Ultima Genomics says it is emerging from “stealth mode” with millions in fresh capital and technology capable of sequencing whole human genomes for a fraction of the cost
Investors seem to be optimistic that an emerging genetics company has the proprietary solution to sequence a whole human genome for just $100. If true, this is a development that would be of interest to clinical laboratory managers and pathologists.
The company, Ultima Genomics of Newark, Calif., recently announced that it had raised $600 million from the investment community. In a press release last month, the company announced it has “emerged from stealth mode with a new high-throughput, low-cost sequencing platform that delivers the $100 genome.”
The press release goes on to state that Ultima will unleash a new era in genomics-driven discoveries by developing a “fundamentally new sequencing architecture designed to scale beyond conventional approaches, including completely different approaches to flow cell engineering, sequencing chemistry, and machine learning.”
Are we at the cusp of a revolution in genomics? Ultima Genomics’ founder and CEO, Gilad Almogy, PhD, believes so.
“Our architecture is intended for radical scaling, and the $100 genome is merely the first example of what it can deliver,” he said in the press release. “We are committed to continuously drive down the cost of genomic information until it is routinely used in every part of the healthcare system.”
From an Estimated Cost of $3 Billion to $450 in Just 30 Years!
Whole genome sequencing (WGS) has decreased dramatically in cost since research into the technology required got started in the early 1990s with the publicly-funded Human Genome Project. At that time, the cost to sequence the entire human genome was estimated at around $3 billion. Then, in 1998, John Craig Venter created Celera Genomics (now a subsidiary of Quest Diagnostics) and was the first to sequence the whole human genome (his own) and at a significantly lower cost of around $300 million.
When DNA sequencer Illumina announced in 2014 the arrival of the $1,000 genome, the news was expected to put whole genome sequencing on the road to becoming routine, Forbes reported. But that prediction didn’t pan out.
Ultima Genomics’ $100 price point, however, could be game changing. It would make the cost of decoding a human genome affordable for nearly everyone and accelerate the growth of personalized medicine in clinical laboratory diagnostics.
Applied Physics versus Biological Sciences
According to GEN, Almogy brings a tech background to Ultima—his PhD is in applied physics, not the biological sciences. He founded Ultima in 2016 after serving as founder, president, and CEO at Fulfil Solutions, a manufacturer of custom automation robotics systems. At Ultima, his goal is to “unleash the same relentless scaling in sequencing” that was used to drive down the cost of computing power and transform modern life.
TechCrunch reported that Ultima’s UG100 sequencing machine and software platform can perform a complete sequencing of a human genome in about 20 hours, with precision comparable to existing options, but does so at a far lower cost per gigabase (Gb), equal to one billion base pairs.
According to the Ultima Genomics website, its breakthroughs include:
An open substrate that creates a massive, low-cost reaction surface that delivers many billions of reads while avoiding costly flow cells and complicated fluidics.
Novel scalable chemistry that combines the speed, efficiency, and read lengths of natural nucleotides with the accuracy and scalability of endpoint detection.
A revolutionary sequencing hardware that uses spinning circular wafers that enable efficient reagent use, zero crosstalk, and ultra-high-speed scanning of large surfaces.
Affordable Genomics Will Lead to ‘Millions of Tests per Year’
Exact Sciences’ Chairman and CEO Kevin Conroy—whose Wisconsin-based molecular diagnostics company recently entered into a long-term supply agreement for Ultima Genomic’s NGS technologies—believes low-cost genomic sequencing will improve cancer screening and disease monitoring.
“Exact Sciences believes access to differentiated and affordable genomics technologies is critical to providing patients better information before diagnosis and across all stages of cancer treatment,” Conroy said in a press release. “Ultima’s mission to drive down the cost of sequencing and increase the use of genomic information supports our goal to provide accurate and affordable testing options across the cancer continuum. This is particularly important for applications like cancer screening, minimal residual disease, and recurrence monitoring, which could lead to millions of tests per year.”
GEN pointed out that Ultima’s 20-hour turnaround time is fast and its quality on par with its competitors, but that it is Ultima’s $1/Gb price (noted in the preprint) that will set it apart. That cost would be a fraction of Illumina’s NextSeq ($20/Gb) and Element Biosciences’ AVITI ($5/Gb).
Almogy told TechCrunch that Ultima is working with early access partners to publish more proof-of-concept studies showing the capabilities of the sequencing technique, with broader commercial deployment of the technology in 2023. Final pricing is yet to be determined, he said.
If the $100 genome accelerates the pace of medical discoveries and personalized medicine, clinical laboratory scientists and pathologists will be in ideal positions to capitalize on what the executives and investors at Ultima Genomics hope may become a revolution in whole human genome sequencing and genomics.
Medical laboratories are already using gene sequencing as part of a global effort to identify new variants of the coronavirus and their genetic ancestors
Thanks to advances in genetic sequencing technology that enable medical laboratories to sequence organisms faster, more accurately, and at lower cost than ever before, clinical pathology laboratories worldwide are using that capability to analyze the SARS-CoV-2 coronavirus and identify variants as they emerge in different parts of the world.
The US Centers for Disease Control and Prevention (CDC) now plans to harness the power of gene sequencing through a new consortium called SPHERES (SARS-CoV-2 Sequencing for Public Health Emergency Response, Epidemiology, and Surveillance) to “coordinate SARS-CoV-2 sequencing across the United States,” states a CDC news release. The consortium is led by the CDC’s Advanced Molecular Detection (AMD) program and “aims to generate information about the virus that will strengthen COVID-19 mitigation strategies.”
The consortium is comprised of 11 federal agencies, 20 academic institutions, state public health laboratories in 21 states, nine non-profit research organizations, and 14 lab and IVD companies, including:
Oxford Nanopore Technologies
Verily Life Sciences
‘Fundamentally Changing How Public Health Responds’
Gene sequencing and related technologies have “fundamentally changed how public health responds in terms of surveillance and outbreak response,” said Duncan MacCannell, PhD, Chief Science Officer for the CDC’s Office of Advanced Molecular Detection (OAMD), in an April 30 New York Times (NYT) article, which stated that the CDC SPHERES program “will help trace patterns of transmission, investigate outbreaks, and map how the virus is evolving, which can affect a cure.”
The CDC says that rapid DNA sequencing of SARS-CoV-2 will help monitor significant changes in the virus, support contact tracing efforts, provide information for developers of diagnostics and therapies, and “advance public health research in the areas of transmission dynamics, host response, and evolution of the virus.”
The sequencing laboratories in the consortium have agreed to “release their information into the public domain quickly and in a standard way,” the NYT reported, adding that the project includes standards for what types of information medical laboratories should submit, including, “where and when a sample was taken,” and other critical details.
Sharing Data Between Sequencing Laboratories and Biotech Companies
The CDC announced the SPHERES initiative on April 30, although it launched in early April, the NYT reported.
According to the CDC, SPHERES’ objectives include:
To bring together a network of sequencing laboratories, bioinformatics capacity and subject matter expertise under the umbrella of a massive and coordinated public health sequencing effort.
To identify and prioritize capabilities and resource needs across the network and to align sources of federal, non-governmental, and private sector funding and support with areas of greatest impact and need.
To improve coordination of genomic sequencing between institutions and jurisdictions and to enable more resilience across the network.
To champion concepts of openness, standards-based analysis, and rapid data sharing throughout the United States and worldwide during the COVID-19 pandemic response.
To provide a common forum for US public, private, and academic institutions to share protocols, methods, bioinformatics tools, standards, and best practices.
To establish consistent data and metadata standards, including streamlined repository submission processes, sample prioritization criteria, and a framework for shared, privacy-compliant unique case identifiers.
To align with other national sequencing and bioinformatics networks, and to support global efforts to advance the use of standards and open data in public health.
Implications for Developing a Vaccine
As the virus continues to mutate and evolve, one question is whether a vaccine developed for one variant will work on others. However, several experts told The Washington Post that the SARS-CoV-2 coronavirus is relatively stable compared to viruses that cause seasonal flu (influenza).
Nor, he said, is one variant likely to cause worse clinical outcomes than others. “So far, we don’t have any evidence linking a specific virus [strain] to any disease severity score. Right now, disease severity is much more likely to be driven by other factors.”
Fast improvements in gene sequencing technology have made it faster, more accurate, and cheaper to sequence. Thus, as the COVID-19 outbreak happened, there were many clinical laboratories around the world with the equipment, the staff, and the expertise to sequence the novel coronavirus and watch it mutate from generation to generation and from region to region around the globe. This capability has never been available in outbreaks prior to the current SARS-CoV-2 outbreak.
Genetic testing, gene sequencing done by clinical laboratories and anatomic pathology groups underpin how first-mover hospitals, health networks are improving patient outcomes
In just a few weeks, an unprecedented gathering will bring together the nation’s most prominent first-mover health networks, hospitals, and companies operating programs that deliver precision medicine daily to patients in clinical care settings.
On Sept. 12-13, 2018, “Breakthroughs with Genetic and Precision Medicine: What All Health Network CEOs Need to Know,” will take place at the Hutton Hotel in Nashville, Tenn. “What differentiates these sessions is the emphasis on each organization’s strategy, how it launched its precision medicine programs, what is improving in patient outcomes, and how payers are reimbursing for these services,” stated Robert L. Michel, Executive Director of the Precision Medicine Institute in Austin, Texas. “This is not about the science of precision medicine. Rather, it is about the practical elements required for any hospital, health system, or physician group to actually set up and deliver a precision medicine service to patients on a daily basis.”
Precision Medicine’s First-Mover Hospitals and Providers to Speak
Health systems and hospitals headlining this special conference are:
Exhibitors include the above, plus: Thermo Fisher, Philips, Sunquest, and MyGenetx.
“This meeting will give you the insider’s understanding about delivering precision medicine in real patient care settings that cannot be accessed at other venues,” noted Michel. “The goal is to have first-mover providers share their experiences, thus providing a road map that other hospitals, physician practices, and other providers at this conference can take back and follow with confidence.”
Michel said that sessions will be dedicated to precision medicine strategies, how it is being used in oncology, primary care, the role of pharmacogenomics, and use of healthcare big data. Speakers will describe the clever ways innovative health networks and hospitals are using healthcare big data to inform physicians in ways that improve outcomes, lower the cost of care and, in two real-world case studies, are generating seven-figure reimbursement from shared savings programs with certain health plans.
This year’s keynote address is by Jeffrey R. Balser, MD, PhD (above), President and CEO, Vanderbilt University Medical Center and Dean of the Vanderbilt University School of Medicine, one of the most progressive and innovative health systems in the country. (Photo copyright: Vanderbilt University.)
Using Healthcare Big Data to Achieve Precision Medicine Success, Shared Savings
“Shared savings successes will be one of the breakthrough achievements reported at the Nashville event,” he explained. “We’ve invited two prominent provider organizations to share how they are using healthcare big data to support physicians in achieving improved patient outcomes while at the same time impressively reducing the overall cost of care. To my knowledge, this is the first time these precision medicine case studies have been presented at a national meeting.”
One such presentation will be delivered by Philip Chen, MD, PhD, Chief Healthcare Informatics Officer at Sonic Healthcare USA Austin, Texas. Their precision medicine goal was to use healthcare big data to help physicians better manage diabetes and other chronic conditions in their practices. This program involved a large primary care practice and a major health insurer. Now in its fourth year, Sonic Healthcare USA is earning six- and seven-figure payments as part of a shared savings arrangement with the insurer.
“Shared savings is definitely a Holy Grail for all large health networks and physician groups as payers drop fee-for-service and switch providers to value-based payments,” said Michel. “The experience of Sonic Healthcare in this innovative three-way collaboration with an insurer and a very large physician group demonstrates that a strong data analytics capability and engagement with physicians can simultaneously bend the cost-of-care-curve downward while improving patient outcomes, as measured year-by-year. This is a presentation every C-Suite executive should attend.
Strategic, Business, Operational, and Financial Aspects of Precision Medicine
“This conference—centered upon the strategic, business, operational, and financial aspects of a precision medicine program—came to be because it is the unmet need of every health network CEO and C-Suite administrator,” observed Michel. “Every healthcare leader tasked with developing an effective clinical and financial strategy for his or her institution knows that the real challenge in launching a precision medicine program for patient care is not the science.
“Rather, the true challenges come from how to support clinical needs with the availability of capital, recruiting experienced clinicians, and putting the right informatics capabilities in place,” he stated. “Most hospital and health network administrators recognize the risk of launching a precision medicine program too early. They know such programs can suck up huge amounts of resources without producing significant improvements in patient care. What adds to the risk is that payers may be slow to reimburse for precision medicine.”
Register by September 1 and save $300 on tuition! Plus, take advantage of our special Team Discount Program, so you and your key team members can get the most out of the conference by attending together.
“Breakthroughs with Genetic and Precision Medicine: What All Health Network CEOs Need to Know” is the gold-standard summit for everyone active or interested in succeeding with precision medicine programs. Don’t miss out—register today!
Researchers demonstrated it was feasible to encode digital malware onto a strand of synthesized DNA and infect the gene sequencers and computer networks used by medical laboratories
As if anatomic pathology groups and clinical laboratory leaders don’t already have enough to think about, here comes a security vulnerability right out of a sci-fi thriller. Researchers at the University of Washington (UW) have used synthesized DNA to encode digital malware into a physical strand of DNA capable of establishing a remote connection to the computer network on which the sequenced DNA is read!
Stated differently, researchers have now demonstrated that is possible for bad guys to hack into a medical laboratory’s instrument systems and computer network using a physical strand of synthesized DNA that is encoded with digital malware.
Another Threat to Clinical Laboratories, Pathology Groups?
Does this translate into an immediate security issue for medical laboratories? For now, the threat is only theoretical. While researchers did succeed, their study findings should provide some comfort to pathology groups or medical laboratories worried about the implications of DNA-based malware. The UW researchers published their findings at the 2017 USENIX Security Symposium.
Synthetic DNA Malware Exploit is More Proof-of-Concept than Immediate Threat
At its core, computer code (AKA source code) is similar to DNA in that it is composed of a set number of states—with binary, zeroes, and ones. This led UW researchers to question whether they could translate the AGCT elements (adenine, guanine, cytosine, and thymine) of DNA into binary code capable of hacking DNA sequencers and accessing the information they contain.
In an article in The Atlantic, Tadayoshi Kohno, PhD, Short-Dooley Professor in the Department of Computer Science and Engineering at UW, who led the research team, noted that, “The present-day threat is very small, and people don’t need to lose sleep immediately. But we wanted to know what was possible and what the issues are down the line.”
Complexity of Engineering a DNA-Powered Computer Virus
To begin the process, researchers needed to create a specific DNA strand encoded with the exact proteins that would later convert into their exploit. An article in ArsTechnica suggests this would be a challenge due to the physical properties of DNA’s double-helix design.
In the article, John Timmer, PhD, wrote, “DNA with Gs and Cs forms a stronger double-helix. Too many of them, and the strand won’t open up easily for sequencing. Too few, and it’ll pop open when you don’t want it to.”
The study shows it took multiple attempts to find a DNA sequence that would both carry the malware code and withstand the synthesizing and sequencing processes. Even then, researchers needed an exploit for the software used on sequencers in clinical laboratories and other diagnostics providers to prove their theory. Study authors used their own modified version of an open-source sequencing software, adding an exploit they could target, instead of a version of the software already publicly in use.
Lee Organick (above left), Karl Koscher (center), and Peter Ney (right) worked with Luis Ceze and Tadayoshi Kohno, PhD, at the University of Washington to develop the DNA sequence containing the malware code. The researchers determined that it was feasible for the gene instruments used by clinical laboratories to be infected with the malware, which could then move to infect a clinical lab’s computer network. (Photo copyright: University of Washington.)
With their proteins synthesized and customized software in place, researchers still faced challenges getting the code to trigger. “With reads randomly appearing in an FASTQ file,” the researchers noted, “we would expect the modified program to be exploited 37.4% of the time.”
As with genetic code, the binary code of a program is highly sensitive to errors. Any misread bases or splitting of the code resulted in failure. When sequencers only read a few hundred bases at a time, ensuring the code doesn’t hit one of these splits is a challenge.
One unique difference between binary and genetic code also caused trouble—genetic sequences aren’t direction dependent, while binary sequences are. If the code is read in reverse, it won’t execute properly.
Future Concerns for Clinical Laboratories and Genetic Researchers
Today, the threat to medical laboratories and the sensitive data generated by sequencing is minor. However, tomorrow that threat could be more common.
In a WIRED article on the subject, Jason Callahan, Chief Information Security Officer for Illumina stated, “This is interesting research about potential long-term risks. We agree with the premise of the study—that this does not pose an imminent threat and is not a typical cyber security capability.”
Don Rule, founder of Translational Software, agrees. When asked about the threat posed to clinical laboratories, he said, “… if you have to pre-introduce the hack in the analytics program, this is a pretty circuitous way to take over a computer. I can see how it is feasible and right now Norton Antivirus is not looking for viruses encoded in the AGCT code set, but we are right not to lose a lot of sleep over it.”
However, as genetic sequencing becomes a common part of medicine, attackers might have increased reason to disrupt services or intercept data. The UW researchers cite “important domains like forensics, medicine, and agriculture” as potential targets.
While their successful attack was highly engineered, their research into open-source sequencing software revealed a range of common security weaknesses. Many clinical laboratories and anatomic pathology groups also run proprietary analysis software or use hardware with embedded software.
They recommend that medical laboratories work to centralize software updates and create ways to verify data and patches through digital signatures or other secure measures.
Already, genetic researchers take care to avoid synthesizing potentially dangerous sequences, and to contain tests and data. But this study shows that not all threats come from within the research or clinical laboratory environment. Both engineers of sequencing technology and hardware—and the medical laboratories using them—will need to optimize operations and monitor trends closely to see how security issues evolve alongside sequencing capabilities.
Few anatomical tools hold more potential to revolutionize the science of diagnostics than biomarkers, and pathologists and medical laboratories will be first in line to put these powerful tools to use helping patients with chronic diseases
Clinical laboratories rely on biomarkers for pathology tests and procedures that track and identify infections and disease during the diagnostic process. Thus, trends that highlight the critical role biomarkers play in medical research are particularly relevant to pathology groups and medical laboratories.
Here’s an overview of critical trends in biomarker research and development that promise to improve diagnosis and treatment of chronic disease.
Emerging Use of Predictive Biomarkers in Precision Medicine
PM involves an approach to healthcare that is fine-tuned to each patient’s unique condition and physiology. As opposed to the conventional one-size-fits-all approach, which looks at the best options for the average person without examining variations in individual patients.
Predictive biomarkers identify individuals who will most likely respond either favorably or unfavorably to a drug or course of treatment. This improves a patient’s chance to receive benefit or avoid harm and goes to the root of Precision Medicine. (Image copyright: Pennside Partners.)
The National Institutes of Health (NIH) defines PM as “an emerging approach for disease treatment and prevention that considers individual variability in genes, environment, and lifestyle for each person.” It gives physicians and researchers the ability to more accurately forecast which prevention tactics and treatments will be optimal for certain patients.
Combining Drugs for Specific Outcomes
Cancer treatment will be complimented by the utilization of combination drugs that include two or more active pharmaceutical ingredients. Many drug trials are currently being performed to determine which combination of drugs will be the most favorable for specific cancers.
Combination drugs should become crucial in the treatment of different cancers treatments, such as immunotherapy, which involves treating disease by inducing, enhancing, or suppressing an immune response.
Biomarkers associated with certain cancers may enable physicians and researchers to determine which combination drugs will work best for each individual patient.
Developing More Effective Diagnostics
In Vitro diagnostics (IVDs) are poised for massive growth in market share. A report by Allied Market Research, states the worldwide IVD market will reach $81.3 billion by 2022. It noted that IVD techniques in which bodily fluids, such as blood, urine, stool, and sputum are tested to detect disease, conditions, and infections include important technologies such as:
Allied Market Research expects growth of the IVD market to result from these factors:
Increases in chronic and infectious diseases;
An aging population;
Growing knowledge of rare diseases; and
Increasing use of personalized medicines.
The capability to sequence the human genome is further adding to improvements in diagnostic development. Pharmaceutical companies can generate diagnostic counterparts alongside related drugs.
Biopsies from Fluid Sources
Millions of dollars have been spent on developing liquid biopsies that detect cancer from simple blood draws. The National Cancer Institute Dictionary of Cancer Terms defines a liquid biopsy as “a test done on a sample of blood to look for cancer cells from a tumor that are circulating in the blood or for pieces of DNA from tumor cells that are in the blood.”
At present, liquid biopsies are typically used only in the treatment and monitoring of cancers already diagnosed. Companies such as Grail, a spinoff of Illumina, and Guardant Health are striving to develop ways to make liquid biopsies a crucial part of cancer detection in the early stages, increasing long-term survival rates.
“The holy grail in oncology has been the search for biomarkers that could reliably signal the presence of cancer at an early stage,” said Dr. Richard Klausner, Senior Vice President and Chief Medical Officer at Grail.
Grail hopes to market a pan-cancer screening test that will measure circulating nucleic acids in the blood to detect the presence of cancer in patients who are experiencing no symptoms of the disease.
Clinical Trials and Precision Medicine
The Precision Medicine Initiative (PMI), launched by the federal government in 2015, investigates ways to create tailor-made treatments and prevention strategies for patients based on their distinctive attributes.
Two ongoing studies involved in PMI research are MATCH and TAPUR:
MATCH (Molecular Analysis for Therapy Choice) is a clinical trial run by The National Cancer Institute. The researchers are studying tumors to learn if they possess gene abnormalities that are treatable by known drugs.
TAPUR (Targeted Agent and Profiling Utilization Registry), is a non-randomized clinical trial being conducted by the American Society of Clinical Oncology (ASCO). The researchers are chronicling the safety and efficacy of available cancer drugs currently on the market.
New Tools for Pathologists and Clinical Laboratories
The attention and funds given to these types of projects expand the possibilities of being able to develop targeted therapies and treatments for patients. Such technological advancements could someday enable physicians to view and treat cancer as a product of specific gene mutations and not just a disease.
These trends will be crucial and favorable for clinical laboratories in the future. As tests and treatments become unique to individual patients, pathologists and clinical laboratories will be on the frontlines of providing advanced services to healthcare professionals.