With improved genetic sequencing comes larger human genome databases that could lead to new diagnostic and therapeutic biomarkers for clinical laboratories
As the COVID-19 pandemic grabbed headlines, the human genome database at the US Department of Veterans Affairs Million Veterans Program (MVP) quietly grew. Now, this wealth of genomic information—as well as data from other large-scale genomic and genetic collections—is expected to produce new biomarkers for clinical laboratory diagnostics and testing.
In December, cancer genomics company Personalis, Inc. (NASDAQ:PSNL) of Menlo Park, Calif., achieved a milestone and delivered its 100,000th whole human genome sequence to the MVP, according to a news release, which also states that Personalis is the sole sequencing provider to the MVP.
The VA’s MVP program, which started in 2011, has 850,000 enrolled veterans and is expected to eventually involve two million people. The VA’s aim is to explore the role genes, lifestyle, and military experience play in health and human illness, notes the VA’s MVP website.
Health conditions affecting veterans the MVP is researching include:
The VA has contracted with Personalis through September 2021, and has invested $175 million, Clinical OMICS reported. Personalis has earned approximately $14 million from the VA. That’s about 76% of the company’s revenue, according to 2nd quarter data, Clinical OMICS noted.
“The VA MVP is the largest whole genome sequencing project in the United States, and this is a significant milestone for both the program and for Personalis,” said John West (above with wife Judy), Founder and CEO of Personalis, in the news release. “Population-scale sequencing projects of this nature represent a cornerstone in our effort to accelerate the advancement of precision medicine across a wide range of disease areas,” he added. (Photo copyright: MIT Technology Review.)
Database of Veterans’ Genomes Used in Current Research
What has the VA gained from their investment so far? An MVP fact sheet states researchers are tapping MVP data for these and other veteran health-related studies:
Differentiating between prostate cancer tumors that require treatment and others that are slow-growing and not life-threatening.
How genetics drives obesity, diabetes, and heart disease.
How data in DNA translates into actual physiological changes within the body.
Gene variations and patients’ response to Warfarin.
NIH Research Program Studies Effects of Genetics on Health
Another research program, the National Institutes of Health’s All of Us study, recently began returning results to its participants who provided blood, urine, and/or saliva samples. The NIH aims to aid research into health outcomes influenced by genetics, environment, and lifestyle, explained a news release. The program, launched in 2018, has biological samples from more than 270,000 people with a goal of one million participants.
“We’re changing the paradigm for research. Participants are our most important partners in this effort, and we know many of them are eager to get their genetic results and learn about the science they’re making possible,” said Josh Denny, MD, CEO of the NIH’s All of Us research program in the news release. Denny, a physician scientist, was Professor of Biomedical Informatics and Medicine, Director of the Center for Precision Medicine and Vice President for Personalized Medicine at Vanderbilt University Medical Center prior to joining the NIH. (Photo copyright: National Institutes of Health.)
Inclusive Data Could Aid Precision Medicine
The news release notes that more than 80% of biological samples in the All of Us database come from people in communities that have been under-represented in biomedical research.
“We need programs like All of Us to build diverse datasets so that research findings ultimately benefit everyone,” said Brad Ozenberger, PhD, All of Us Genomics Program Director, in the news release.
Precision medicine designed for specific healthcare populations is a goal of the All of Us program.
“[All of Us is] beneficial to all Americans, but actually beneficial to the African American race because a lot of research and a lot of medicines that we are taking advantage of today, [African Americans] were not part of the research,” Chris Crawford, All of US Research Study Navigator, told the Birmingham Times. “As [the All of Us study] goes forward and we get a big diverse group of people, it will help as far as making medicine and treatment that will be more precise for us,” he added.
Large Databases Could Advance Care
Genome sequencing technology continues to improve. It is faster, less complicated, and cheaper to sequence a whole human genome than ever before. And the resulting sequence is more accurate.
Thus, as human genome sequencing databases grow, researchers are deriving useful scientific insights from the data. This is relevant for clinical laboratories because the new insights from studying bigger databases of genomic information will produce new diagnostic and therapeutic biomarkers that can be the basis for new clinical laboratory tests as well as useful diagnostic assays for anatomic pathologists.
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Embrace full bi-directional synchronization with third-party services such as:
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Software Reviews
“Outstanding Anatomic Pathology solution with great flexibility”
The system is highly customizable; there is “almost” nothing you can’t do. We are able to produce beautiful reports that are easy to read; this is a huge physician satisfier! The support team is very well versed and able to devise creative solutions to challenging issues; they are a pleasure to work with. – Kristen Conley, Director of IT and Business Development, Eastern Connecticut Pathology Consultants (Waterbury, CT) – Read this and other LigoLab reviews at Capterra
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“Great customization”
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Video Testimonials
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RECENT PRESS RELEASES/OTHER RESOURCES
Press Releases
February 2021 – Atlas Genomics Detects UK Coronavirus Variant with PCR Test, Result Confirmed with RNA Sequencing – Read Press Release
January 2021 – LigoLab’s TestDirectly Direct-to-Consumer Portal Helps Labs Prevent Lost Revenue – Read Press Release
December 2020 – Avunjian Earns Top Honor for the LigoLab and TestDirectly Response to COVID-19 – Read Press Release
November 2020 – Process Thousands of HRSA Patients in Minutes with LigoLab – Read Press Release
November 2020 – LigoLab’s LIS & RCM Operating Platform Supports Pooled Testing – Read Press Release
October 2020 – TestDirectly Eliminates the Paper Requisitions That Cause Accessioning Headaches – Read Press Release
September 2020 – LigoLab’s Fully Integrated Platform Features No-Touch Auto-Billing – Read Press Release
September 2020 – TestDirectly Simplifies Workflows and Improves Turnaround Times – Read Press Release
August 2020 – LigoLab Offers a Pricing Model That Aligns With Laboratory Goals and an Implementation Plan That Minimizes Lab Disruption – Read Press Release
Blogs
LigoLab Gives Labs a Convenient and User-Friendly Way to Incentivize Patients and Accelerate Payments – Read Blog Unite Your LIS & RCM and Truly Revolutionize Your Business – Read Blog
Operational Excellence – It’s Possible With the Right Laboratory Operating Platform – Read Blog
The Connected Laboratory: A New Approach to Laboratory Billing – Read Blog
How Modern Laboratories Produce and Distribute Reports – Read Blog
What Do Lab Leaders Want From Their Laboratory Information Systems? – Read White Paper
COMPANY BIOS
Suren Avunjian, Founder and Chief Executive Officer, oversees the management of all operations for the company and is responsible for creating, planning, and integrating LigoLab’s strategic direction. In February of 2020, he and his team swiftly built TestDirectly, a direct-to-consumer portal that facilitates safe and easy sample collecting, processing, and reporting. He co-founded LigoLab in 2006 after serving as CTO for the largest privately held laboratory in California. While there, he managed the implementation of cutting-edge technologies that enabled the laboratory to scale up its testing volume by 20 times in just seven years. He passionately leads LigoLab by applying his experience of driving strategy, operational excellence, and innovation at the right time and with the right opportunity.
Tony Oganesian, Founder and Managing Partner, oversees a talented group of developers and the development of all LigoLab Information System products. He has domain expertise in healthcare and the clinical and anatomic pathology lab industry verticals. For the last 20 years, he’s successfully developed software and supervised development efforts while employing a variety of programming platforms and deploying systems across desktop, server, and mobile operating systems. He has a strong background in RDBMS systems, in implementing Electronic Data Interchange (EDI) for different industries, and in deploying systems using Web (thin client) technologies as well as rich workstation applications.
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What Hospital and Health System Labs Need to Know About Operational Support and Logistics During the COVID-19 Outbreak Dark Daily and COVID-19 STAT Intelligence Briefings is offering this FREE webinar as a service to our clinical lab and pathology colleagues Held Wednesday, April 1, 2020 Now a Streaming Webinar How are other clinical laboratories successfully working their way through the COVID-19 outbreak? What are different health networks doing to provide SARS-CoV-2 tests?...
The scientist also employed machine learning “to gauge how easily accessible genes are for transcription” in research that could lead to new clinical laboratory diagnostic tests
Anatomic pathologists and clinical laboratories are of course familiar with the biological science of genomics, which, among other things, has been used to map the human genome. But did you know that a three-dimensional (3D) map of a genome has been created and that it is helping scientists understand how DNA regulates its organization—and why?
The achievement took place at St. Jude Children’s Research Hospital (St. Jude) in Memphis, Tenn. Scientists there created “the first 3D map of a mouse genome” to study “the way cells organize their genomes during development,” a St. Jude news release noted.
Some experts predict that this new approach to understanding how changes happen in a genome could eventually provide new insights that anatomic pathologists and clinical laboratory scientists could find useful when working with physicians to diagnose patients and using the test results to identify the most appropriate therapy for those patients.
In addition to 3D modeling, the researchers applied machine learning to data from multiple sources to see how the organization of the genome changed at different times during development. “The changes are not random, but part of the developmental program of cells,” Dyer said in the news release.
The St. Jude study focused on the rod cells in a mouse retina. That may seem like a narrow scope, but there are more than 8,000 genes involved in retinal development in mice, during which those genes are either turned on or off.
To see what was happening among the cells, the researchers used HI-C analysis, an aspect of ultra-deep chromosome conformation capture, in situ. They found that the loops in the DNA bring together regions of the genome, allowing them to interact in specific ways.
Until this study, how those interactions took place was a
mystery.
“Understanding the way cells organize their genomes during development will help us to understand their ability to respond to stress, injury and disease,”Michael Dyer, PhD (above), Chair of St. Jude’s Developmental Neurobiology Department, co-leader of the Developmental Biology and Solid Tumor Program, and Investigator at Howard Hughes Medical Institute (HHMI), said in the news release. (Photo copyright: St. Jude Children’s Research Hospital.)
The scientists also discovered there were DNA promoters, which encourage gene expression, and also DNA enhancers that increase the likelihood gene expression will occur.
“The research also included the first report of a powerful regulator of gene expression, a super enhancer, that worked in a specific cell at a specific stage of development,” the news release states. “The finding is important because the super enhancers can be hijacked in developmental cancers of the brain and other organs.”
St. Jude goes on to state, “In this study, the scientists determined that when a core regulatory circuit super-enhancer for the VSX2 gene was deleted, an entire class of neurons (bipolar neurons) was eliminated. No other defects were identified. Deletion of the VSX2 gene causes many more defects in retinal development, so the super-enhancer is highly specific to bipolar neurons.”
The St. Jude researchers developed a genetic mouse model of
the defect that scientists are using to study neural circuits in the retina,
the news release states.
Research Technologist Victoria Honnell (left); Developmental Neurobiologist Jackie Norrie, PhD (center); and Postdoctoral Researcher Marybeth Lupo, PhD (right), work in the St. Jude clinical laboratory of Michael Dyer, PhD, using 3D genomic mapping to study gene regulation during development and disease. (Photo copyright: St. Jude Children’s Research Hospital.)
DNA Loops May Matter to Pathology Sooner Rather than
Later
Previous researcher studies primarily used genomic sequencing technology to locate and investigate alterations in genes that lead to disease. In the St. Jude study, the researchers examined how DNA is packaged. If the DNA of a single cell could be stretched out, it would be more than six feet long. To fit into the nucleus of a cell, DNA is looped and bundled into a microscopic package. The St. Jude scientists determined that how these loops are organized regulates how the cell functions and develops.
Scientists around the world will continue studying how the loops in DNA impact gene regulation and how that affects the gene’s response to disease. At St. Jude Children’s Research Hospital, Dyer and his colleagues “used the same approach to create a 3D genomic map of the mouse cerebellum, a brain structure where medulloblastoma can develop. Medulloblastoma is the most common malignant pediatric brain tumor,” noted the St. Jude’s news release.
In addition to providing an understanding of how genes
function, these 3D studies are providing valuable insight into how some
diseases develop and mature. While nascent research such as this may not impact
pathologists and clinical laboratories at the moment, it’s not a stretch to
think that this work may lead to greater understanding of the pathology of
diseases in the near future.
Suren Avunjian, Founder and Chief Executive Officer, oversees the management of all operations for the company and is responsible for creating, planning, and integrating LigoLab’s strategic direction. In February of 2020, he and his team swiftly built TestDirectly, a direct-to-consumer portal that facilitates safe and easy sample collecting, processing, and reporting. He co-founded LigoLab in 2006 after serving as CTO for the largest privately held laboratory in California. While there, he managed the implementation of cutting-edge technologies that enabled the laboratory to scale up its testing volume by 20 times in just seven years. He passionately leads LigoLab by applying his experience of driving strategy, operational excellence, and innovation at the right time and with the right opportunity.
Tony Oganesian, Founder and Managing Partner, oversees a talented group of developers and the development of all LigoLab Information System products. He has domain expertise in healthcare and the clinical and anatomic pathology lab industry verticals. For the last 20 years, he’s successfully developed software and supervised development efforts while employing a variety of programming platforms and deploying systems across desktop, server, and mobile operating systems. He has a strong background in RDBMS systems, in implementing Electronic Data Interchange (EDI) for different industries, and in deploying systems using Web (thin client) technologies as well as rich workstation applications.
