Findings are ‘a vital first step in discovering potentially valuable targets for development of new [COVID-19] treatments,’ noted co-first author of the study
Researchers at King’s College London (KCL) have determined that levels of certain blood proteins specific to each person’s blood type can be “causally linked” to an increased risk of hospitalization and death from a COVID-19 infection. The scientists also found that a person’s genetics play a key role in establishing the levels of those proteins in the blood.
This is relevant for clinical laboratories—particularly hospital/health system laboratories—because testing for specific proteins in the blood by medical laboratories could help flag incoming patients at higher risk for an acute COVID-19 infection.
Also, “By identifying this suite of proteins, the research has highlighted a number [of] possible targets for drugs that could be used to help treat severe COVID-19,” noted a KCL news release.
Identifying certain drugs that would be more effective for specific individuals or healthcare groups is a core goal of precision medicine.
“We have used a purely genetic approach to investigate a large number of blood proteins and established that a handful have causal links to the development of severe COVID-19,” said Alish Palmos, PhD (above), Postdoctoral Research Associate, King’s College London Social, Genetic and Developmental Psychiatry Center, and co-first author of the study. “Honing in on this group of proteins is a vital first step in discovering potentially valuable targets for development of new treatments.” Medical laboratories may soon be able to use this knowledge as a way to determine risk for severe COVID-19 hospitalization, as well as to guide decisions on how to use new precision medicine drugs for combating the infection. (Photo copyright: Twitter.)
Genetic Variants Linked to Causality
Since the COVID-19 pandemic began in late 2019, scientists and researchers have been vigorously trying to understand the SARS-CoV-2 coronavirus and determine why some patients have more severe symptoms than others.
To conduct their study, the KCL researchers screened more than 3,000 blood proteins to identify which proteins have a causal link to hospitalization risk, the need for respiratory support, and death from a severe COVID-19 infection.
“Causality between exposure and disease can be established because genetic variants inherited from parent to offspring are randomly assigned at conception similar to how a randomized controlled trial assigns people to groups,” said Vincent Millischer, MD, PhD, Medical University of Vienna and co-first author of the study in the KCL news release.
“In our study, the groups are defined by their genetic propensity to different blood protein levels, allowing an assessment of causal direction from high blood protein levels to COVID-19 severity whilst avoiding influence of environmental effects,” he added.
The scientists selected genetic variants, known as single nucleotide polymorphisms, that were strongly associated with blood protein levels. They then performed their analysis using Mendelian randomization to test the causal associations of those blood proteins with the development of severe COVID-19 infections.
“Mendelian randomization uses genetic variants associated with a trait [e.g., protein level] and measures their causal effect on disease outcomes, [avoiding] environmental confounding factors, such as lifestyle, being physically ill, etc.,” Alish Palmos, PhD, told Medical News Today. Palmos is a Postdoctoral Research Associate at King’s College London’s Social, Genetic, and Developmental Psychiatry Center and co-first author of the study.
Blood Groups Linked to COVID-19 Hospitalization, Death
One of the most important findings of the KCL research is a causal association between COVID-19 severity and an enzyme called ABO, which determines blood type. This discovery suggests that blood groups perform an instrumental role in whether individuals develop severe forms of the illness.
“The enzyme helps determine the blood group of an individual and our study has linked it with both risk of hospitalization and the need of respiratory support or death,” said Christopher Hübel, PhD, Postdoctoral Research Associate, King’s College and co-last author of the study in the press release. “Our study does not link precise blood group with risk of severe COVID-19, but since previous research has found that proportion of people who are group A is higher in COVID-19 positive individuals, this suggests that blood group A is more likely candidate for follow-up studies.”
The KCL researchers uncovered several compelling findings regarding blood proteins and COVID-19, including:
The discovery of six blood markers that were significantly associated with an elevated risk of hospitalization.
The discovery of nine blood markers that were significantly associated with a decreased risk of hospitalization.
Consistent results indicating hospitalization being significantly associated with decreased levels of macrophage inflammatory protein.
Five blood markers associated with the need for respiratory support or death.
Eight blood markers causally associated with a statistically significantly decreased risk of need for respiratory support or death.
Consistent results with respiratory support or death being significantly causally associated with decreased levels of neprilysin.
Developing New COVID-19 Treatments and Preventative Therapies
“What we have done in our study is provide a shortlist for the next stage of research,” said Gerome Breen, PhD, in the KCL news release. Breen is Professor of Psychiatric Genetics at King’s College London’s Institute of Psychiatry, Psychology and Neuroscience, and co-last author of the study.
“Out of 1000s of blood proteins we have whittled it down to about 14 that have some form of causal connection to the risk of severe COVID-19 and present a potentially important avenue for further research to better understand the mechanisms behind COVID-19 with an ultimate aim of developing new treatments but potentially also preventative therapies,” he added.
Further research and clinical investigation are needed to validate the King’s College London researchers’ findings. However, their insights could result in new clinical laboratory tests and personalized treatments for COVID-19.
Since all Americans have access to free COVID-19 vaccines, many pathologists and clinical lab managers will ask if this test is even necessary. Some experts say “maybe”
Here’s another example of genetic test developers who are willing to push boundaries and sell a diagnostic test directly to consumers that has some diagnostic experts and pathologists challenging its clinical validity.
The test was developed by molecular diagnostics company Genetic Technologies Ltd. (NASDAQ:GENE) of Melbourne, Australia, and, according to an article in Science, is an at-home saliva test that “combines genetic data with someone’s age, sex, and pre-existing medical conditions to predict their risk of becoming extremely ill from COVID-19.”
In a non-peer-reviewed preprint, titled, “Development and Validation of a Clinical and Genetic Model for Predicting Risk of Severe COVID-19,” Genetic Technologies’ Chief Scientific Officer Richard Allman, PhD, and Senior Biostatistician and the study’s first author, Gillian Dite, PhD, wrote, “Using SARS-CoV-2 positive participants from the UK Biobank, we developed and validated a clinical and genetic model to predict risk of severe COVID-19. … Accurate prediction of individual risk is possible and will be important in regions where vaccines are not widely available or where people refuse or are disqualified from vaccination, especially given uncertainty about the extent of infection transmission among vaccinated people and the emergence of SARS-CoV-2 variants of concern.”
But since every American already has access to free COVID-19 vaccines, one wonders why this test would be launched in the US?
Determining Risk for COVID-19 Infection
Can a genetic test predict an individual’s risk of contracting a SARS-CoV-2 infection that would require hospitalization or cause death? Genetic Technologies and its US partner, Infinity BiologiX (IBX) of Piscataway, N.J., believe so.
According to a Genetic Technologies news release, the saliva test, which reportedly costs $175, enables a “leading-edge risk assessment that estimates your personal risk of severe disease,” IBX says on its website.
The at-home saliva-based test, which is intended for people age 18 and older, gives a risk score for contracting a serious COVID-19 case based on genetic and clinical information, IBX stated in its own news release.
The two companies partnered with Vault Health, a “virtual platform for telemedicine and diagnostics” developer, to distribute, and sell the COVID-19 Serious Disease Risk Test in the US.
In the IBX news release, IBX’s Chief Executive Officer, Robin Grimwood, said, “We see this initial agreement for the sale and distribution of Genetic Technologies’ COVID-19 Risk Test (above) as a critical collaboration in line with our mission to understand the genetic causes of common, complex diseases and to discover diagnoses, treatments and, eventually, cures for these diseases.” However, as Dark Daily’s sister publication The Dark Report previously reported, some geneticists, epidemiologists, and clinical laboratory professionals have expressed concerns. (Photo copyright: Infinity BiologiX.)
Is There a Place for Genetic COVID-19 Risk Test in the US?
“Alongside existing treatment options and vaccines, we believe this test will enable more insightful decisions for states, workplaces, and individuals,” said Simon Morriss, Genetic Technologies’ CEO, in the news release.
Meanwhile, some experts are uncertain about predictive types of testing for the SARS-CoV-2 coronavirus. “I think it’s premature to use a genetic test to predict a person’s likely COVID-19 severity. We don’t understand exactly what these genetic variants mean or how they affect disease,” epidemiologist Priya Duggal PhD, a professor in the Genetics Epidemiology Division at the Johns Hopkins University School of Public Health, told Science.
According to Science, “The test debuts in a regulatory gray zone …. The two companies did not seek [FDA] approval for validity because, [Genetic Technologies Chief Scientific Officer Richard Allman] says, the test is not a direct-to-consumer product that falls under its review. After a customer receives results from IBX’s federally-approved labs, they can consult with a ‘telehealth’ physician.”
“We are uniquely and strategically positioned with our partners to deliver the test and provide remote telehealth services and reporting, utilizing our extensive array capability and capacity across a number of platforms,” Grimwood said in the IBX news release.
However, Science reported that “Several geneticists who reviewed the company’s preprint” said “the test needs to be validated in other, more diverse populations than one detailed in the UK Biobank, and they wonder whether its predictions are reliable for people infected with new SARS-CoV-2 variants.”
“It’s a good start, but by no means is it calibrated or validated sufficiently to say this is a test I would take, or my wife should take,” cancer geneticist Stephen Chanock, MD, Director of the Division of Cancer Epidemiology and Genetics at the National Cancer Institute, National Institutes of Health, told Science.
The question remains unanswered as to why a genetic risk test for SARS-CoV-2 and its variants is needed in the United States. Nevertheless, clinical laboratory leaders and pathologists may want to monitor these developments for new biomarkers and COVID-19 diagnostics.
With 100% of the human genome mapped, new genetic diagnostic and disease screening tests may soon be available for clinical laboratories and pathology groups
Utilizing technology developed by two different biotechnology/genetic sequencing companies, an international consortium of genetic scientists claim to have sequenced 100% of the entire human genome, “including the missing parts,” STAT reported. This will give clinical laboratories access to the complete 3.055 billion base pair (bp) sequence of the human genome.
If validated, this achievement could greatly impact future genetic research and genetic diagnostics development. That also will be true for precision medicine and disease-screening testing.
Completing the First “End-to-End” Genetic Sequencing
In June of 2000, the Human Genome Project (HGP) announced it had successfully created the first “working draft” of the human genome. But according to the National Human Genome Research Institute (NHGRI), the draft did not include 100% of the human genome. It “consists of overlapping fragments covering 97% of the human genome, of which sequence has already been assembled for approximately 85% of the genome,” an NHGRI press release noted.
“The original genome papers were carefully worded because they did not sequence every DNA molecule from one end to the other,” Ewan Birney, PhD, Deputy Director General of the European Molecular Biology Laboratory (EMBL) and Director of EMBL’s European Bioinformatics Institute (EMBL-EBI), told STAT. “What this group has done is show that they can do it end-to-end. That’s important for future research because it shows what is possible,” he added.
In their published paper, the T2T scientists wrote, “Addressing this remaining 8% of the genome, the Telomere-to-Telomere (T2T) Consortium has finished the first truly complete 3.055 billion base pair (bp) sequence of a human genome, representing the largest improvement to the human reference genome since its initial release.”
Tale of Two Genetic Sequencing Technologies
Humans have a total of 46 chromosomes in 23 pairs that represent tens of thousands of individual genes. Each individual gene consists of numbers of base pairs and there are billions of these base pairs within the human genome. In 2000, scientists estimated that humans have only 30,000 to 35,000 genes, but that number has since been reduced to just above 20,000 genes.
According to STAT, “The work was possible because the Oxford Nanopore and PacBio technologies do not cut the DNA up into tiny puzzle pieces.”
PacBio used HiFi sequencing, which is only a few years old and provides the benefits of both short and long reads. STAT noted that PacBio’s technology “uses lasers to examine the same sequence of DNA again and again, creating a readout that can be highly accurate.” According to the company’s website, “HiFi reads are produced by calling consensus from subreads generated by multiple passes of the enzyme around a circularized template. This results in a HiFi read that is both long and accurate.”
Oxford Nanopore uses electrical current in its sequencing devices. In this technology, strands of base pairs are pressed through a microscopic nanopore one molecule at a time. Those molecules are then zapped with electrical currents to enable scientists to determine what type of molecule they are and, in turn, identify the full strand.
The T2T Consortium acknowledge in their paper that they had trouble with approximately 0.3% of the genome, but that, though there may be a few errors, there are no gaps.
“You’re just trying to dig into this final unknown of the human genome,” Karen Miga (above), Assistant Professor in the Biomolecular Engineering Department at the University of California, Santa Cruz (UCSC), Associate Director at the UCSC Genomics Institute, and lead author of the T2T Consortium study, told STAT. “It’s just never been done before and the reason it hasn’t been done before is because it’s hard.” (Photo copyright: University of California, Santa Cruz.)
Might New Precision Medicine Therapies Come from T2T Consortium’s Research?
The researchers claim in their paper that the number of known base pairs has grown from 2.92 billion to 3.05 billion and that the number of known genes has increased by 0.4%. Through their research, they also discovered 115 new genes that code for proteins.
The T2T Consortium scientists also noted that the genome they sequenced for their research did not come from a person but rather from a hydatidiform mole, a rare growth that occasionally forms on the inside of a women’s uterus. The hydatidiform occurs when a sperm fertilizes an egg that has no nucleus. As a result, the cells examined for the T2T study contained only 23 chromosomes instead of the full 46 found in most humans.
Although the T2T Consortium’s work is a huge leap forward in the study of the human genome, more research is needed. The consortium plans to publish its findings in a peer-reviewed medical journal. In addition, both PacBio and Oxford Nanopore plan to develop a way to sequence the entire 46 chromosome human genome in the future.
The future of genetic research and gene sequencing is to create technologies that will allow researchers to identify single nucleotide polymorphisms (SNPs) that contain longer strings of DNA. Because these SNPs in the human genome correlate with medical conditions and response to specific genetic therapies, advancing knowledge of the genome can ultimately provide beneficial insights that may lead to new genetic tests for medical diagnoses and help medical professionals determine the best, personalized therapies for individual patients.
High-Density Sequencing Chips Will Soon Be Able To Sequence Five Million SNPs
Rapid gene sequencing is catching the interest of progressive anatomic pathologists. These medical laboratory professionals are interested in using rapid gene sequencing technology to allow them to study tens and hundreds of genes on a patient specimen.
The technologies used in rapid gene sequencing are being developed and improved by a handful of biotech companies who are racing each other be first to deliver systems to the marketplace that can sequence whole human genomes at a cost of $1,000 or less. Some innovative medical laboratories are beginning to acquire these sequencing systems and explore how they might be used for clinical pathology laboratory testing. (more…)
Nation’s largest public health district wants to promote personalized medicine
Here’s an unusual development in genetic testing that shows clinical laboratory managers how fast the lab testing marketplace is changing. Two-hospital Palomar Pomerado Health (PPH), California’s largest public health district, recently partnered with 23andMe to introduce a personalized medicine service in North San Diego County.
PPH now sells 23andMe genetic test kits for $399 at express care centers in two grocery stores and an outpatient center. The test kit, Time magazine’s 2008 pick for Invention of the Year, comes with a 30-minute education session by a nurse practitioner.
