Project aims to create a new pangenome for genetic testing that will ensure better clinical laboratory testing and healthcare outcomes
Recent advances in genetics are motivating some scientists to proclaim the need to update the existing “master human genome”—currently based on a single individual’s genetic sequence—to make it more inclusive. This international research effort will have implications for personalized clinical laboratory testing and precision medicine.
Genetic scientists at the Human Pangenome Reference Consortium (HPRC), a project funded by the National Human Genome Research Institute (NHGRI), are working “to sequence and assemble genomes from individuals from diverse populations in order to better represent [the] genomic landscape of diverse human populations,” according to the organization’s website.
The project plans to evaluate a wide variety of reference genomes and develop a more diverse human pangenome (a multi-genome reference sequence) that will contain a larger cross-section of the human population. The HPRC scientists will be looking at genomes from specific countries, including Denmark, Japan, South Korea, Sweden, and the United Arab Emirates, The Guardian reported.
The increased diversity of reference genetic data will enable genomic researchers to increase the accuracy of precision medicine diagnostics and clinical laboratory testing.
“One person is not representative of the world,” Pui-Yan Kwok, MD, PhD (above), Henry Bachrach Distinguished Professor, Cardiovascular Research Institute at the University of California, San Francisco, told The Guardian. “As a result, most genome sequencing is fundamentally biased.” And that bias, the researchers claim, affects the accuracy of clinical laboratory treatments and diagnostics. (Photo copyright: UCSF.)
Reference Genome for Genetic Sequencing is Based on One Person
Launched in 1990, The Human Genome Project studied all DNA in a select set of organisms. The project completed its first sequence of the human genome in 2003, which became the reference genome for thousands of genomic discoveries since then.
But there’s a problem.
Although a revolutionary breakthrough in genetic sequencing, that reference genome came from just one person. This means a significant portion of the human population is not represented in genetic research, and that bias, according to some scientists, “limits the kind of genetic variation that can be detected, leaving some patients without diagnoses and potentially without proper treatment,” according to The Guardian.
“Getting the right medicine to the right patient at the right time is the tagline,” Neil Hanchard, MD, DPhil, physician scientist and senior investigator for precision health research at the NHGRI in Bethesda, Maryland, told The Guardian.
The HPRC’s goal is to help mitigate reference biases that could hamper disease diagnoses and ensure all populations receive the best treatments for illness.
According to its website, the organization’s main purpose includes:
Gene sequencing from a diverse set of samples with the newest technologies.
Fostering an ecosystem of assembly and pangenome tools.
Creating and releasing high-quality assemblies and pangenomes.
Embedding a team of scholars to address ethical, legal, and social implications of their work.
Forming international partnerships for the research.
HPRC Scientists Find Never-Sequenced Genetic Variants in Africa
Standard gene sequencing works by dividing DNA into tiny portions known as short reads, then sequencing and organizing the reads into a genome using an existing reference as a guide. However, this process renders larger blocks of variants, called structural variants (SVs), more difficult to read or even remain undetected, which can translate to a sequence that does not completely represent personal variations.
In 2019, the HPRC team of scientists analyzed genetic samples from 154 people from various parts of the world and discovered SV content that was missing from their reference sequence. A further study of genetic samples from 338 individuals that examined only extra inserted DNA detected the presence of almost 130,000 new sequences.
More recently, the HPRC researchers sampled 426 individuals from 50 ethnolinguistic groups from Africa and discovered a few million new single nucleotide variants (SNVs). Most of these distinct SNVs derived from populations that had not been previously sampled.
“We haven’t even touched SVs,” Hanchard told The Guardian. “But our preliminary data suggests it’s going to be more of the same.”
“We may miss risk variants in those regions not represented in the reference,” he added.
HPRC Receives Clearance from NHGRI to Continue Research
Hanchard recognizes the benefits of regional references in genomic sequencing and is optimistic about the future of genomics and the ability to sequence more diverse populations.
“I would love to get to a point where everyone feels represented and that this is for them, as much as it is for any particular group,” he told The Guardian. “We are from one humanity, that’s the important part.”
On February 13, the HPRC received concept clearance for renewal of the program from the NHGRI, which plans to commit up to $10 million in total costs per year for the program over the next five years.
Genetic sequencing continues to emerge as a vital tool in the diagnoses and treatment of diseases. Ensuring that as many diverse populations as possible are included in genomic research is an important element for precision medicine and optimal healthcare.
Clinical laboratory managers and pathologists will want to stay updated on these developments, because much of this new knowledge about the pangenome will need to be incorporated when interpreting genetic sequences and developing diagnoses in support of personalized medicine.
Clinical laboratory scientist who aided in the investigation compared DNA test results with publicly available genetic information
In an interesting twist in the solving of crime, genetic test results—along with help from a clinical laboratory scientist (CLS) turned amateur genealogist—guided relatives of Melissa Highsmith to her whereabouts after she was allegedly kidnapped as a toddler over half a century ago. According to The Guardian, the CLS helped locate Melissa by “interpreting the key DNA results and mining publicly available records.”
Highsmith’s abduction was one of the oldest missing person cases in the country and demonstrates how clinical laboratory skills can be applied outside the laboratory to help solve other problems—in this case, helping a family search for a kidnapped daughter—using genetic testing technologies that until recently were not available to the general public.
Thanks to a 23andMe at-home DNA test—and a tenacious clinical laboratory scientist/amateur genealogist—Melissa Highsmith (shown above at time of kidnapping and today) has been reunited with her birth family. This shows how genetic testing is being used in remarkable ways outside of the clinical laboratory. (Photo copyright: Highsmith family/People.)
Thanksgiving Reunion
Back in 1971, Melissa’s mother, Alta Apantenco, placed an advertisement in a local newspaper in Fort Worth, Texas, to hire a babysitter to care for her 21-month-old daughter. Apantenco hired Ruth Johnson to babysit her daughter without meeting the woman in person. Because Apantenco had to be at work, the child was handed over to Johnson by Apantenco’s roommate. The babysitter then allegedly abducted Melissa and disappeared with her.
Melissa’s family reported her missing to the police and searched for the snatched baby for more than 51 years. The family even organized a Facebook page called “Finding Melissa Highsmith” and sought outside assistance from the National Center for Missing and Exploited Children (NCMEC) in locating their lost relative, according to the New York Post.
The police and the FBI also got involved in the case, but few leads emerged over the decades.
Then, in September of 2022, Melissa’s family received a new lead regarding her location based on her father’s 23andMe DNA test results. Those results, along with a birthmark and date of birth, confirmed that Melissa was alive and well and residing in the Charleston, South Carolina area.
Over Thanksgiving weekend, Melissa was reunited with her mother, her father Jeffrie Highsmith, and two of her four siblings at a church in Fort Worth. She hopes to meet her remaining two siblings over the Christmas holidays.
“I can’t describe my feelings. I’m so happy to see my daughter that I didn’t ever think I would see again,” Apantenco told Saint Paul, Minnesota, television station KSTP.
“I couldn’t stop crying,” said Melissa’s sister Victoria Garner in a family statement. “I was overjoyed, and I’m still walking around in a fog trying to comprehend that my sister [was] right in front of me and that we found her,” The Guardian reported.
Clinical Laboratory Scientist Aids in the Investigation
The 23andMe test results alerted the family to the existence of a few unknown relatives that could be connected to the DNA of Melissa’s father. The family then contacted a genealogist and clinical laboratory scientist from Minnesota named Lisa Jo Schiele to help them interpret the results and potentially locate the missing woman. Schiele compared the DNA results with public records to help find Melissa Highsmith.
“I was able to use what we call traditional genealogy to find marriage records and things like that to find where Melissa was right now,” Schiele told KSTP. “At first glance, you look at these matches, but I’m like, ‘Holy cow, is this too good to be true?’ I’m very happy to help them navigate all of this.”
One of Melissa’s sisters, Sharon Highsmith, stated that her mother experienced deep feelings of guilt after Melissa’s abduction and had even faced accusations that she had something to do with the disappearance of her daughter.
“My mom did the best she could with the limited resources she had. She couldn’t risk getting fired, so she trusted the person who said they’d care for her child,” Sharon said in a family statement. “I’m grateful we have vindication for my mom,” The Guardian reported.
“I keep having to pinch myself to make sure I’m awake,” Melissa, who now resides in Fort Worth, told KSTP.
“It’s a miracle,” Apantenco said.
“A Christmas miracle,” Melissa added.
Due to the statute of limitations, which expired 20 years after Melissa turned 18, the babysitter who allegedly took Melissa cannot be criminally prosecuted.
“I’m angry our family was robbed for 51 years,’’ Melissa told Fort Worth news station WFAA.
This remarkable story illustrates how clinical laboratory skills combined with genetic testing results can be used outside of medical laboratory testing purposes to aid in solving criminal cases and other mysteries involving missing people.
Further advances in DNA testing combined with genetic databases that include DNA from greater numbers of people could result in more reunions involving missing persons who were identified because of genetic matching.
DNA analysis of early plague victims pinpoints Black Death’s start on Silk Road trading communities in mountain region of what is now modern-day Kyrgyzstan in Central Asia
Microbiologists and clinical laboratory scientists will likely find it fascinating that an international team of scientists may have solved one of history’s greatest mysteries—the origin of the bubonic plague that ravaged Afro-Eurasia in the mid fourteenth century. Also known as the Black Death, the plague killed 60% of the population of Europe, Asia, and North Africa between 1346-1353 and, until now, the original source of this disease has largely gone unsolved.
In their study published in the journal Nature, titled, “The Source of the Black Death in Fourteenth-Century Central Eurasia,” the authors outlined their investigation of cemeteries in the Chüy Valley of modern-day Kyrgyzstan. The tombstone inscriptions showed a disproportionally high number of burials dating between 1338 and 1339 with inscriptions stating “pestilence” as the cause of death.
Archeological evidence combined with ancient DNA analysis of early plague victims enabled scientists to pinpoint the Black Death’s origins in Kyrgyzstan. “We have basically located the origin in time and space, which is really remarkable,” geneticist Johannes Krause, PhD (above), Professor at the Max Planck Institute for Evolutionary Anthropology, who co-led the study, told The Guardian. “We found not only the ancestor of the Black Death, but the ancestor of the majority of the plague strains that are circulating in the world today.” These new research findings may help microbiologists and clinical pathologists gain new insights into how current strains of Yersinia pestis can be better diagnosed. (Photo copyright: Max Planck Institute.)
Big Bang of Plague
Using 30 skeletons that were excavated from these cemeteries in the late 1880s and moved to St. Petersburg, Russia, the scientists analyzed the DNA of ancient pathogens recovered from the remains of seven people. They discovered Yersinia pestis (Y. pestis) DNA in three burials from Kara-Djigach, which lies in the foothills of the Tian Shan mountains.
According to another article in Nature, the scientists showed that a pair of full Y. pestis genomes from their data were direct ancestors of strains linked to the Black Death, and that the Kara-Djigach strain was an ancestor of the vast majority of Y. pestis lineages circulating today.
“It was like a big bang of plague,” Krause stated at a press briefing, Nature reported.
The research team concluded that the Tian Shan region was the location where Y. pestis first spread from rodents to people, and that the local marmot colonies likely the prevalent rodent carriers of plague.
“We found that modern strains [of the plague] most closely related to the ancient strain are today found in plague reservoirs around the Tian Shan mountains, so very close to where the ancient strain was found. This points to an origin of Black Death’s ancestor in Central Asia,” Krause explained in a Max Planck Institute news release.
He told Nature that fleas likely passed the marmot-based infection on to humans, sparking a local Kyrgyzstan epidemic. The disease then spread along the Silk Road trade routes, eventually reaching Europe, where rats (and the fleas that they carried) spread the disease.
Understanding Context of Plague
Writing in The Conversation, Associate Professor of Medieval and Environmental History Philip Slavin, PhD, University of Stirling, who co-authored the study, explained that Kara-Djigach is unlikely to be “the specific source of the pandemic,” but rather that the “disaster started somewhere in the wider Tian Shan area, perhaps not too far from that site,” where marmot colonies were likely the source of the 1338-1339 outbreak.
Making a modern-day comparison, Krause told Nature, “It is like finding the place where all the strains come together, like with coronavirus where we have Alpha, Delta, Omicron all coming from this strain in Wuhan.”
Slavin maintains that understanding the “big evolutionary picture” is key when studying the phenomenon of emerging epidemic diseases.
“It is important to see how these diseases develop evolutionary and historically, and avoid treating different strains as isolated phenomena,” he wrote in The Conversation. “To understand how the diseases develop and get transmitted, it is also crucial to consider the environmental and socioeconomic contexts.”
Scientists have spent centuries debating the source of the Black Death that devastated the medieval world. The multidisciplinary process used by the Slavin/Krause-led team provides a lesson to clinical laboratory managers and pathologists on the important role they play when collaborating with colleagues from different fields on scientific investigations.
Even as Balwani’s trial moves ahead, Hulu’s miniseries ‘The Dropout’ chronicles the pair’s romance and the company’s downfall while providing controversial subject matter for various media outlets
Unlike Theranos founder Elizabeth Holmes’ criminal trial for fraud which generated daily headlines across the nation, the related fraud trial of ex-Theranos COO Ramesh “Sunny” Balwani is not getting the same news coverage. Therefore, media have shifted their reporting to Balwani’s personal relationship with the Holmes, which is clearly having its moment in the media spotlight.
The release of the Hulu miniseries “The Dropout”—which chronicles Holmes’ failed attempt to revolutionize the clinical laboratory industry by developing a device capable of performing multiple clinical blood tests using a finger-stick of blood—created the initial media and TV-viewer buzz.
Now a diverse range of media, including Fortune, The New York Post, and The Guardian, are turning their attention to the former Theranos executives’ private relationship during the time when they were in charge at the failed medical laboratory company.
As “The Dropout” outlines, Holmes gained celebrity status after dropping out of Stanford University at age 19 and founding Theranos in 2003. Years later, when Theranos claimed its Edison blood-testing device could conduct hundreds of blood tests using a finger-prick of blood, the startup’s valuation soared to nearly $9 billion in 2014, making Holmes a billionaire based on her 50% stake in the company, Investopedia reported.
In “What Happened to Elizabeth Holmes and Sunny Balwani? Where the Shamed Theranos Execs are Today,” Fortune used the release of “The Dropout” to publish an update on Holmes and Balwani. The magazine notes Holmes’ family connections—she was a descendant of the founders of America’s first yeast company and the daughter of a former Enron executive and congressional aide—helped her early efforts at fundraising for Theranos.
Fortune also stated that Holmes’ “pedigreed background” enabled her to attract “luminaries” such as former Secretary of State Henry Kissinger and former CDC Director William Foege to the Theranos board and gained her access to high-profile investors.
In U.S. District Court Northern District of California, ex-Theranos president and COO Ramesh “Sunny” Balwani (above) faces charges for allegedly defrauding patients and investors about Theranos. His defense team has attempted to distance their client from the day-to-day decision-making in the clinical laboratory company, while prosecution witnesses are attempting to show Balwani not only invested money in the startup but orchestrated many of the company’s actions. Balwani has pleaded not guilty to all charges. (Photo copyright: David Paul Morris, Fortune.)
Theranos, Holmes Cloaked in Secrecy, according to Fortune
While Holmes sought the spotlight when promoting Theranos, Fortune maintains the company’s work culture and Holmes herself were clocked in secrecy. The article states Holmes hired bodyguards to serve as her chauffeurs, installed bulletproof glass in her office windows, and did not allow workers in separate departments to discuss projects with one another.
Balwani met Holmes in 2002 while both were studying in Beijing as part of a Mandarin language summer program. He was 37 and married at the time, while Holmes was an 18-year-old high school student. Balwani was attending an MBA program at the University of California, Berkeley, which he entered after selling his shares in software company Commerce One in 2000 for nearly $40 million.
The New York Post reported Balwani sold the upscale Silicon Valley home he previously shared with Holmes for $15.8 million this past January. The 6,800-square-foot, five-bedroom, seven-bathroom house in Atherton, Calif., is a one-acre property, which The Post states was purchased by the couple for $9 million in 2013. Balwani bought out Holmes’ 50% stake in 2018.
Aron Solomon, a Chief Legal Analyst for legal marketing firm Esquire Digital, is not surprised by the interest in all things Theranos-related.
“We are seeing a ton of interest following the Holmes trial, and I don’t think it’s going to go away,” he told The Guardian.
Potential Reason for Delay in Holmes’ Sentencing
Holmes was convicted in January on four counts of fraud, but she is not expected to be sentenced until September. Amanda Kramer, JD, a partner in the White Collar Defense and Investigations practice at Covington and Burling, LLP, and a former federal prosecutor, suggests that Holmes’ sentencing date may have been delayed until after Balwani’s trial due to the potential for new information to come to light.
“It’s not typical for a case to be sentenced eight months out, but this is not a typical case in many senses,” Kramer told NPR. “And some facts established in Balwani’s trial might prove to be relevant in Holmes’ sentencing.”
So, it appears clinical laboratory directors and pathologists may find more interesting insights about the problems at Theranos emerging from court testimony when it is time for Holmes to be sentenced and during the remaining days of Balwani’s trial. Stay tuned. Dark Daily will continue to bring you the relevant facts of the case.
Decision is part of UK effort to diagnose 75% of all cancers at stage I or stage II by 2028 and demonstrates to pathologists that the technology used in liquid biopsy tests is improving at a fast pace
Pathologists and medical laboratory scientists know that when it comes to liquid biopsy tests to detect cancer, there is plenty of both hope and hype. Nevertheless, following a successful pilot study at the Christie NHS Foundation Trust in Manchester, England, which ran from 2015-2021, the UK’s National Health Service (NHS) is pushing forward with the use of liquid biopsy tests for certain cancer patients, The Guardian reported.
NHS’ decision to roll out the widespread use of liquid biopsies—a screening tool used to search for cancer cells or pieces of DNA from tumor cells in a blood sample—across the UK is a hopeful sign that ongoing improvements in this diagnostic technology are reaching a point where it may be consistently reliable when used in clinical settings.
The national program provides personalized drug therapies based on the genetic markers found in the blood tests of cancer patients who have solid tumors and are otherwise out of treatment options. The liquid biopsy creates, in essence, a match-making service for patients and clinical trials.
Liquid Biopsy Genetic Testing for Cancer Patients
“The learnings from our original ‘Target’ study in Manchester were that genetic testing needs to be done on a large scale to identify rare genetic mutations and that broader access to medicines through clinical trials being undertaken across the country rather than just one site are required,” Matthew Krebs, PhD, Clinical Senior Lecturer in Experimental Cancer Medicine at the University of Manchester, told The Guardian.
Krebs, an honorary consultant in medical oncology at the Christie NHS Foundation Trust, led the Target National pilot study.
“This study will allow thousands of cancer patients in the UK to access genetic testing via a liquid biopsy. This will enable us to identify rare genetic mutations that in some patients could mean access to life-changing experimental medicines that can provide great treatment responses, where there are otherwise limited or no other treatment options available.”
Detecting cancers at earlier stages of disease—when treatment is more likely to result in improved survival—has become a strategic cancer planning priority in the UK, theBMJ noted.
“The NHS is committed to diagnosing 75% of all cancers at stage I or II by 2028, from around 50% currently,” the BMJ wrote. “Achieving such progress in less than a decade would be highly ambitious, even without disruption caused by the COVID-19 pandemic. In this context, considerable hope has been expressed that blood tests for circulating free DNA—sometimes known as liquid biopsy—could help achieve earlier detection of cancers.”
The Guardian noted that the UK’s initiative will use a liquid biopsy test made by Swiss-healthcare giant Roche.
“We can’t guarantee that we will find a fault in the genetic code of every cancer patient we recruit, or that if we do, there will be a suitable drug trial for them,” Matthew Krebs, PhD (above), lead scientist of the NHS’ Target National pilot study, told The Guardian. “However, as we learn more about the genetics of cancer in this study, it will help doctors and scientists develop new treatments to help people in the future. Ultimately, we hope liquid biopsy testing will be adopted into routine NHS care, but we need studies such as this to show the benefit of the test on a large scale and provide the evidence that patients can benefit from being matched to targeted medicines on the basis of the blood test.” (Photo copyright: Cancer Research UK Manchester Centre.)
In her article “The Promise of Liquid Biopsies for Cancer Diagnosis,” published in the American Journal of Managed Care (AJMC) Evidence-based Oncology, serial healthcare entrepreneur and faculty lecturer at Harvard Medical School Liz Kwo, MD, detailed the optimism surrounding the “revolutionary screening tool,” including its potential for:
identifying mechanisms of resistance to therapies,
measuring remaining disease after treatment,
assessing cancer relapse or resistance to treatment, and
eliminating risk surrounding traditional biopsies.
The AJMC article estimated the liquid biopsy market will be valued at $6 billion by 2030. However, Kwo also noted that clinical adoption of liquid biopsies in the US continues to face challenges.
Welch compared the investor hype surrounding liquid biopsies to that of the now-defunct blood testing company Theranos, which lured high-profile investors to pour millions into its unproven diagnostic technology.
“Effective cancer screening requires more than early detection. It also requires that starting therapy earlier helps people live to older ages than they would if they started treatment later,” he wrote. “If that doesn’t happen, liquid biopsies will only lead to people living longer with the knowledge they have a potentially incurable disease without extending their lives. These people would be subjected to cancer therapies and their toxicities earlier, but at a time when they would otherwise be experiencing no cancer-related signs or symptoms.”
And so, while there’s much excitement about the possibility of a minimally invasive way to detect cancer, anatomic pathology groups and clinical laboratories will have to wait and see if the hype and hope surrounding liquid biopsies is substantiated by further research.
