Aug 6, 2018 | Digital Pathology, Instruments & Equipment, Laboratory Instruments & Laboratory Equipment, Laboratory Management and Operations, Laboratory News, Laboratory Operations, Laboratory Pathology, Laboratory Testing
Researchers in Boston are working to develop DNA as a low-cost, effective way to store data; could lead to new molecular technology industries outside of healthcare
Even as new insights about the role of DNA in various human diseases and health conditions continue to tumble out of research labs, a potential new use for DNA is emerging. A research team in Boston is exploring how to use DNA as a low-cost, reliable way to store and retrieve data.
This has implications for the nation’s clinical laboratories and anatomic pathology groups, because they are gaining experience in sequencing DNA, then storing that data for analysis and use in clinical care settings. If a way to use DNA as a data storage methodology was to become reality, it can be expected that medical laboratories will have the skillsets, experience, and information technology infrastructure already in place to offer a DNA-based data storage service. This would be particularly true for patient data and healthcare data.
Finding a way to reduce the cost of data storage is a primary reason why scientists are looking at ways that DNA could be used as a data storage technology. These scientists and technology developers seek ways to alleviate the world’s over-crowded hard drives, cloud servers, and databases. They hope this can be done by developing technologies that store digital information in artificially-made versions of DNA molecules.
The research so far suggests DNA data storage could be used to store data more effectively than existing data storage solutions. If this proves true, DNA-based data storage technologies could play a key role in industries outside of healthcare.
If so, practical knowledge of DNA handling and storage would be critical to these companies’ success. In turn, this could present unique opportunities for medical laboratory professionals.
DNA Data Storage: Durable but Costly
Besides enormous capacity, DNA-based data storage technology offers durability and long shelf life in a compact footprint, compared to other data storage mediums.
“DNA has an information-storage density several orders of magnitude higher than any other known storage technology,” Victor Zhirnov, PhD, Chief Scientist and Director, Semiconductor Research Corporation, told Wired.
However, projected costs are quite high, due to the cost of writing the information into the DNA. However, Catalog Technologies Inc. of Boston thinks it has a solution.
Rather than producing billions of unique bits of DNA, as Microsoft did while developing its own DNA data storage solution, Catalog’s approach is to “cheaply generate large quantities of just a few different DNA molecules, none longer than 30 base pairs. Then [use] billions of enzymatic reactions to encode information into the recombination patterns of those prefab bits of DNA. Instead of mapping one bit to one base pair, bits are arranged in multidimensional matrices, and sets of molecules represent their locations in each matrix.”
The Boston-based company plans to launch an industrial-scale DNA data storage service using a machine that can daily write a terabyte of data by leveraging 500-trillion DNA molecules, according to Wired. Potential customers include the entertainment industry, federal government, and information technology developers.
Catalog is supported by $9 million from investors. However, it is not the only company working on this. Microsoft and other companies are reportedly working on DNA storage projects as well.
“It’s a new generation of information storage technology that’s got a million times the information density, compared to flash storage. You can shrink down entire data centers into shoeboxes of DNA,” Catalog’s CEO, Hyunjun Park, PhD (above center, between Chief Science Officer Devin Leake on left and Milena Lazova, scientist, on right), told the Boston Globe. (Photo copyright: Catalog.)
Microsoft, University of Washington’s Synthetic DNA Data Storage
Microsoft and researchers at the University of Washington (UW) made progress on their development of a DNA-based storage system for digital data, according to a news release. What makes their work unique, they say, is the large-scale storage of synthetic DNA (200 megabytes) along with the ability to the retrieve data as needed.
“Synthetic DNA is durable and can encode digital data with high density, making it an attractive medium for data storage. However, recovering stored data on a large-scale currently requires all the DNA in a pool to be sequenced, even if only a subset of the information needs to be extracted,” the researchers wrote in their paper published in Nature Biotechnology.
“Here, we encode and store 35 distinct files (over 200 megabytes of data ) in more than 13-million DNA oligonucleotides and show that we can recover each file individually and with no errors, using a random access approach,” the researchers explained.
“Our work reduces the effort, both in sequencing capacity and in processing, to completely recover information stored in DNA,” Sergey Yekhanin, PhD, Microsoft Senior Researcher, told Digital Trends.
Successful research by Catalog, Microsoft, and others may soon lead to the launch of marketable DNA data storage services. And medical laboratory professionals who already know the code—the life code that is—will likely find themselves more marketable as well!
—Donna Marie Pocius
Related Information:
The Rise of DNA Data Storage
The Next Big Thing in Data Storage is Actually Microscopic
Catalog Hauls in $9 Million to Make DNA-Based Data Storage Commercially Viable
UW and Microsoft Researchers Achieve Random Access in Large-Scale DNA Data Storage
Random Access in Large-Scale DNA Data Storage
Microsoft and University of Washington Show DNA Can Store Data in Practical Way
Aug 1, 2018 | Digital Pathology, Instruments & Equipment, Laboratory Instruments & Laboratory Equipment, Laboratory Management and Operations, Laboratory News, Laboratory Operations, Laboratory Pathology, Laboratory Testing, Management & Operations
Identifying patients who will likely develop prolonged concussion symptoms could lead to new clinical laboratory tests and personalized medicine treatments
Researchers are homing in on a new diagnostic assay for concussion that could potentially generate significant numbers of test referrals to the nation’s clinical laboratories. This innovative work is targeting how concussions are diagnosed and treated.
Each year, thousands of children receive sports-related injuries, including concussions. There are ways for anatomic pathologists and hospital medical laboratories to diagnose concussions; however, testing can be invasive and doesn’t always reveal a complete picture of the injury state.
Additionally, about one third of children with concussions develop prolonged symptoms. However, when prescribing treatment plans, physicians have been unable to predict which patients are likely to recover quickly versus those who will have a longer recovery.
Now, researchers at Penn State College of Medicine (Penn State) believe they have discovered five microRNAs in saliva that could be used to identify patients who will likely experience prolonged concussion symptoms even one month after the initial injury.
The study also found that certain materials in saliva can help diagnose the severity of concussions and could hold the key to more effective clinical laboratory tests and personalized medicine treatments.
The Penn State researchers published their study results in JAMA Pediatrics, a publication of the Journal of the American Medical Association (JAMA).
Concussion Leading Sports-related Brain Injury
There are approximately 3.8 million sports and recreation-related traumatic brain injuries in the United States each year and the majority of those cases are concussions, according to The Concussion Place. Most concussions treated in emergency rooms are due to falls, motor-vehicle related injuries, being struck by an object, assaults, or playing sports.
Also known as mild traumatic brain injuries (mTBI), concussions are caused by blows or jolts to the head or body that cause the brain to move with excessive force inside the skull. The sudden impact damages brain cells and causes chemical changes within the brain that alter normal functioning. Though usually not life threatening, the damage can be serious and linger for months.
Symptoms of concussion include: headaches, fatigue, nausea, vomiting, dizziness, balance problems, confusion, memory problems, sleep disturbances, and double or blurry vision. Symptoms usually occur immediately, but could take days or even weeks to appear.
Identifying Severity/Predicting Prolonged Symptoms of Traumatic Brain Injuries
After a concussion occurs, brain cells release small fragments of genetic material known as microRNAs while they attempt to repair themselves. A portion of these microRNAs appear in the injured person’s blood and saliva.
In order to determine whether these microRNAs could be used to determine the severity of a traumatic brain injury and predict whether prolonged symptoms would occur, the prospective cohort study researchers gathered saliva samples from 52 concussion patients between the ages of seven and 21:
- The average age of the subjects was 14;
- Twenty-two of the participants were female;
- They were all athletes; and,
- The majority of the samples were collected one to two weeks after the initial injury.
The researchers examined distinct microRNAs in the samples and identified some that enabled them to predict how long a patient’s concussion symptoms might last. In addition, they found one microRNA in children and young adults that accurately predicted which subjects would experience memory and problem-solving difficulties as part of their symptomatology.
The researchers also evaluated the concussion patients using the Sport Concussion Assessment Tool (SCAT-3), Third Edition. Physicians use this questionnaire to assess the symptoms and severity of concussions. The researchers also asked the parents of the concussed patients for observations about their children’s symptoms.
During follow up visits, which occurred at four- and eight-week increments following the original assessment, the Penn State researchers collected additional saliva samples and re-evaluated the patients using SCAT-3.
New Biomarkers Based on MicroRNAs Instead of Protein
“There’s been a big push recently to find more objective markers that a concussion has occurred, instead of relying simply on patient surveys,” Steven Hicks, MD, PhD, Assistant Professor of Pediatrics, Penn State College of Medicine, Hershey, Pa., one of the study researchers, told Penn State News.
“Previous research has focused on proteins, but this approach is limited because proteins have a hard time crossing the blood-brain barrier. What’s novel about this study is we looked at microRNAs instead of proteins, and we decided to look in saliva rather than blood,” he noted.
According to Steven Hicks, MD, PhD (above), who worked on the Penn State College of Medicine study, microRNAs could be more accurate than the traditional questionnaire when diagnosing and forecasting the effects of concussions. “The microRNAs were able to predict whether symptoms would last beyond four weeks with about 85% accuracy,” he told Penn State News. “In comparison, using the SCAT-3 report of symptoms alone is about 64% accurate. If you just go off the parent’s report of symptoms, it goes down to the mid-50s. In this pilot study, these molecular signatures are outperforming survey tools.” (Photo copyright: MD Magazine.)
The goal of this research was to develop a way to definitively ascertain that a concussion had occurred, predict the length and type of symptoms, and then use that data to improve and personalize care for children and young adults who have had a concussion.
“With that knowledge physicians could make more informed decisions about how long to hold a child out of sports, whether starting more aggressive medication regimens might be warranted, or whether involving a concussion specialist might be appropriate,” Hicks told MD Magazine. “Anytime we can use accurate, objective measures to guide medical care, I think that represents an opportunity to improve concussion treatment.”
Further research and clinical trials will be needed to solidify the effectiveness and accuracy of these new biomarkers. However, a rapid, non-invasive saliva test that can determine the severity of a concussion, and predicted whether prolonged symptoms will likely occur, would be widely used and could be an important assay for clinical laboratories. Particularly those associated with hospital medical laboratories and emergency rooms.
—JP Schlingman
Related Information:
Association of Salivary MicroRNA Changes with Prolonged Concussion Symptoms
Saliva Test May Detect Biomarker for Prolonged Concussion
Molecules in Spit May be Able to Diagnose and Predict Length of Concussions
Prolonged Concussion Symptoms Identifiable by Salivary MicroRNA
Spit Test May Help Reveal Concussion Severity
Saliva Test May Lead to Improved Concussion Care for Youths
Jul 25, 2018 | Digital Pathology, Instruments & Equipment, Laboratory Instruments & Laboratory Equipment, Laboratory Management and Operations, Laboratory News, Laboratory Operations, Laboratory Pathology, Laboratory Testing, Management & Operations
While Apple recently debuted features to bring personal health records and protected health information to its mobile devices, Microsoft shuttered HealthVault in favor of focusing on AI-powered healthcare advances
As clinical laboratories and anatomic pathology groups know, lab testing data comprise more than 70% of the average patient’s health record. Thus, creating a universal platform on which consumers can share or review health information and medical histories with caregivers is a critical, yet elusive goal for most major tech companies, including tech giants Apple (Nasdaq:AAPL) and Microsoft (Nasdaq:MSFT).
Apple has big plans for patient health records and is working to bring protected health information (PHI) and healthcare advice to iPhones, iPads, and Apple Watch. Meanwhile, Microsoft is reducing its footprint in the mobile device healthcare market. Instead, it appears to be banking on its Artificial Intelligence (AI) platform. How these two diverging paths play out could have ramifications for the pathology and clinical laboratory industries.
HealthVault Insights versus AI versus Apple Health Mobile Apps
Launched in February 2017, Microsoft’s HealthVault Insights combined machine learning and AI with patients’ PHI and mobile activity tracking. The intent was to create an accessible, interactive platform for patients to monitor important health trends.
However, as of January 2018, Microsoft pulled the mobile app from Android, iOS, and Windows App stores. While summary information that draws on previously collected data is still available from the HealthVault website, new data and detailed insights are no longer available.
“We launched HealthVault Insights as a research project … with the goal of helping patients generate new insights about their health,” states Microsoft’s HealthVault Insights website. “Since then, we’ve learned a lot about how machine learning can be used to increase patient engagement and are now applying that knowledge to other projects.”
According to ZDNet, the closing of HealthVault Insights does not impact the Microsoft Health platform or the HealthVault patient-records system.
However, Microsoft’s shuttering of HealthVault Insights, and Google’s shuttering its Google Health platform in 2012, does seem to make Apple the last major tech company developing apps target at healthcare consumers designed to help them exchange private health information with caregivers through mobile devices. Dark Daily reported on Apple’s update earlier this year. (See, “Apple’s Update of Its Mobile Health App Consolidates Data from Multiple EHRs and Makes It Easier to Push Clinical Laboratory Data to Patients,” March 21, 2018.)
AI Will ‘Dramatically Transform Healthcare’
Shuttering HealthVault highlighted Microsoft’s shift away from consumer-facing health efforts and toward assisting medical laboratories, physicians, and research groups discover and implement treatments driving modern personalized medicine.
In a Microsoft blog post, Peter Lee, Corporate VP of Microsoft Healthcare, stated that Microsoft hopes its Healthcare NeXT platform will “dramatically transform healthcare, will deeply integrate Greenfield research and health technology product development, as well as establish a new model at Microsoft for strategic health industry partnerships.”
HealthVault Insights was one of several projects in Microsoft’s Healthcare NeXT initiative. Run by Microsoft’s AI and Research Group and partnering with major healthcare and research facilities across the country, other projects in the Healthcare NeXT initiative include:
Speaking with Business Insider, Lee noted that healthcare is becoming a “very large business” for Microsoft. “We don’t talk publicly about the dollars, but it’s large,” he concluded.
Microsoft’s EmpowerMD website states the eventual goal is to use the system to connect conversations with the growing trove of healthcare data available. “Our long-term vision is a learning system that incorporates data from longitudinal medical records, medical devices, genomics, population health, research papers, and more.”
AI a ‘Sleeping Giant for Healthcare’
“AI can be viewed as a sleeping giant for healthcare,” Eric Horvitz, PhD, Director of Microsoft Research Labs, told Nasdaq, when discussing Microsoft’s view of technology and healthcare. “AI methods show promise for multiple roles in healthcare. [This includes] inferring and alerting about hidden risks of potential adverse outcomes, selectively guiding attention, care, and interventional programs where [they are] most needed and reducing errors in hospitals.”
One such project involves a strategic partnership with the University of Pittsburg Medical Center (UPMC), which is a “$13-billion Pittsburgh-based system, comprising more than 25 hospitals, a three-million-member health plan, and 3,600 physicians, [that] will be a core partner in our efforts to improve healthcare delivery through a series of projects, beginning with a focus on transforming clinician empowerment and productivity,” according to Microsoft.
“Despite UPMC’s efforts to stay on the leading edge of technology, too often our clinicians and patients feel as though they’re serving the technology rather than the other way around. With Microsoft, we have a shared vision of empowering clinicians by reducing the burden of electronic paperwork and allowing the doctor to focus on the sacred doctor-patient relationship,” Steven D. Shapiro, MD (above), Chief Medical and Scientific Officer of UPMC and President of UPMC’s Health Services division, stated in the Microsoft blog. [Photo copyright: University of Pittsburg Medical Center.]
Medical laboratories and anatomic pathology groups may soon contribute health information to databases that one day will power AI systems. These trends highlight opportunities to both educate physicians on the tools available to utilize patient health data in an effective manner, and on new platforms that clinical laboratories could use to further streamline operations, reduce costs, and boost efficiency.
—Jon Stone
Related Information:
How Microsoft Is Using Advanced Technology in Healthcare
Microsoft Scrapping Personal Health Data App-Based Research Project
An Update on HealthVault Insights
How Microsoft’s Top Scientists Have Built a Big Business in Hacking Healthcare and Helped a Lot of People Along the Way
Microsoft Abandons Its Own HealthVault App: Is This Part of Something Larger?
Here’s How Microsoft Is Investing in AI
Microsoft Rolls Out More AI-Infused Healthcare Services, Software
Microsoft and Partners Combine the Cloud, AI, Research and Industry Expertise to Focus on Transforming Health Care
In Healthcare Push, Microsoft Launches Genomics Service on Azure Cloud
Apple’s Update of Its Mobile Health App Consolidates Data from Multiple EHRs and Makes It Easier to Push Clinical Laboratory Data to Patients
Jul 20, 2018 | Digital Pathology, Instruments & Equipment, Laboratory Instruments & Laboratory Equipment, Laboratory Management and Operations, Laboratory News, Laboratory Operations, Laboratory Pathology, Laboratory Testing
Should greater attention be given to protein damage in chronic diseases such as Alzheimer’s and diabetes? One life scientist says “yes” and suggests changing how test developers view the cause of age-related and degenerative diseases
DNA and the human genome get plenty of media attention and are considered by many to be unlocking the secrets to health and long life. However, as clinical laboratory professionals know, DNA is just one component of the very complex organism that is a human being.
In fact, DNA, RNA, and proteins are all valid biomarkers for medical laboratory tests and, according to one life scientist, all three should get equal attention as to their role in curing disease and keeping people healthy.
Along with proteins and RNA, DNA is actually an “equal partner in the circle of life,” wrote David Grainger, PhD, CEO of Methuselah Health, in a Forbes opinion piece about what he calls the “cult of DNA-centricity” and its relative limitations.
Effects of Protein Damage
“Aging and age-related degenerative diseases are caused by protein damage rather than by DNA damage,” explained Grainger, a Life Scientist who studies the role proteins play in aging and disease. “DNA, like data, cannot by itself do anything. The data on your computer is powerless without apps to interpret it, screens and speakers to communicate it, keyboards and touchscreens to interact with it.”
“Similarly,” he continued, “the DNA sequence information (although it resides in a physical object—the DNA molecule—just as computer data resides on a hard disk) is powerless and ethereal until it is translated into proteins that can perform functions,” he points out.
According to Grainger, diseases such as cystic fibrosis and Duchenne Muscular Dystrophy may be associated with genetic mutation. However, other diseases take a different course and are more likely to develop due to protein damage, which he contends may strengthen in time, causing changes in cells or tissues and, eventually, age-related diseases.
“Alzheimer’s disease, diabetes, or autoimmunity often take decades to develop (even though your genome sequence has been the same since the day you were conceived); the insidious accumulation of the damaged protein may be very slow indeed,” he penned.
“But so strong is the cult of DNA-centricity that most scientists seem unwilling to challenge the fundamental assumption that the cause of late-onset diseases must lie somewhere in the genome,” Grainger concludes.
Shifting Focus from Genetics to Proteins
Besides being CEO of Methuselah Health, Grainger also is Co-Founder and Chief Scientific Advisor at Medicxi, a life sciences investment firm that backed Methuselah Health with $5 million in venture capital funding for research into disease treatments that focus on proteins in aging, reported Fierce CEO.
Methuselah Health, founded in 2015 in Cambridge, UK, with offices in the US, is reportedly using post-translational modifications for analysis of many different proteins.
“At Methuselah Health, we have shifted focus from the genetics—which tells you in an ideal world how your body would function—to the now: this is how your body functions now and this is what is going wrong with it. And that answer lies in the proteins,” stated Dr. David Grainger (above), CEO of Methuselah Health, in an interview with the UK’s New NHS Alliance. Click on this link to watch the full interview. [Photo and caption copyright: New NHS Alliance.]
This is how Methuselah Health analyzes damaged proteins using mass spectrometry, according to David Mosedale, PhD, Methuselah Health’s Chief Technology Officer, in the New NHS Alliance story:
- Protein samples from healthy individuals and people with diseases are used;
- Proteins from the samples are sliced into protein blocks and fed slowly into a mass spectrometer, which accurately weighs them;
- Scientists observe damage to individual blocks of proteins;
- Taking those blocks, proteins are reconstructed to ascertain which proteins have been damaged;
- Information is leveraged for discovery of drugs to target diseases.
Mass spectrometry is a powerful approach to protein sample identification, according to News-Medical.Net. It enables analysis of protein specificity and background contaminants. Interactions among proteins—with RNA or DNA—also are possible with mass spectrometry.
Methuselah Health’s scientists are particularly interested in the damaged proteins that have been around a while, which they call hyper-stable danger variants (HSDVs) and consider to be the foundation for development of age-related diseases, Grainger told WuXi AppTec.
“By applying the Methuselah platform, we can see the HSDVs and so understand which pathways we need to target to prevent disease,” he explained.
For clinical laboratories, pathologists, and their patients, work by Methuselah Health could accelerate the development of personalized medicine treatments for debilitating chronic diseases. Furthermore, it may compel more people to think of DNA as one of several components interacting that make up human bodies and not as the only game in diagnostics.
—Donna Marie Pocius
Related Information:
The Cult of DNA-Centricity
Methuselah Health CEO David Grainger Out to Aid Longevity
VIDEO: Methuselah Health, Addressing Diseases Associated with Aging
Understanding and Slowing the Human Aging Clock Via Protein Stability
Using Mass Spectrometry for Protein Complex Analysis
Jul 13, 2018 | Digital Pathology, Instruments & Equipment, Laboratory Instruments & Laboratory Equipment, Laboratory Management and Operations, Laboratory News, Laboratory Operations, Laboratory Pathology, Management & Operations, News From Dark Daily
Popularity of the pocket-sized gene-sequencing device continues to prove that DNA testing away from clinical laboratories in remote clinics and outlying field laboratories is not just possible, but in some cases preferable
Once again, Oxford Nanopore Technologies (ONT) is demonstrating how next-generation gene sequencing technology can make it cheaper, simpler, and faster to sequence without the need for big clinical laboratories. And its successful raising of $180 million to expand development worldwide shows the support it has with capital funding investors.
Dark Daily has repeatedly reported on the development of the UK-based company’s point-of-care DNA sequencer going back to 2011. Called MinION, we predicted in 2015, that once brought to market, the pocket-sized gene sequencing machine “could help achieve the NIH’s goal of $1,000 human genome sequencing and, in remote clinics and outbreak zones, shift testing away from medical laboratories.” (See Dark Daily, “Point-of-Care DNA Sequencer Inching Closer to Widespread Use as Beta-Testers Praise Oxford Technologies’ Pocketsize, Portable Nanopore Device,” November 4, 2015.)
Since then, MinION’s use worldwide “for a number of biological analysis techniques including de novo sequencing, targeted sequencing, metagenomics, epigenetics, and more” has only expanded, according to multiple sources and ONT’s website.
How Does MinION Work as a Gene Sequencer?
The MinION nanopore sequencing device weighs about 100 grams (less than four ounces), is about the size of a standard deck of cards, operates off a laptop USB plug, and can sequence genetic material in a matter of minutes.
To perform the nanopore sequencing, a strand of deoxyribonucleic acid (DNA) or ribonucleic acid (RNA) is pushed through small pores in a membrane. An ionic current is then applied to the material and voltage is implemented to measure any disruptions in the current. The resulting measurement represents an electrical signal that is converted to human-readable sequence.
“It’s like the ultimate barcode,” Gordon Sanghera, PhD, Chief Executive Officer at Oxford Nanopore, told BBC News.
Oxford Nanopore Technologies’ diminutive MinION gene-sequencing device has the capacity to directly recognize epigenetic markers that control gene activity and cellular processes involved in the onset and development of disease. Early detection of cancers, testing for birth defects and infectious diseases, and blood screening are possible future clinical laboratory applications for the MinION. Click on this link to watch video on MinION. (Photo copyright: Oxford Nanopore Technologies.)
Why is MinION Important?
One advantage to this technology is that it has the ability to sequence much longer strands of DNA when compared to existing technologies. The MinION can sequence over a million letters or bases, around 2% of a DNA strand or chromosome with 96% or above accuracy. The device can read remarkably long stretches of consecutive DNA letters. Readouts of several thousand letters are common and the record for the MinION is 882,000 consecutive DNA letters, Technology Review noted.
“One of the most important findings of this research was that, even though the human genome reference was completed or thought to have been completed a while ago, it still contains many missing pieces and we were able to close some of those gaps in the sequence by developing a new method for developing these extremely long reads using nanopore sequencing,” Nick Loman, PhD, Professor of Microbial Genomics and Bioinformatics at the School of Biosciences at the University of Birmingham, UK, told Pharmaphorum. Loman worked on research with Oxford Nanopore on nanopore sequencing.
“We’ve gone from a situation where you can only do genome sequencing for a huge amount of money in well-equipped labs to one where we can have genome sequencing literally in your pocket just like a mobile phone,” Loman told BBC News. “That gives us a really exciting opportunity to start having genome sequencing as a routine tool, perhaps something people can do in their own home.”
Using MinION in the Field
According to the Oxford Nanopore website, the MinION:
- Is pocket-sized and portable;
- Has up to 512 nanopore channels;
- Has a simple 10-minute sample preparation time;
- Allows real-time analysis for rapid and efficient results; and,
- Is adaptable to direct DNA or RNA sequencing.
The MinION Starter Pack is available for purchase on the company’s website with prices starting at $1,000. The kit includes:
- The MinION device;
- Flow cells;
- Sequencing kits;
- Wash kits; and,
- MinION community support.
Researchers at The Kinghorn Center for Clinical Genomics at the Garvan Institute of Medical Research in Darlinghurst, Australia, are currently using the MinION for research purposes.
Members of the Zebra Project (above), an international group of scientists, used Oxford Nanopore Technologies’ MinION to sequence genomes during epidemics in Latin America. With just a laptop computer for power, MinION can run complex gene-sequencing and achieve superior results than other similar technologies. It is in use worldwide bringing clinical laboratory testing to patients in remote, outlying locations. (Photo copyright: Ricardo Funari.)
“I think it’s really expanding the arsenal of tools we have to peer into cell biology and the root causes of cancer and various diseases,” Dr. Martin Smith, Head of Genomic Technologies at the center, told Australian Financial Review. “It’s really just starting to open the lid off the jar and peer more deeply into the genomics of the cell.”
Dr. Sanghera hopes the gadget could be utilized in the future to identify common infections at home and help consumers avoid unnecessary trips to doctors, clinics, and hospitals, and avert the misuse and overuse of prescription medications. He also feels MinION has applications outside the healthcare industry, such as detecting the presence of harmful microbes in food and water supplies.
As gadgets like MinION become more popular, the potential to move DNA sequencing closer to the patient (and out of the core lab) has implications for clinical laboratories and anatomic pathology groups. However, core labs would still be a preferred source to collect the raw data, store that data, then do the annotation of the DNA sequences and report the findings to the referring physician.
—JP Schlingman
Related Information:
How Knowing Your Genetic Code Could Lengthen Your Life
Genome in the Palm of Your Hand
Molecular Machines and the Place of Physics in the Biology Curriculum
Oxford Nanopore’s Hand-Held DNA Analyzer Has Traveled the World
Hostplus Sinks $27m Into Hand-held DNA Sequencing Firm Oxford Nanopore
GIC, Others Invest £100m In Hand-held DNA Sequencing firm Oxford Nanopore
Handheld Device Sequences Human Genome
Breakthrough Leads to Sequencing of a Human Genome Using a Pocket-sized Device
Oxford Nanopore’s Tech Reaches Genome Sequencing Landmark
Point-of-Care DNA Sequencer Inching Closer to Widespread Use as Beta-Testers Praise Oxford Technologies’ Pocketsize, Portable Nanopore Device
$900 Point-of-Care DNA Nanopore Sequencer May Hit Market in Next 12 Months
Is Whole-genome Sequencing Reaching a Tipping Point for Clinical Pathology Laboratories?
Jun 27, 2018 | Digital Pathology, Instruments & Equipment, Laboratory Instruments & Laboratory Equipment, Laboratory Management and Operations, Laboratory News, Laboratory Operations, Laboratory Pathology, Laboratory Testing, Management & Operations
Using GPIIb/IIIa inhibition, and ion chelation, researchers have developed a “universal” method for preserving blood up to 72 hours while keeping it viable for advanced rare-cell applications
Through microfluidics and automation, clinical laboratories and anatomic pathologists have been able to detect ever-smaller quantities of biomarkers and other indicators of chronic disease.
However, preserving sample quality is an essential part of analytical accuracy. This is particularly true in precision oncology and other specialties where isolating rare cells (aka, low abundance cells), such as circulating tumor cells (CTCs), is a key component to obtaining information and running diagnostics.
Publishing their finding in Nature, researchers at Massachusetts General Hospital Center for Engineering in Medicine (MGH-CEM) have developed a whole blood stabilization method that is ideal for rare-cell applications, and which preserves sample integrity for up to 72 hours.
Should further testing validate their findings and methodology, this change could allow greater use of central laboratories and other remote testing facilities that previously would not be available due to distance and sample travel time.
Keeping Blood Alive Is Not Easy
“At Mass. General, we have the luxury of being so integrated with the clinical team that we can process blood specimens in the lab typically within an hour or two after they are drawn,” stated lead author Keith Wong, PhD, former Research Fellow, MGH-CEM, and now Senior Scientist at Rubius Therapeutics, Boston, in a Mass General press release. “But to make these liquid biopsy technologies routine lab tests for the rest of the world, we need ways to keep blood alive for much longer than several hours, since these assays are best performed in central laboratories for reasons of cost-effectiveness and reproducibility.”
Study authors Wong and co-lead author Shannon Tessier, PhD, Investigator at MGH-CEM, noted that current FDA-approved blood stabilization methods for CTC assays use chemical fixation—a process that can result in degradation of sensitive biomolecules and kill the cells within the sample.
Without stabilization, however, breakdown of red cells, activation of leukocytes (white blood cells), and clot formation can render the results of analyzing a sample useless, or create issues with increasingly sensitive equipment used to run assays and diagnostics.
“We wanted to slow down the biological clock as much as possible by using hypothermia, but that is not as simple as it sounds,” says Tessier. “Low temperature is a powerful means to decrease metabolism, but a host of unwanted side effects occur at the same time.”
Researchers started by using hypothermic treatments to slow degradation and cell death. However, this created another obstacle—aggressive platelet coagulation. By introducing glycoprotein IIb/IIIa inhibitors, they found they could minimize this aggregation.
Keith Wong, PhD (left), a former Research Fellow, MGH-CEM, and now Senior Scientist at Rubius Therapeutics in Boston; and Shannon Tessier, PhD (right), Investigator at MGH-CEM, co-authored a study to develop a whole blood stabilization method that preserves sample integrity for up to 72 hours, making it possible to transport blood specimens further distances to central clinical laboratories for processing. (Photo copyrights: LinkedIn.)
Prior to microfluidic processing of their test samples, researchers applied a brief calcium chelation treatment. The result was efficient sorting of rare CTCs from blood drawn up to 72 hours prior, while keeping RNA intact and retaining cell viability.
“The critical achievement here,” says Tessier, “Is that the isolated tumor cells contain high-quality RNA that is suitable for demanding molecular assays, such as single-cell qPCR, droplet digital PCR, and RNA sequencing.”
Their testing involved 10 patients with metastatic prostate cancer. Sample integrity was verified by comparing CTC analysis results between fresh samples and preserved samples from the same patients using MGH-CEM’s own microfluidic CTC-iChip device.
Results showed a 92% agreement across 12 cancer-specific gene transcripts. For AR-V7, their preservation method achieved 100% agreement. “This is very exciting for clinicians,” declared David Miyamoto, MD, PhD, of Massachusetts General Hospital Cancer Center in the press release. “AR-V7 mRNA can only be detected using CTCs and not with circulating tumor DNA or other cell-free assays.”
Methodology Concerns and Future Confirmations
“Moving forward, an extremely exciting area in precision oncology is the establishment of patient-specific CTC cultures and xenograft models for drug susceptibility,” the study authors noted. “The lack of robust methods to preserve viable CTCs is a major roadblock towards this Holy Grail in liquid biopsy. In our preliminary experiments, we found that spiked tumor cells in blood remain highly viable (>80%) after 72 hours of hypothermic preservation.”
Despite this, they also acknowledge limitations on their current findings. The first is the need for larger-scale validation, as their testing involved a 10-patient sample group.
Second, they note that further studies will be needed to “more completely characterize whole-transcriptome alterations as a result of preservation, and to what extent they can be stabilized through other means, such as further cooling (e.g., non-freezing sub-zero temperatures) or metabolic depression.”
Researchers also note that their approach has multiple advantages for regulatory approval and further testing—GPIIb/IIIa inhibitors are both low-cost and already approved for clinical use, implementation requires no modification of existing isolation assays, and cold chain protocols are already in place allowing for easy adaptation to fit the needs of pathology groups, medical laboratories, and other diagnostics providers handling samples.
While still in its early stages, the methods introduced by the researchers at MGH-CEM show potential to allow both the facilities collecting samples and the clinical laboratories processing them greater flexibility and increased accuracy, as high-sensitivity assays and diagnostics continue to power the push toward personalized medicine and expand laboratory menus across the industry.
—Jon Stone
Related Information:
Whole Blood Stabilization for the Microfluidic Isolation and Molecular Characterization of Circulating Tumor Cells
Improved Blood Stabilization Should Expand Use of Circulating Tumor Cell Profiling
Genentech Scientists Zero In on “Liquid Biopsies” as a Way to Replace Tissue Biopsies in Breast Cancer
University of Michigan Researchers Use “Labyrinth” Chip Design in Clinical Trial to Capture Circulating Tumor Cells of Different Cancer Types
Super-Fast Microscope Captures Circulating Tumor Cells with High Sensitivity and Resolution in Real Time
