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.
Genetic scientists show how rapid WGS is helping doctors determine best treatments for patients with life-threatening conditions
Clinical laboratory scientists will recall that last year, Dark Daily covered how researchers at Stanford University School of Medicine had developed a method for performing rapid whole genomic sequencing (WGS) in as little as five hours. We predicted that their new ultra-rapid genome sequencing approach could lead to significantly faster diagnostics and improved clinical laboratory treatments for cancer and other diseases. And it has.
The research scientist responsible for that breakthrough is cardiologist and Associate Dean of Stanford University School of Medicine, Euan Ashley, MD, PhD. Ashley is also a professor of genomics and precision health, cardiovascular medicine, genetics, and biomedical data science and pathology.
Ashley’s success demonstrates that the drive to reduce the diagnostic time to answer is a market dynamic encouraging research companies to continue finding ways to make WGS faster to accomplish, cheaper to perform, and the DNA sequences generated more accurate.
It is precisely these developments that will provide clinical laboratories and anatomic pathology groups with new means for improving diagnosis and the identification of the most appropriate therapies for individual patients—a core element of precision medicine.
Ashley’s team is now looking at how faster genetic sequencing results could help physicians make life-and-death treatment decisions, STAT reported.
“There’s just never been a better time to be doing genomics,” cardiologist Euan Ashley, MD, PhD, Associate Dean of the Stanford University School of Medicine, told STAT. “Now there are lots of choices. If you’re a genome center and you need to do half a million genomes, you’re going to be extremely price-sensitive. If you’re a clinical lab, where you get a few exomes and a few genomes every day, and what really matters to you is the highest possible accuracy for diagnosis, then you’re definitely going to make a different choice,” he added. (Photo copyright: euanangusashley.com.)
Getting Crucial Genetic Information Faster
Ashley believes that if doctors who work with rare and deadly diseases get crucial genetic information faster, they can more precisely determine which surgical procedures are best for their patients during life-or-death situations.
Already, his work is proving highly successful. In a letter his team published in the New England Journal of Medicine (NEJM), the researchers reported 12 cases of sequencing seriously ill patients, five of whom were diagnosed in seven hours and 18 minutes. Every single case resulted in tangible changes in treatments given to the patients.
“We continue to be interested in sequencing genomes faster and more accurately, for a broader range of clinical applications. We’re recruiting from intensive care units similar kinds of patients to the ones we did before, but with every aspect of the pipeline upgraded, which helps both from a speed but also from an accuracy perspective,” he told STAT.
Ashley and his team continue to delve into the patient care aspects, striving to continue to make a big impact. In addition, the group is being sought out by cancer doctors who need faster diagnoses.
“We also have a lot of interest from cancer doctors saying it’s really important to make a cancer diagnosis quickly. And of course, there is no person who’s ever had the specter of cancer hanging over them for a moment that didn’t want some kind of an answer faster. If you can have it in the next minute, you would take it rather than waiting several weeks,” he noted.
As a result, the group has initiated pilot studies “to look at returning results faster in the same way that we were speeding up the intensive care unit with whole genome sequencing,” Ashley told STAT.
Though the work is in the early stages, the team has a few scenarios where access to genetic data changes medical decision making. For instance, when genetic test results showing a positive BRCA variant alter a doctor’s surgical plan.
“We don’t wait for a cardiac enzyme [test] if somebody’s having a heart attack. That comes back within 10 minutes to a few hours from the lab. I don’t see why you should have to wait for a test to tell you if you’re positive for BRCA variant,” he told STAT.
“Another very obvious place is acute leukemia. And there’s a number of actionable conditions where if they can be detected rapidly, then treatment can be started faster,” he added.
Improving Genetic Sequencing Accuracy while Lowering Costs
STAT asked Ashley about a claim that his team could cut their Guinness World Record sequencing time in half.
“It’s easy to throw that number around, harder to deliver on it. But I think we’re definitely on track to knock hours, not minutes, off that record,” he said.
Additionally, the team continues to work on decreasing cost per genome. In just the time since the record was set, there has already been great strides in this area. The market is filled with new companies and the competition has lowered costs.
“It has definitely come down,” Ashely noted. “In fact, by the time we ended up publishing the [NEJM] paper—as opposed to when we first did this calculation—the cost was already lower. And that was actually before the entry of these new companies to the market, which added downward pressure on costs of sequencing,” he added.
Getting Payers to Reimburse for Genetic Sequencing
Even though costs for WGS is dropping, getting health plans to reimburse for genetic testing remains difficult.
“The challenge now is persuading payers to the very obvious fact that this technology makes patients’ lives better and saves them money,” Ashley told STAT. “And that’s the amazing part. There are so many cost-effectiveness studies now for this technology and yet we are still paying people to sit on the phone all day long and debate with insurance companies.
“And in a world where we pay a very large amount of money for therapeutics, these diagnostics can be cost-saving and lifesaving. At some level, it’s hard to understand why it hasn’t been deployed much more readily,” he concluded.
Clinical laboratory leaders, pathologists, and research scientists should continue to monitor the development of rapid genetic sequencing for diagnostic purposes.
New Orleans, LA (April 26, 2016) — A top-flight roster of lab experts and innovators gather in New Orleans April 26-27, 2016, for the annual Executive War College on Lab and Pathology Management. This event—the nation’s largest, most respected gathering on lab management and operations—is taking place at the Sheraton Hotel on Canal Street. Now in its 21st year, Executive War College this year expects record-breaking attendance by senior lab executives, administrators, and pathologists from all over the world.
“Never before has the clinical laboratory industry and anatomic pathology profession experienced such a fast-paced transformation of the American healthcare system as is happening now,” says Robert L. Michel, producer of Executive War College and Editor-In-Chief of The Dark Report. “As one example, the profession of lab medicine has the unprecedented opportunity to take the leading role in advancing the practice of precision medicine, informed by knowledge derived from genetic testing and whole-human genome sequencing.
Specifically addressing these precision medicine opportunities are General Sessions Tuesday, April 27, and Wednesday, April 28, noted Michel. These are world-class sessions, from esteemed speakers with international academic and clinical research reputations.”
The Executive War College 2016 General Session presentations will include:
“Genome Sequencing and Genetic Medicine: How It’s Changing Healthcare Today and What Providers Can Expect Moving Forward,” Wednesday, April 27 at 9:40 am, featuring Brad Perkins, M.D., Chief Medical Officer with Human Longevity in San Diego, CA
“Genomics, Data & Personalized Medicine – The UK Experience of Transforming Care for the Future,” Wednesday, April 27 at 10:40 am, featuring Professor Sue Hill, OBE, Ph.D., Dsc, CBiol, FlBiol, Hon FRCP, Chief Scientific Officer with the NHS England
A panel discussion Tuesday afternoon, April 26 at 4:30 pm, entitled “Understanding the New Ways that Payers and Labs are Interacting as Healthcare Transforms, Different Payment Models Emerge, and Genetic Testing Creates New Opportunities to Improve Patient Outcomes,” bringing together experts with a range of perspectives on these issues.
In addition to the above one-of-a-kind forums, Executive War College 2016 offers more than 50 more information-packed presentations comprising an enlightening and expansive range of topics, plus special sessions for pathology professionals, and interactive roundtables for lab CFOs, CIOs, Sales Managers, and Marketing Officers. For more information on Executive War College 2016, visit http://www.executivewarcollege.com. You may also contact Chris Garcia at 210-912-7716.
About THE DARK REPORT
Established in 1995, THE DARK REPORT is the leading source of exclusive business intelligence for laboratory CEOs, COOs, CFOs, Pathologists and Senior industry executives. It is widely read by leaders in laboratory medicine and diagnostics. The Dark Report produces the famous Executive War College on Laboratory and Pathology Management every spring, which showcases innovations by the nation’s and globe’s leading laboratory organizations. Dark Daily is an Internet-based e-briefing intelligence service, read worldwide by thought leaders in laboratory and pathology management. Other well-known conferences conducted by THE DARK REPORT are Lab Quality Confab (on the use of Lean and Six Sigma methods in labs and hospitals) and Molecular Summit (on the integration of in vivo and in vitro diagnostics). THE DARK REPORT co-produces Frontiers in Laboratory Medicine annually in the United Kingdom; Executive Edge bi-annually in Canada; and The Business of Pathology bi-annually in Australia.
World’s largest medical laboratory management conference will take place on April 26-27 and showcase how innovative labs are delivering more value with lab testing services
By now, most pathologists and clinical laboratory professionals recognize that healthcare is prepared to accept the use of whole human genome sequencing for diagnostic and therapeutic purposes. It is no longer a question of “will it happen?” Rather, the questions are now: “how fast will this happen and what must my lab do to be ready to support physicians in how they use the knowledge derived from whole human genome sequencing?”
Funded by both for-profit and not-for-profit organizations, this new gene sequencing center is preparing to offer its first genetic tests for use in patient care
Next-generation gene sequencing for clinical diagnostic applications is moving forward at the New York Genome Center (NYGC). Located in New York City, the center is designed to be a genetic medicine technology incubator and has funding from a number of for-profit and not-for-profit sources.
For pathologists and medical laboratory administrators, this creation and operation of this independent sequencing center is a notable development. It shows the willingness of different organizations to come together and fund a collaborative venture to advance exome sequencing and whole-genome sequencing for clinical purposes.
