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Researchers at Wellcome Sanger Institute Develop New Tool to Analyze Genetic Changes and Role of Cell Division in Human Tissue

Nanorate sequencing allows researchers to identify changes to individual genetic sequencing letters among millions of DNA letters contained in a single cell

Detecting genetic mutations in cells requires genomic sequencing that, until now, has not been accurate enough to spot minute changes in DNA sequences. Many clinical laboratory scientists know this restricted the ability of genetic scientists to identify cancerous mutations early in individual cells.

Now, researchers at the Wellcome Sanger Institute in the United Kingdom have developed a new method of genetic sequencing that “makes it possible to more accurately investigate how genetic changes occur in human tissues,” according to Genetic Engineering and Biotechnology News (GEN).

This development suggests a new, more sensitive tool may soon be available for anatomic pathologists to speed evaluation of pre-cancerous and cancerous tissues, thereby achieving earlier detection of disease and clinical intervention.

Called Nanorate Sequencing (NanoSeq for short), the new technology enables researchers to detect genetic changes in any human tissues “with unprecedented accuracy,” according to a news release.

The Wellcome Sanger Institute researchers published their findings in the journal Nature, titled, “Somatic Mutation Landscapes at Single-Molecule Resolution.”

How Somatic Mutations Drive Cancer, Aging, and Other Diseases

NanoSeq enables the detection of new mutations in most human cells—the non-dividing cells—GEN explained, calling Wellcome Sangar Institute’s new technology a “breakthrough” in the use of duplex sequencing.

Until now, genomic sequencing has not been “accurate enough” for this level of detection, Sanger stated in the news release. Thus, there was little opportunity to enhance exploration of new mutations in the majority of human cells.

Further, the findings of the Sanger study suggest that cell division may not be the primary cause of somatic mutations (changes in the DNA sequence of a biological cell).

In their paper, the researchers discussed the importance of somatic mutations. “Somatic mutations drive the development of cancer and may contribute to aging and other diseases. Despite their importance, the difficulty of detecting mutations that are only present in single cells or small clones has limited our knowledge of somatic mutagenesis to a minority of tissues.

“Here, to overcome these limitations, we developed Nanorate Sequencing (NanoSeq), a duplex sequencing protocol with error rates of less than five errors per billion base pairs in single DNA molecules from cell populations. This rate is two orders of magnitude lower than typical somatic mutation loads, enabling the study of somatic mutations in any tissue independently of clonality,” the researchers wrote in Nature.

Refining Duplex Sequencing and Improving PCR Testing

In their study, Sanger researchers assessed duplex sequencing and found errors concentrated at DNA fragment ends. To them, this suggested “flaws” in preparation for DNA sequencing.

Duplex sequencing is an established technique “which sequences both strands of a DNA molecule to remove sequencing and polymerase chain reaction (PCR) errors,” explained a Science Advisory Board article.

Robert Osborne, PhD

“Detecting somatic mutations that are only present in one or a few cells is incredibly technically challenging. You have to find a single letter change among tens of millions of DNA letters and previous sequencing methods were simply not accurate enough,” said Robert Osborne, PhD (above), former Principal Staff Scientist at Sanger who led development of NanoSeq, in the news release. Osborne is now COO of Biofidelity, a cancer diagnostics developer in Cambridge, United Kingdom. This research may eventually give clinical laboratories and surgical pathologists useful new tools that enable earlier, more accurate diagnosis of cancer. (Photo copyright: Cambridge Independent.)

Re-evaluating Mutagenesis and Cell Division with NanoSeq

It took the Sanger researchers four years to create NanoSeq. They “carefully refined” duplex sequencing methods using more specific enzymes to aid DNA cutting and bioinformatics analysis, Clinical OMICS noted.

Then, they put NanoSeq’s sensitivity to the test. They wanted to know if its low error rate meant that NanoSeq could enable study of somatic mutations in any tissue. This would be important, they noted, because genetic mutations naturally occur in cells in a range of 15 to 40 mutations per year with some changes leading to cancer.

The scientists compared the rate and pattern of mutation in both stem cells (renewing cells supplying non-dividing cells) and non-dividing cells (the majority of cells) in blood, colon, brain, and muscle tissues.

The Sanger study found:

  • Mutations in slowly dividing stem cells are on track with progenitor cells, which are more rapidly dividing cells.
  • Cell division may not be the “dominant process causing mutations in blood cells.”
  • Analysis of non-dividing neurons and rarely-dividing muscle cells found “mutations accumulate throughout life in cells without cell division and at a similar pace” to blood cells.

“It is often assumed that cell division is the main factor in the occurrence of somatic mutations, with a greater number of divisions creating a greater number of mutations. But our analysis found that blood cells that had divided many times more than others featured the same rates and patterns of mutation. This changes how we think about mutagenesis and suggests that other biological mechanisms besides cell divisions are key,” said Federico Abascal, PhD, First Author and Sanger Postdoctoral Fellow, in the news release.

Using NanoSeq to Scale Up Somatic Mutation Analyses

“NanoSeq will also make it easier, cheaper, and less invasive to study somatic mutation on a much larger scale. Rather than analyzing biopsies from small numbers of patients and only being able to look at stem cells or tumor tissue, now we can study samples from hundreds of patients and observe somatic mutations in any tissue,” said Inigo Martincorena, PhD, Senior Author and Sanger Group Leader, in the news release.

More research is needed before NanoSeq finds its way to diagnosing cancer by anatomic pathology groups. Still, for diagnostics professionals and clinical laboratory leaders, NanoSeq is an interesting development. It appears to be a way for scientists to see genetic changes in single cells and mutations in a handful of cells that evolve into cancerous tumors, as compared to those that do not.

The Sanger scientists plan to pursue larger follow-up NanoSeq studies.

—Donna Marie Pocius

Related Information:

NANOSEQ: Nanorate Sequencing, Ultra-Accurate Detection of Somatic Mutations

Major Advance Enables Study of Genetic Mutations in Any Tissue

NanoSeq Technique Improved to Detect New Non-Dividing Cell Mutations

Somatic Mutation Landscape at Single-Molecule Resolution

New Method Allows for Study of Genetic Changes in Individual DNA Molecules

Sanger Institute Improves NanoSeq Method to Detect New Mutations in Non-Dividing Cells

Wellcome Sanger Institute’s NanoSeq Sequencing Breakthrough Enables Study of DNA Mutations from Any Human Tissue

Ex-Theranos CEO Elizabeth Holmes Takes Witness Stand in Her Own Defense: Admits to Using Pharma Giants’ Logos on Reports to Investors, But Claims No Intent to Deceive

Former CEO also testified that she believed company’s proprietary blood-testing technology could perform ‘any’ clinical laboratory blood test

One relevant question in the federal fraud trial of ex-Theranos CEO Elizabeth Holmes was whether she would testify on her own behalf. That question was answered shortly after the government rested its criminal fraud case against the former Silicon Valley clinical laboratory testing company founder. Holmes took the stand in her own defense, a risk her defense team hopes will pay off in her favor.

During her first three days of testimony leading up to the Thanksgiving holiday break, Holmes—who faces 11 counts of fraud and conspiracy related to her tenure as founder and CEO of Theranos—made headlines by admitting she did personally put the logos of pharmaceutical giants Pfizer and Schering-Plough on reports she sent to Theranos investors and executives at Walgreens and Safeway. She expressed regret for doing so to the jury, but claimed her intent was not to deceive but to give credit to others.

“This work was done in partnership with these companies, and I was trying to convey that,” she testified, according to a trial coverage from Ars Technica.

When asked if she realized that others would assume the pharmaceutical companies—not Theranos—were the authors of the report, Holmes replied, “I’ve heard that testimony in this case, and I wish I’d done it differently.”

If found guilty, Holmes—who once claimed Theranos’ Edison proprietary blood-testing technology would to be able to complete as many as 200 clinical laboratory tests using a single finger-stick of blood—could face maximum penalties of 20 years in prison, a $2.75 million fine, and possible restitution.

Illustration depicting ex-Theranos CEO Elizabeth Holmes testifying in court

The illustration above depicts ex-Theranos CEO Elizabeth Holmes testifying on her own behalf. Former Santa Clara County prosecutor Steven Clark, JD, told The Mercury News, “(T)he best person to say what Elizabeth Holmes’ intent was is Elizabeth Holmes, and that’s why I think she’s taking the stand. … I think the jury will like her.” That remains to be seen. But there’s no doubt that Clinical Laboratory Directors should take a strong interest in the outcome of this trail. (Graphic copyright: Vicki Behringer/Reuters.)

Holmes Testifies She Believed the Edison Device Could Perform “Any” Blood Test

In its trail coverage, NPR described Holmes’ first three days of testimony “as having involved deflecting responsibility, pointing to the expertise of the Theranos board of directors, lab staff, and other company employees whom Holmes has suggested were close to how [Theranos’] blood analyzers worked.”

According to Reuters, Holmes’ defense team is arguing that Holmes’ always-rosy forecasts about her company’s technology and finances were based on her belief the proprietary Edison device worked as advertised, which, in turn, was based on feedback from pharmaceutical companies, her own employees, and the military.

During her testimony, Holmes compared a traditional blood-testing device to Theranos’ “3.0” device, which she said would reduce the human-error rate that can occur during blood sampling.

“If we had the ability to automate much of that process, we could reduce the error associated with traditional lab testing,” she told the court.

Reuters reported that Holmes told jurors her confidence in the Theranos device was in part due to how well the unit had performed in studies completed in 2008 and 2009, including those run by drug companies such as Novartis.

The Mercury News described Holmes as speaking with “confidence—and frequently a small smile”—during her opening day of testimony.

Asked by one of her lawyers, “Did you believe that Theranos had developed technology that was capable of performing any blood test?” Holmes responded, “I did.”

Holmes Testifies about Military’s Alleged Use of Edison Device

Prosecutors maintain that Holmes knew Theranos’ proprietary blood-testing technology had serious accuracy issues yet lied about its capabilities and use to lure investors. One of those false claims included allegedly stating the US military was using the Edison device on the battlefield. Earlier in the trial, CNBC reported, prosecution witness Brian Grossman, Chief Investment Officer at PFM Health Sciences, which invested $96 million into Theranos, testified he was told in a 2013 meeting with Holmes and Balwani that Theranos technology was being used in medical-evacuation helicopters.

Dark Daily covered court testimony on the military’s alleged use of the Theranos blood-testing device in “Prosecutors in Elizabeth Holmes’ Federal Fraud Trial Question Witnesses about Theranos’ Edison Technology and the Inaccurate Medical Laboratory Test Results It Produced.”

However, on the witness stand, Holmes described Theranos’ projects with the US military as much more limited in scope than the descriptions outlined by investors testifying for the prosecution.

According to The Wall Street Journal (WSJ), Holmes told jurors a 2010 partnership between Theranos and a US Army Institute of Surgical Research doctor in Texas looked into using the Theranos device to measure blood markers to detect kidney performance. A second project involved the military’s Africa Command, which was determining whether the device could withstand high temperatures. Holmes testified the devices used in Africa “held up well,” though some modifications were needed, and some issues were revealed with the touchscreen.

Should Holmes Have Testified on Her Own Behalf?

Trial experts maintain Holmes’ decision to testify in her own defense could backfire.

“It’s always a risk to put your client on because if they make a mistake they can sink the whole case,” former Santa Clara County prosecutor Steven Clark, JD, told The Mercury News. He added, “what’s at issue here is Elizabeth Holmes’ intent. And the best person to say what Elizabeth Holmes’ intent was is Elizabeth Holmes, and that’s why I think she’s taking the stand. She’s very charismatic. She’s really good on her feet. And I think the jury will like her.

“This is the pitch meeting of her life,” Clark added. “She’s going to be explaining herself to 12 people as to what was in her mind.”

Judge Drops One Count Due to Prosecution Error, Government Rests Its Case

Holmes is now charged with nine counts of wire fraud and two counts of conspiracy to commit wire fraud after the government dropped one count of fraud from the indictment. According to WSJ coverage of the trial, US District Judge Edward Davila blocked a patient named in the indictment as “B.B.” from testifying because of a filing error by the prosecution. The judge’s decision resulted in the government dropping one count.

The government rested its case against Holmes on November 19 following testimony from independent journalist Roger Parloff, who wrote a flattering 2014 Fortune magazine story on Holmes. He later redacted his earlier writing in another Fortune article, titled, “How Theranos Misled Me.”

The government alleged Holmes used media publicity as part of her scheme to defraud investors, patients, and physicians. All totaled, 29 witnesses appeared for the prosecution, the WSJ reported

Former Theranos Chief Operating Officer Ramesh “Sunny” Balwani—Holmes’ one-time boyfriend—faces similar charges of defrauding patients, investors, and physicians. His trial is expected to begin in January 2022.

Clinical laboratory managers and pathologists who have watched the federal court proceedings with keen interest should expect the trial to wrap up at the conclusion of Holmes’ testimony, just in time for the Balwani fraud trial to begin. 

—Andrea Downing Peck

Related Information:

Elizabeth Holmes Claims She Forged Pharma Reports—for All the Right Reasons

Elizabeth Holmes Describes Limited Military Research Partnerships

Government Rest Its Case Against Elizabeth Holmes

Elizabeth Holmes Takes Witness Stand in Theranos Trial after Prosecution Rests its Case

Holmes Defends Belief in Theranos Technology at Her Fraud Trial

Elizabeth Holmes Testifies That Theranos Had ‘Successes’ with Pharmaceutical Companies

Hedge Fund Investor Tells Jurors in Holmes Trial That Theranos Lied about Finger-Prick Tech and Military Use

This CEO Is Out for Blood

How Theranos Misled Me

Another Former Theranos Clinical Laboratory Director Testifies in Holmes’ Fraud Trial about Irregularities with Proprietary Edison Blood-Testing Technology

Corporate Executives and Mega-Rich Investors Testify in Elizabeth Holmes’ Federal Fraud Trial That They Were Misled by Theranos’ Claims about the Edison Blood-Testing Device

Prosecutors in Elizabeth Holmes’ Federal Fraud Trial Question Witnesses about Theranos’ Edison Technology and the Inaccurate Medical Laboratory Test Results It Produced

Retail Giant Nordstrom Now Sells Viome Life Sciences’ Microbiome Testing Kit Online, Will Stock the Test Kit in Some Retail Locations Next Year

Although there are healthcare providers who see the potential in microbiome testing, many clinical laboratories are not yet ready to embrace microbiome-based testing

In an unlikely string of events, no less than Nordstrom, the national department store chain, announced in September that it would offer microbiome-based test claimed to “check gut health.” Apparently, its customers were interested in this clinical laboratory test, as the Nordstrom website currently indicates that the “Health Intelligence Test Kit by Viome” is already sold out!

What does it say about consumer interest in clinical laboratory self-testing that Nordstrom has decided to offer at-home microbiome tests to its store customers? Can it be assumed that Nordstrom conducted enough marketing surveys of its customers to determine: a) that they were interested in microbiome testing; and b) they would buy enough microbiome tests that Nordstrom would benefit financially from either the mark-up on the tests or from the derived goodwill for meeting customer expectations?

Whatever the motivation, the retail giant recently announced it had partnered with Viome Life Sciences to sell Viome’s microbiome testing kits to its customers online, and in 2022, at some Nordstrom retail locations. These tests are centered around helping consumers understand the relationship between their microbiome and nutrition.

Pathologists and clinical laboratories will want to track Nordstrom’s success or failure in selling microbiome-based assays to its consumers. Microbiomics is in its infancy and remains a very unsettled area of diagnostics. Similarly, Viome, a self-described precision health and wellness company that conducts mRNA analysis at scale, will need to demonstrate that its strategy of developing precision medicine diagnostics and therapeutics based on the human microbiome has clinical relevance.

Helping Consumers with ‘Precision Nutrition’

In a September news release, Viome founder and CEO Naveen Jain, a serial entrepreneur, said, “Both Viome and Nordstrom believe that true health and beauty start from within. There is no such thing as a universal healthy food or healthy supplement. What is right for one person can be wrong for someone else, especially when it comes to nutrition which is key to human longevity and vitality. Precision nutrition is the future!”

If you are not familiar with the term “Precision Nutrition” here’s how Harvard’s T.H. Chan School of Public Health describes it: “Precision nutrition may sound like a new fad diet, but it is actually a credible emerging area of research supported by the National Institutes of Health under the umbrella of precision medicine.

“Precision medicine seeks to improve the personalized treatment of diseases, and precision nutrition is specific to dietary intake. Both develop interventions to prevent or treat chronic diseases based on a person’s unique characteristics like DNA, race, gender, health history, and lifestyle habits. Both aim to provide safer and more effective ways to prevent and treat disease by providing more accurate and targeted strategies.

“Precision nutrition assumes that each person may have a different response to specific foods and nutrients, so that the best diet for one individual may look very different than the best diet for another.

“Precision nutrition also considers the microbiome, trillions of bacteria in our bodies that play a key role in various daily internal operations. What types and how much bacteria we have are unique to each individual. Our diets can determine which types of bacteria live in our digestive tracts, and according to precision nutrition the reverse is also true: the types of bacteria we house might determine how we break down certain foods and what types of foods are most beneficial for our bodies.”

Medical Laboratory Testing, not Guessing

Viome Life Sciences is a microbiome and RNA analysis company based in Bellevue, Wash. The test kit that Nordstrom is selling is called the Health Intelligence Test. It is an at-home mRNA test that can provide users with some insights regarding their health. Consumers use the kit to collect blood and fecal samples, then return those samples to Viome for testing.

In a press release announcing its collaboration with Nordstrom, Viome said, “In a world overwhelmed by information relating to diet and supplement advice, Viome believes in testing, not guessing and empowering its users with actionable insights. To date, Viome has helped over 250,000 individuals improve their health through precision nutrition powered by microbial and human gene expression insights.”

Nordstrom began offering Viome’s Health Intelligence Test kit for $199 on its website starting in September. As of this writing and noted above, the kits are sold out. Nordstrom plans to stock the kit in select stores starting in 2022.

Viome’s Health Intelligence Test kit

Viome’s Health Intelligence Test kit (above) looks at the microbiome to determine gut health, cellular health, healthy aging, immune health, and stress responses. Test results offer consumers personalized nutritional suggestions and recommendations for supplements, probiotics, and prebiotics based on an individual’s biology. Test are performed by Viome’s own clinical laboratories and results sent directly to Nordstrom’s customers. (Photo copyright: Viome Life Sciences.)

Individuals who purchase the test submit blood and stool samples to Viome’s lab which performs an analysis of gene activity patterns in the user’s cells and microbiome. Viome provides the results to consumers within two to three weeks.

“This partnership is a giant step towards making our technology more accessible, so people can understand what’s right for their unique body,” Jain said in the news release. “We are inspired each day by the incredible changes our customers are seeing in their health including improvements in digestion, weight, stress, ability to focus, and more.”

According to the news release, Viome conducted blind studies earlier this year that revealed significant successes based on their precision nutritional approach to wellness. Study participants, Viome claims, improved their outcomes to four diseases through nutrition:

Is Microbiome Diagnostics Testing Ready for Clinical Use?

Microbiomics is a relatively new field of diagnostics research. Much more research and testing will be needed to prove its clinical value and efficacy in healthcare diagnostics. Nevertheless, companies are offering microbiomics testing to consumers and that has some healthcare providers concerned.

In the GeekWire article, David Suskind, MD, a gastroenterologist at Seattle Children’s Hospital and Professor of Pediatrics at the University of Washington, described Viome’s study methodology as “questionable,” adding, “I think this is a very interesting and exciting space and I do think there are definite potential implications, down the road. [However] we are not there in terms of looking at microbiome and making broad recommendation for individuals, as of yet.”

Will at-home clinical laboratory testing kits that analyze an individual’s microbiome someday provide data that help people lead healthier lives and ward off diseases? That’s Jain’s prediction.

In an article published in Well+Good, Jain said, “COVID-19 has, of course, been such a dark time, but one positive that did come from it is that more people are taking control of their own health. I really believe that the future of healthcare will be delivered not at the hospital, but at home.”

If this collaboration between Nordstrom and Viome proves successful, similar partnerships between at-home diagnostics developers and established retail chains may become even more common. And that should be on the radars of pathologists and clinical laboratories.

—JP Schlingman

Related Information:

Test Order Page on Nordstrom Website for ‘Health Intelligence Test Kit by Viome’

Gut Check at Nordstrom: Retail Giant to Sell Microbiome Test from Seattle-Area Startup Viome

Viome Announces Retail Launch at Nordstrom

Nordstrom Is the Latest Retailer to Expand Its Health and Wellness Assortment

Viome’s At-Home Microbiome Testing Kit Hits Nordstrom’s Digital Shelves

More Countries Are Now Capable of Genome Sequencing and Contributing to Global COVID-19 GISAID Database than Ever Before

GISAID hosts a vast, open database of genomic sequences of SARS-CoV-2 coronavirus samples, and medical laboratory scientists in countries across the globe are contributing

Clinical laboratories around the world have been contributing to the global scientific community’s database of knowledge about SARS-CoV-2, the coronavirus that caused the COVID-19 pandemic, and its variants, through an ingenious and crucial network known as GISAID. This cooperative sharing of the coronavirus’ genetic data (now four million genomic sequences strong) has greatly contributed to understanding the spread of infections and progress obtained in developing effective treatments and vaccines.

Headquartered in Munich, Germany, GISAID, which stands for Global Initiative on Sharing Avian Influenza Data, was created in 2008 during the Avian Influenza (Bird Flu) pandemic. The GISAID initiative promotes “the rapid sharing of data from all influenza viruses and the coronavirus causing COVID-19. This includes genetic sequence and related clinical and epidemiological data associated with human viruses, and geographical as well as species-specific data associated with avian and other animal viruses, to help researchers understand how viruses evolve and spread during epidemics and pandemics,” according to the GISAID website.

Clinical pathologists are likely familiar with GISAID. The initiative has become an indispensable tool for researchers battling SARS-CoV-2. GISAID allows scientists and organizations worldwide to upload genetic sequences of COVID-19 samples. Those sequences can then be used in research for treatments, vaccines, and to track emerging variants. The information is invaluable, freely available, and represents the collaborative efforts of scientists around the world in the fight against COVID-19 and other infectious diseases.

An article published in The World, titled, “From Congo to Chile, Small Labs Are Playing a Growing Role in Global Understanding of COVID,” noted that more than four million genomic sequences have been submitted as of October 15, 2021. The more countries around the world that submit sequences to GISAID, the more understanding scientists have of how the virus is mutating. And, as the cost of performing genomic sequencing declines, the number of countries submitting genomes of SARS-CoV-2 to GISAID is rising.

How GISAID Ensures Contributors Receive Credit for Their Work

One of the reasons that GISAID has been so successful in gathering data is that it requires anyone who uses data downloaded from the massive database to give credit to the person or organization who uploaded it. In other words, if a scientist in the United Kingdom (UK) does breakthrough research using genomes that were originally uploaded to GISAID by a scientist in the Congo, the UK scientist must credit the work of the scientist from the Congo.

Other genomic databases do not have this requirement and genetic researchers are often hesitant to share information due to fear their work will be co-opted by others. According to The World, scientists in lower income countries are particularly vulnerable to having their work appropriated.

Even worse is having one’s work appropriated, used to create a product, and then not being given access to that product.

Christian Happi, PhD

“Unfortunately, we’ve seen also the situation whereby people have leveraged that data and created the solution and refused to share the solution with those that shared the data,” virologist Christian Happi, PhD (above), who directs the African Center of Excellence for Genomics of Infectious Diseases (ACEGID) at Redeemer’s University in Nigeria, told The World. “And that is definitely going to roll back this whole open data sharing and access principle.” Happi is also a Visiting Scientist in the Department of Immunology and Infectious Diseases at Harvard’s T.H. Chan School of Public Health. (Photo copyright: Pius Utomi Ekpei/AFP/News 24.)

That is why GISAID’s policy of giving credit is so important, as molecular biologist Francine Ntoumi, PhD, told The World. “This means that we are going to participate in the game. We are able to say what is circulating. You are no more an observer and I think it makes a difference.” Ntoumi is Founder and Executive Director of the Congolese Foundation for Medical Research (CFMR) in the Republic of Congo, a lecturer in Immunology at Marien Ngouabi University, and Associate Professor and Head of a Research Group at the Institute of Tropical Medicine at the University of Tübingen, Germany.

The guarantee that credit will be given softens some of those fears and explains why the GISAID database is so vast, and increasingly contains sequences from scientists in Africa, South American, and other places where genomic sequencing was not widespread prior to the pandemic. Information from all over the world is crucial for scientists monitoring the mutations of the SARS-CoV-2 coronavirus.

Criticisms of GISAID

The fact that more countries are contributing to the GISAID database is certainly a positive, but the non-profit is not without its critics. There have been complaints about the lack of transparency, and some researchers claim to have had their access denied to the data without any explanation.

An article published in Science reported that “Scientists live in fear of losing access to the GISAID database.”

One scientist who requested anonymity told Science, “I am so tired of being scared all the time, of being terrified that if I take a step wrong, I will lose access to the data that I base my research on. [GISAID] has that sword hanging over any scientist that works on SARS-CoV-2.”

In response to these criticisms, GISAID said in a statement, “Any individual who registers with GISAID and agrees to the GISAID terms of use will be granted access credentials. … On rare occasions, GISAID has found it necessary to temporarily suspend access credentials to protect the GISAID sharing mechanism,” The World reported.

The strict sharing rules may be necessary to encourage researchers in lower income countries to contribute their genomic data on SARS-CoV-2. Charles Rotimi, PhD, a geneticist at the National Human Genome Research Institute (NHGRI), told Science, “To make scientists, especially from developing countries, more comfortable—making sure that they are recognized in the work that they are doing—sometimes you have to create an extra layer [of protection].”

GISAID has certainly accomplished much in its assembling four million SARS-CoV-2 genetic sequences. The initiative’s efforts have contributed to a substantial increase in the number of countries around the world that now have gene sequencing capabilities.

This is another illustration for clinical laboratory managers and pathologists of how continual technology advances in gene sequencing equipment and data analysis software make it significantly cheaper, faster, and more accurate to do genetic sequencing. This was not true, just a few years ago.

—Dava Stewart

Related Information:

From Congo to Chile, Small Labs Are Playing a Growing Role in Global Understanding of COVID

Africa CDC Ramps Up Training on SARS-CoV-2 Genomics and Bioinformatics

The Cost of Sequencing a Human Genome

Critics Decry Access, Transparency Issues with Key Trove of Coronavirus Sequences

McMaster University Researchers Develop Bioinformatics ‘Shortcut’ That Speeds Detection and Identification of Pathogens, including Sepsis, SARS-CoV-2, Others

Molecular probes designed to spot minute amounts of pathogens in biological samples may aid clinical laboratories’ speed-to-answer

Driven to find a better way to isolate minute samples of pathogens from among high-volumes of other biological organisms, researchers at Canada’s McMaster University in Hamilton, Ontario, have unveiled a bioinformatics algorithm which they claim shortens time-to-answer and speeds diagnosis of deadly diseases.

Two disease pathogens the researchers specifically targeted in their study are responsible for sepsis and SARS-CoV-2, the coronavirus causing COVID-19. Clinical laboratories would welcome a technology which both shortens time-to-answer and improves diagnostic accuracy, particularly for pathogens such as sepsis and SARS-CoV-2.

Their design of molecular probes that target the genomic sequences of specific pathogens can enable diagnosticians and clinical laboratories to spot extremely small amounts of viral and bacterial pathogens in patients’ biological samples, as well as in the environment and wildlife.

“There are thousands of bacterial pathogens and being able to determine which one is present in a patient’s blood sample could lead to the correct treatment faster when time is very important,” Zachery Dickson, a lead author of the study, told Brighter World. Dickson is a bioinformatics PhD candidate in the Department of Biology at McMaster University. “The probe makes identification much faster, meaning we could potentially save people who might otherwise die,” he added.

Sepsis is a life-threatening response to infection that leads to organ failure, tissue damage, and death in hospitals worldwide. According to Sepsis Alliance, about 30% of people diagnosed with severe sepsis will die without quick and proper treatment. Thus, a “shortcut” to identifying sepsis in its early stages may well save many lives, the McMaster researchers noted.

And COVID-19 has killed millions. Such a tool that identifies sepsis and SARS-CoV-2 in minute biological samples would be a boon to hospital medical laboratories worldwide.

Hendrik Poinar, PhD

“We currently need faster, cheaper, and more succinct ways to detect pathogens in human and environmental samples that democratize the hunt, and this pipeline does exactly that,” Hendrik Poinar, PhD (above), McMaster Professor of Anthropology and a lead author of the study, told Brighter World. Poinar is Director of the McMaster University Ancient DNA Center. Hospital medical laboratories could help save many lives if sepsis and COVID-19 could be detected earlier. (Graphic copyright: McMaster University.)

Is Bioinformatics ‘Shortcut’ Faster than PCR Testing?

The National Human Genome Research Institute defines a “probe” in genetics as a “single-stranded sequence of DNA or RNA used to search for its complementary sequences in a sample genome.”

The McMaster scientists call their unique probe design process, HUBDesign, or Hierarchical Unique Bait Design. “HUB is a bioinformatics pipeline that designs probes for targeted DNA capture,” according to their paper published in the journal Cell Reports Methods, titled, “Probe Design for Simultaneous, Targeted Capture of Diverse Metagenomic Targets.”

The researchers say their probes enable a shortcut to detection—even in an infection’s early stages—by “targeting, isolating, and identifying the DNA sequences specifically and simultaneously.”

The probes’ design makes possible simultaneous targeted capture of diverse metagenomics targets, Biocompare explained.

But is it faster than PCR (polymerase chain reaction) testing?

The McMaster scientists were motivated by the “challenges of low signal, high background, and uncertain targets that plague many metagenomic sequencing efforts,” they noted in their paper.

They pointed to challenges posed by PCR testing, a popular technique used for detection of sepsis pathogens as well as, more recently, for SARS-CoV-2, the coronavirus causing COVID-19.

“The (PCR) technique relies on primers that bind to nucleic acid sequences specific to an organism or group of organisms. Although capable of sensitive, rapid detection and quantification of a particular target, PCR is limited when multiple loci are targeted by primers,” the researchers wrote in Cell Reports Methods.

According to LabMedica, “A wide array of metagenomic study efforts are hampered by the same challenge: low concentrations of targets of interest combined with overwhelming amounts of background signal. Although PCR or naive DNA capture can be used when there are a small number of organisms of interest, design challenges become untenable for large numbers of targets.”

Detecting Pathogens Faster, Cheaper, and More Accurately

As part of their study, researchers tested two probe sets:

  • one to target bacterial pathogens linked to sepsis, and
  • another to detect coronaviruses including SARS-CoV-2.

They were successful in using the probes to capture a variety of pathogens linked to sepsis and SARS-CoV-2.

“We validated HUBDesign by generating probe sets targeting the breadth of coronavirus diversity, as well as a suite of bacterial pathogens often underlying sepsis. In separate experiments demonstrating significant, simultaneous enrichment, we captured SARS-CoV-2 and HCoV-NL63 [Human coronavirus NL 63] in a human RNA background and seven bacterial strains in human blood. HUBDesign has broad applicability wherever there are multiple organisms of interest,” the researchers wrote in Cell Reports Methods.

The findings also have implications to the environment and wildlife, the researchers noted.

Of course, more research is needed to validate the tool’s usefulness in medical diagnostics. The McMaster University researchers intend to improve HUBDesign’s efficiency but note that probes cannot be designed for unknown targets.

Nevertheless, the advanced application of novel technologies to diagnose of sepsis, which causes 250,000 deaths in the US each year, according to the federal Centers for Disease Control and Prevention, is a positive development worth watching.

The McMaster scientists’ discoveries—confirmed by future research and clinical studies—could go a long way toward ending the dire effects of sepsis as well as COVID-19. That would be a welcome development, particularly for hospital-based laboratories.

—Donna Marie Pocius

Related Information:

DNA Researchers Develop Critical Shortcut to Detect and Identify Known and Emerging Pathogens

Probe Design for Simultaneous, Targeted Capture of Diverse Metagenomic Targets

New Tool Designs Probes for Targeted DNA Capture

Novel Tool Developed to Detect and Identify Pathogens

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Junk DNA May Not be “Junk” Afterall, but Perform Significant Functions in Ensuring Fertility, and Preventing Cancer and Other Diseases

Recent research into transposons within DNA dark matter may produce new biomarkers for clinical laboratory testing and diagnostics

There’s been another interesting development in the study of genetic “dark matter” which may give rise to new biomarkers for clinical laboratory diagnostics and testing. This is worth noting, because biological dark matter has long been considered non-critical and immaterial to the human organism or human evolution. Researchers often refer to it as junk DNA.

However, newly-released research suggests that transposons (aka, transposable elements) contained within our genetic dark matter may play a “critical role in mammalian development,” according to a UC Berkeley news release. Transposons, the release notes, are “viral elements [that] have invaded mammalian genomes for millions of years and currently make up nearly half the DNA in the genomes of all living mammals.”

The study, led by researchers at the University of California, Berkeley, and Washington University in St. Louis, found at least one family of transposons that affected the viability of test mice. They believe the transposon could play a similar role in all mammals—including humans.

The researchers published their study in the journal Cell, titled, “A Mouse-Specific Retrotransposon Drives a Conserved Cdk2ap1 Isoform Essential for Development.”

Lin He, PhD

Molecular biologist Lin He, PhD (above), led the study conducted at the University of California, Berkeley, and Washington University in St. Louis, which found that bits of DNA once considered “junk” may actually perform important functions, such as ensuring fertility. These findings may one day confirm new biomarkers for clinical laboratory testing. (Photo copyright: MacArthur Foundation.)

How Removal of a Transposon Led to Death

The researchers found that the function of one type of transposon affected whether a mouse fetus could form properly and survive birth. The transposon “regulates the proliferation of cells in the early fertilized embryo and the timing of implantation in the mother’s uterus,” the news release notes.

To perform the research, the scientists removed a specific transposon that controls the proliferation of cells in the early fertilization of an embryo from the mice. After extracting that transposon, half of the mouse pups died before birth.

The researchers then looked at other mammalian species—including humans—and “found virus-derived regulatory elements linked to cell proliferation and timing of embryo implantation, suggesting that ancient viral DNA has been domesticated independently to play a crucial role in early embryonic development in all mammals,” UC Berkeley noted.

The researchers suggest that some of our dark matter DNA has an important function in our embryonic maturation and survival.

“The mouse and humans share 99% of their protein coding genes in their genomes—we are very similar with each other,” said molecular biologist and senior author of the study Lin He, PhD, Associate Professor, Department of Molecular and Cell Biology, UC Berkeley, in the news release.

“So, what constitutes the differences between mice and humans? One of the major differences is gene regulation—mice and humans have the same genes, but they can be regulated differently. Transposons have the capacity to generate a lot of gene regulatory diversity and could help us to understand species-specific differences in the world.”

“The real significance of this story is it tells us how evolution works in the most unexpected manner possible,” said geneticist and study co-author Ting Wang, PhD, Sanford and Karen Loewentheil Distinguished Professor of Medicine, Department of Genetics, Washington University School of Medicine, in the UC Berkeley news release.

“Transposons were long considered useless genetic material, but they make up such a big portion of the mammalian genome. A lot of interesting studies illustrate that transposons are a driving force of human genome evolution. Yet, this is the first example that I know of where deletion of a piece of junk DNA leads to a lethal phenotype, demonstrating that the function of specific transposons can be essential,” he added.

Their research could have implications for human fertility as many miscarriages in humans are due to undiagnosed conditions or have no apparent genetic component.

“If 50% of our genome is non-coding or repetitive—this dark matter—it is very tempting to ask the question whether or not human reproduction and the causes of human infertility can be explained by junk DNA sequences,” he said.

Other Studies Involving So-called ‘Junk DNA’

In “Researchers Discover Links Between Non-Coding DNA and Cancer Growth That Could Lead to New Clinical Laboratory Biomarkers for Cancer and Other Chronic Diseases,” Dark Daily reported on studies conducted at the Ontario Institute for Cancer Research (OICR) and the Cancer Research UK in England which also concluded that portions of mammalian DNA previously considered “junk” may in fact be performing critical functions, such as, for example, preventing cancer.

Thus, the UC Berkeley/Washington University study is building on prior research demonstrating that dark matter DNA may not be “junk” after all. More specifically, transposons may eventually have value as biomarkers for clinical laboratory tests and diagnostics.

Of course, additional research and studies are needed to validate these findings and provide greater knowledge about the function of specific transposons. But it’s an intriguing development that’s worth following.

—JP Schlingman

Related Information:

So-called Junk DNA Plays Critical Role in Mammalian Development

Transposons: The Jumping Genes

A Mouse-specific Retrotransposon Drives a Conserved Cdk2ap1 Isoform Essential for Development

Efficient Mouse Genome Engineering by CRISPR-EZ Technology

Researchers Discover Links Between Non-Coding DNA and Cancer Growth That Could Lead to New Clinical Laboratory Biomarkers for Cancer and Other Chronic Diseases

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