News, Analysis, Trends, Management Innovations for
Clinical Laboratories and Pathology Groups

Hosted by Robert Michel

News, Analysis, Trends, Management Innovations for
Clinical Laboratories and Pathology Groups

Hosted by Robert Michel
Sign In

Australian Company Launches At-Home Genetic Test in the US That Claims to Identify a Person’s ‘Risk’ for Contracting the SARS-CoV-2 Coronavirus. But What Science Supports the Test’s Ability to Accurately Assess Risk?

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.

Genetic Technologies’ COVID-19 Risk Test

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.

Launched without FDA Clearance?

A recent Intelligence Briefing from Dark Daily’s sister publication The Dark Report, noted that the companies introduced the test in the US without a US Food and Drug Administration (FDA) review.

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.

—Donna Marie Pocius

Related Information

Test Improves COVID-19 Prevention and Management Capabilities for Employers, Governments, and Public Health Decision Makers; Gene’s COVID-19 Risk Test Released for Sale in the US

Infinity BiologiX, Genetic Technologies, and Vault Health Launch New Test to Assess Severity of COVID-19 in Individuals

Intelligence Briefing: The Dark Report

Would You Have Your DNA Tested to Predict How Hard COVID-19 Would Strike? Should You?

Development and Validation of a Clinical and Genetic Model for Predicting Risk of Severe COVID-19

Mapping the Human Genetic Architecture of COVID-19 Using Worldwide Meta-Analysis

International Team of Genetic Researchers Claim to Have Successfully Mapped the Entire Human Genome

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.

Pacific Biosciences (PacBio) of Menlo Park, Calif., and Oxford Nanopore Technologies of Oxford Science Park, United Kingdom (UK), independently developed the technologies that aided the group of scientists, known collectively as the Telomere-to-Telomere (T2T) Consortium, in the complete mapping 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.

The T2T scientists presented their findings in a paper, titled, “The Complete Sequence of a Human Genome,” published in bioRxiv, an open-access biology preprint server hosted by Cold Spring Harbor Laboratory.

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.

Karen Miga

“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.

—JP Schlingman

Related Information

Scientists Say They’ve Finally Sequenced the Entire Human Genome. Yes, All of It.

Researchers Claim They Have Sequenced the Entirety of the Human Genome—Including the Missing Parts

The Complete Sequence of a Human Genome

HiFi Reads for Highly Accurate Long-Read Sequencing

President Clinton Announces the Completion of the First Survey of the Entire Human Genome

Genome the Crowning Achievement of Medicine in 2000

International Human Genome Sequencing Consortium Announces “Working Draft” of Human Genome

Use of “Long Read” Gene Sequencing Allows University of Washington Researchers to Uncover Thousands of Never-before Seen Gene Variations

This and similar research initiatives expected to increase the number of genetic markers that would be useful for creating clinical pathology laboratory tests and therapeutic drugs

Whole human genome sequencing continues to become faster, easier, cheaper, and more accurate to do. Because of these advances, the sheer number of human genomes being sequenced is skyrocketing. This huge increase in data is helping researchers unlock many new insights that, in turn, are fueling efforts to develop useful new medical laboratory tests and therapeutic drugs.

This is happening at the University of Washington (UW), where researchers using new genome sequencing technology are uncovering thousands of never-before-seen genetic variants. The application of “long read” gene sequencing technologies is allowing these researchers to identify genetic variants previously unknown, and that are made up of between 50 and 5,000 base pairs.

The discovery is important for two reasons. First, it could close existing gaps in the genome map. Second, it could help scientists identify new genomic variations that are closely associated with difficult-to-diagnose diseases. Of interest to pathologists and clinical laboratory professionals, such discoveries could point to expanded use of genetic testing for diagnosis and treatment of disease. (more…)

Pathologists May Be Healthcare’s Rock Stars of Big Data in Genomic Medicine’s ’Third Wave’

Pathologists are positioned to be the primary interpreters of big data as genomic medicine further evolves

Pathologists and clinical laboratory managers may be surprised to learn that at least one data scientist has proclaimed pathologists the real big data rock stars of healthcare. The reason has to do with the shift in focus of genomic medicine from therapeutics and presymptomatic disease assessment to big data analytics.

In a recent posting published at Forbes.com, data scientist Jim Golden heralded the pronouncement of Harvard pathologist Mark S. Boguski, M.D., Ph.D., FACM. He declared that “The time of the $1,000 genome meme is over!” (more…)

Is Whole-genome Sequencing Reaching a Tipping Point for Clinical Pathology Laboratories?

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…)

;