learned that the longer the telomeres the better, as shorter telomeres are associated with accelerated aging.
“The length of certain telomeres gives a history of all the assaults a person has been subject to over the course of her lifetime,” a Wired article noted, quoting Joseph Raffaele, MD, co-founder of PhysioAge Medical Group, a clinical practice in New York City that specializes in “proactive” medicines. He goes on to call telomeres “the new cholesterol.” (Photo copyright: drraffaele.com.)
More Study into STS is Needed
GenomeWeb summarized the Mayo study’s methodology as follows:
“An analysis of data from 17 patients with STS confirmed by flow-FISH (fluorescence in situ hybridization) occurred;
Two were of unknown significance in TERT and RTEL1
Study authors concluded that while some genetic mutations are common to short telomeres, they were found in only about 40% of the people in their study. So, more research is needed to discover other causes of short telomeres.
The study found that when compared to people with normal blood telomeres, people with shorter telomere lengths and more rapidly aging blood cells:
Were 50% more likely to develop new or increasing respiratory symptoms;
Were nine times more likely to die; and,
Had worse health status and quality of life.
“It is known that short telomeres are associated with common morbidities of COPD, but it was not known if there is a relationship between blood telomeres and patient-related outcomes in COPD,” Don Sin, MD, a chest physician who led the research at the Centre for Heart Lung Innovation at St. Paul’s Hospital, stated in a news release.
Other Takes on Telomeres
A Harvard Medical blog noted, however, that short telomeres do not necessarily mean disease is imminent, nor that long ones guarantee optimal health.
“There is mounting evidence that a healthy lifestyle buffers your telomeres,” stated Immaculata De Vivo, PhD, a Harvard Medical School Professor and Genetics Researcher at the Dana-Farber/Harvard Cancer Center, in the blog post.
However, another expert questions the value of measuring telomeres for disease risk.
“In short, telomere lengths are too variable within a population, too variable within an individual, and too sensitive to environmental factors to offer any reliable information for common disease risk,” wrote Ricki Lewis, PhD, in PLOS.
Although there are many pitfalls to overcome, some doctors are pushing to use telomere information in patient treatment, and these studies from the Mayo Clinic and other researchers have contributed important data for diagnostic test developers.
In the end, vast and varied content about telomeres exists and clinical laboratory professionals may be called on to help clarify and assess the information. And that’s the long and the short of it.
