Technologies developed by Pääbo to sequence Neanderthal DNA are being widely used in many clinical laboratory settings, including to study infectious disease outbreaks
Pääbo is considered to be the founder of paleogenetics. This field of science studies the past through examination of preserved genetic material found in remains of ancient organisms. It was his development of pioneering technologies that allowed for the genomic sequencing of Neanderthal DNA.
“[Pääbo’s] work has revolutionized our understanding of the evolutionary history of modern humans,” said German electrochemist Martin Stratmann, PhD, President of the Max Planck Society for the Advancement of Science (MPG), in a press release. “Svante Pääbo, for example, demonstrated that Neanderthals and other extinct hominids made a significant contribution to the ancestry of modern humans.”
“The thing that’s amazing to me is that you now have some ability to go back in time and actually follow genetic history and genetic changes over time,” Svante Pääbo, PhD (above), director of the Max Planck Institute for Evolutionary Anthropology, stated in a news conference, Reuters reported. “It’s a possibility to begin to actually look on evolution in real time, if you like.” Development of modern clinical laboratory techniques for identifying and tracking disease outbreaks have already evolved due to these findings. (Photo copyright: Max Planck Institute for Evolutionary Anthropology.)
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Comparing Neanderthal DNA to That of Modern Humans
Back in the mid-1990s, Pääbo and a team of researchers decoded relatively short fragments of mitochondrial DNA of a Neanderthal male. They discovered through their analysis that the DNA from the Neanderthal varied considerably from the genome of contemporary humans. This validated the belief that modern humans are not direct descendants of the Neanderthals.
Pääbo’s research team found nearly all (99.9%) of the Neanderthal DNA they studied to be heavily colonized by bacteria and fungi. That required them to create solutions for assembling the short components of mitochondrial DNA like a huge puzzle.
To accomplish this, the team had to:
Work under clean room conditions to prevent the accidental introduction of their own DNA into their experiments.
Establish more efficient extraction methods to enhance the output of Neanderthal DNA.
Generate complex computer programs that could compare the ancient DNA fragments with reference genomes of both humans and chimpanzees.
“Neanderthals are the closest relatives of humans today” said Pääbo in the press release. “Comparisons of their genomes with those of modern humans and with those of apes enable us to determine when genetic changes occurred in our ancestors. In the future, it could also be clarified why modern humans eventually developed a complex culture and technology that enabled them to colonize almost the entire world.”
Pääbo’s team succeeded in reconstructing their first version of the Neanderthal genome in 2010. Their comparisons between the genomes of Neanderthal and modern humans proved that the two groups had produced common offspring about 50,000 years ago and that this genetic contribution did influence human evolution.
The genome of modern non-African people still contains about 2% Neanderthal DNA.
“We have found around 30,000 positions in which the genomes of almost all modern humans differ from those of Neanderthals and great apes,” Pääbo added. “They answer what makes anatomically modern humans ‘modern’ in the genetic sense as well. Some of these genetic changes may be the key to understanding what distinguishes the cognitive abilities of today’s humans from those of now extinct hominids.”
Those with Neanderthal DNA More Susceptible to Severe COVID-19 Infection
Pääbo’s research also found that Neanderthal DNA may have affected the immune systems of modern people. During the COVID-19 pandemic, his work verified that individuals who carry a gene variant inherited from Neanderthals are more prone to severe forms of the illness than those who do not have that gene variant.
“We can make an average gauge of the number of the extra deaths we have had in the pandemic due to the contribution from the Neanderthals,” Pääbo said in a 2022 lecture, Reuters reported. “It is quite substantial, it’s more than one million extra individuals who have died due to this Neanderthal variant that they carry.”
Pääbo’s research team continues to develop new methods for reconstructing DNA fragments that are even more biodegraded, and which present in smaller amounts. Their ultimate goal is to investigate even older DNA and genetic material that is scarce due to climate conditions.
The DNA technologies pioneered by Pääbo to sequence Neanderthal DNA are being used widely in many clinical laboratory and research settings today. They include forensic science and the ability to collect DNA from human remains hundreds of years old to identify infectious disease outbreaks and study how today’s human genome has adopted new mutations.
And in less than eight hours, they had diagnosed a child with a rare genetic disorder, results that would take clinical laboratory testing weeks to return, demonstrating the clinical value of the genomic process
In another major genetic sequencing advancement, scientists at Stanford University School of Medicine have developed a method for rapid sequencing of patients’ whole human genome in as little as five hours. And the researchers used their breakthrough to diagnose rare genetic diseases in under eight hours, according to a Stanford Medicine news release. Their new “ultra-rapid genome sequencing approach” could lead to significantly faster diagnostics and improved clinical laboratory treatments for cancer and other diseases.
“A few weeks is what most clinicians call ‘rapid’ when it comes to sequencing a patient’s genome and returning results,” said cardiovascular disease specialist Euan Ashley, MD, PhD (above), professor of medicine, genetics, and biomedical data science, at Stanford University in the news release. “The right people suddenly came together to achieve something amazing. We really felt like we were approaching a new frontier.” Their results could lead to faster diagnostics and clinical laboratory treatments. (Photo copyright: Stanford Medicine.)
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Need for Fast Genetic Diagnosis
In their NEJM paper, the Stanford scientists argue that rapid genetic diagnosis is key to clinical management, improved prognosis, and critical care cost savings.
“Although most critical care decisions must be made in hours, traditional testing requires weeks and rapid testing requires days. We have found that nanopore genome sequencing can accurately and rapidly provide genetic diagnoses,” the authors wrote.
To complete their study, the researchers sequenced the genomes of 12 patients from two hospitals in Stanford, Calif. They used nanopore genome sequencing, cloud computing-based bioinformatics, and a “custom variant prioritization.”
Their findings included:
Five people received a genetic diagnosis from the sequencing information in about eight hours.
Diagnostic rate of 42%, about 12% higher than the average rate for diagnosis of genetic disorders (the researchers noted that not all conditions are genetically based and appropriate for sequencing).
Five hours and two minutes to sequence a patient’s genome in one case.
Seven hours and 18 minutes to sequence and diagnose that case.
How the Nanopore Process Works
To advance sequencing speed, the researchers used equipment by Oxford Nanopore Technologies with 48 sequencing units called “flow cells”—enough to sequence a person’s whole genome at one time.
The Oxford Nanopore PromethION Flow Cell generates more than 100 gigabases of data per hour, AI Time Journal reported. The team used a cloud-based storage system to enable computational power for real-time analysis of the data. AI algorithms scanned the genetic code for errors and compared the patients’ gene variants to variants associated with diseases found in research data, Stanford explained.
According to an NVIDIA blog post, “The researchers accelerated both base calling and variant calling using NVIDIA GPUs on Google Cloud. Variant calling, the process of identifying the millions of variants in a genome, was also sped up with NVIDIA Clara Parabricks, a computational genomics application framework.”
Rapid Genetic Test Produces Clinical Benefits
“Together with our collaborators and some of the world’s leaders in genomics, we were able to develop a rapid sequencing analysis workflow that has already shown tangible clinical benefits,” said Mehrzad Samadi, PhD, NVIDIA Senior Engineering Manager and co-author of the NEJM paper, in the blog post. “These are the kinds of high-impact problems we live to solve.”
In their paper, the Stanford researchers described their use of the rapid genetic test to diagnose and treat an infant who was experiencing epileptic seizures on arrival to Stanford’s pediatric emergency department. In just eight hours, their diagnostic test found that the infant’s convulsions were attributed to a mutation in the gene CSNK2B, “a variant and gene known to cause a neurodevelopmental disorder with early-onset epilepsy,” the researchers wrote.
“By accelerating every step of this process—from collecting a blood sample to sequencing the whole genome to identifying variants linked to diseases—[the Stanford] research team took just hours to find a pathogenic variant and make a definitive diagnosis in a three-month-old infant with a rare seizure-causing genetic disorder. A traditional gene panel analysis ordered at the same time took two weeks to return results,” AI Time Journal reported.
New Benchmarks
The Stanford research team wants to cut the sequencing time in half. But for now, the five-hour rapid whole genome sequence can be considered by clinical laboratory leaders, pathologists, and research scientists a new benchmark in genetic sequencing for diagnostic purposes.
Stories like Stanford’s rapid diagnosis of the three-month old patient with epileptic seizures, point to the ultimate value of advances in genomic sequencing technologies.
Goal is to demonstrate how whole human genome sequencing of newborns can deliver important diagnostic findings associated with 250 genetic conditions
Clinical laboratory testing and genetics are moving closer to the delivery room than ever before. In the largest study of its kind in North America, genomic scientists plan to supplement traditional screening for inherited diseases—traditionally performed on a blood sample taken shortly after birth—with whole genome sequencing (WGS) on 100,000 newborns in New York City during their first five years of life, LifeSciencesIntelligence reported.
Conducted by genetic scientists at NewYork-Presbyterian (NYP) and Columbia University, in collaboration with genetic company GeneDx, a wholly-owned subsidiary of health intelligence company Sema4 (NASDAQ:SMFR), the genetic research study, called GUARDIAN (Genomic Uniform-screening Against Rare Diseases In All Newborns), will screen newborn babies for 250 rare diseases that are generally not tested for.
The GUARDIAN program will “drive earlier diagnosis and treatment to improve the health of the babies who participate, generate evidence to support the expansion of newborn screening through genomic sequencing, and characterize the prevalence and natural history of rare genetic conditions,” according to a Sema4 news release.
“The appetite for this is growing. The awareness of this is growing. We all see it as inevitable,” medical geneticist Robert Green, MD, at Brigham and Women’s Hospital and Harvard Medical School told USA Today. “We are grossly underutilizing the life-saving benefits of genetics and we have to get past that.” Clinical laboratory leaders understand the value of early detection of disease and subsequent early treatment. (Photo copyright: Harvard Medical School.)
Improving Health of Babies Through Early Detection of Disease
GUARDIAN aims to use WGS to identify conditions at birth that can affect long-term health and subsequently enhance treatment options and possibly prevent disability or death.
The 250 different diseases GUARDIAN will be screening for typically strike young children. They are mostly rare conditions that:
have an onset before five years of age,
have a greater than 90% probability of the condition developing based on the genetic result,
have effective approaches and treatments that are already available, and/or
have a well-established natural history of the condition.
“We’re entering the therapeutic era and leaving the diagnostic era,” Paul Kruszka, MD, Chief Medical Officer at GeneDx told USA Today. “This potentially has the opportunity to change the way we practice medicine, especially in rare disease.”
Some Parents Reluctant to Agree to Genetic Testing
Green and his research team first began analyzing the genetic sequences of newborns back in 2013. They believe the costs of performing infant WGS is worthwhile because it can improve lives. However, Green also recognizes that some parents are reluctant to agree to this type of genetic testing due to concerns regarding privacy and the fear of discovering their baby may have an illness.
“You’ve gone through all this pregnancy and you’re sitting there with a healthy baby (and I’m) offering you the opportunity to find out something that’s devastating and terrifying,” he told USA Today. “How fun is that?”
Green continued. “We can respect people who don’t want to know, but also respect people who do want to know. Some families will say ‘I treasure the precious ignorance.’ Others will say ‘If I could have known, I would have poured my heart and soul into clinical trials or spent more time with the child when she was healthy.’”
WGS Screening Identifies Undiagnosed Illnesses in Newborn’s Family
The scientists also found that performing WGS in newborns can detect diseases in the infants as well as unknown illnesses in the families of those babies. According to Kruszka, many parents often seek a diagnosis for a rare disease present in their children for several years. Since many common diseases develop as a result of certain combinations of genes, if illnesses are diagnosed at birth, it could extradite the treatment process, prevent complications, and provide better health outcomes for patients.
“We are relentlessly focused on accelerating the adoption and use of genomic information to impact the lives of as many people as possible, particularly newborns and children,” said Katherine Stueland, President and CEO, Sema4, in the Sema4 news release. “As the first commercial laboratory to launch a rapid whole genome sequencing offering, to address broad unmet needs for early diagnosis, participation in this study is an important step forward for healthcare and in delivering on our goal to sequence once, analyze forever.”
The study is open to all babies in New York City who are born in a health system that participates in the GUARDIAN program, regardless of their race, income, or health insurance coverage.
“The results from this study will help us understand the true impact sequencing at birth can have on newborns and their families in comparison to the current standard of care, particularly as we’ll evaluate clinical outcomes in addition to the psychosocial effect on families,” said Kruszka in the Sema4 news release.
Anything that improves the health of newborn babies is a good thing. Regardless of the cost, if DNA analysis can give newborns and their families a better chance at detecting inherited diseases early while clinical laboratory treatment could make a difference, it is worth pursuing.
Regulators and lawmakers are considering proposed changes to CLIA and PAMA involving medical laboratory services
Clinical laboratories and pathology groups should monitor a series of federal regulatory developments underway this fall. The proposals and documents will potentially affect how lab managers and staff do their jobs and how much Medicare reimbursement medical laboratories receive for certain diagnostic tests next year.
Among the initiatives under consideration are the following:
Below are details about these laboratory-related federal bills and regulatory documents that observant laboratory managers will want to track in the coming months.
“Clinical laboratories need to make sure that they have proper requisitions and documentation for genetic testing that involves telemedicine.” Danielle Tangorre, JD (above), a partner at law firm Robinson and Cole LLP in Albany, NY, told Dark Daily. (Photo copyright: Robinson and Cole LLP.)
CLIA Fee Increases and Testing Personnel Changes
The federal Centers for Medicare and Medicaid Services (CMS) is examining fee and personnel changes for CLIA. Officials from CMS are reviewing public comments on the proposal ahead of publishing a final rule.
Among other changes, the proposal would:
Institute a 20% across-the-board increase on existing fees.
Establish a biennial increase of CLIA fees for follow-up surveys, substantiated complaint surveys, and revised certificates.
Add doctoral, master’s, and bachelor’s degrees in nursing to qualify testing personnel for high and moderate complexity testing.
“The Practitioner does not have sufficient contact with or information from the purported patient to meaningfully assess the medical necessity of the items or services ordered or prescribed.
“The Telemedicine Company compensates the Practitioner based on the volume of items or services ordered or prescribed, which may be characterized to the Practitioner as compensation based on the number of purported medical records that the Practitioner reviewed.
“The Telemedicine Company only furnishes items and services to Federal health care program beneficiaries and does not accept insurance from any other payor.
“The Telemedicine Company does not expect Practitioners (or another Practitioner) to follow up with purported patients nor does it provide Practitioners with the information required to follow up with purported patients (e.g., the Telemedicine Company does not require Practitioners to discuss genetic testing results with each purported patient).”
And more.
“In the telehealth space, the issue the OIG has flagged is that genetic tests are being ordered without patient interaction or with only brief telephonic conversations,” Danielle Tangorre, JD, a partner at law firm Robinson & Cole LLP in Albany, N.Y., told Dark Daily.
New Bill May Eliminate 2023 Medical Laboratory Payment Cuts Under PAMA
Medical labs and pathology groups face payment cuts of up to 15% for 800 lab tests on the Medicare Clinical Lab Fee Schedule (CLFS) on Jan. 1, 2023, as part of PAMA.
The bill proposes to move regulatory oversight of LDTs from CLIA to the federal Food and Drug Administration (FDA). Champions of the bill argue that FDA regulation is needed for in vitro clinical tests (IVCTs) because they are similar to medical devices and bring with them patient safety concerns.
The bill seemed ready for a Senate vote over the summer but stalled. On Sept. 30, Congress passed a short-term resolution to keep the federal government funded. During negotiation, the VALID Act was removed from the larger spending package, according to Boston law firm Ropes and Gray.
Expect discussion to renew in Congress about the VALID Act after the mid-term elections.
Clinical laboratory leaders and pathology group managers will want to closely monitor the progress of these four federal legislative and regulatory developments. Each of the possible actions described above would significantly change the status quo in the compliance requirements and reimbursement arrangements for both clinical laboratory testing and anatomic pathology services.
Proof-of-concept study ‘highlights that using AI to integrate different types of clinically informed data to predict disease outcomes is feasible’ researchers say
Artificial intelligence (AI) and machine learning are—in stepwise fashion—making progress in demonstrating value in the world of pathology diagnostics. But human anatomic pathologists are generally required for a prognosis. Now, in a proof-of-concept study, researchers at Brigham and Women’s Hospital in Boston have developed a method that uses AI models to integrate multiple types of data from disparate sources to accurately predict patient outcomes for 14 different types of cancer.
The process also uncovered “the predictive bases of features used to predict patient risk—a property that could be used to uncover new biomarkers,” according to Genetic Engineering and Biotechnology News (GEN).
Should these research findings become clinically viable, anatomic pathologists may gain powerful new AI tools specifically designed to help them predict what type of outcome a cancer patient can expect.
“Experts analyze many pieces of evidence to predict how well a patient may do. These early examinations become the basis of making decisions about enrolling in a clinical trial or specific treatment regimens,” said Faisal Mahmood, PhD (above) in a Brigham press release. “But that means that this multimodal prediction happens at the level of the expert. We’re trying to address the problem computationally,” he added. Should they be proven clinically-viable through additional studies, these findings could lead to useful tools that help anatomic pathologists and clinical laboratory scientists more accurately predict what type of outcomes cancer patient may experience. (Photo copyright: Harvard.)
AI-based Prognostics in Pathology and Clinical Laboratory Medicine
The team at Brigham constructed their AI model using The Cancer Genome Atlas (TCGA), a publicly available resource which contains data on many types of cancer. They then created a deep learning-based algorithm that examines information from different data sources.
Pathologists traditionally depend on several distinct sources of data, such as pathology images, genomic sequencing, and patient history to diagnose various cancers and help develop prognoses.
For their research, Mahmood and his colleagues trained and validated their AI algorithm on 6,592 H/E (hematoxylin and eosin) whole slide images (WSIs) from 5,720 cancer patients. Molecular profile features, which included mutation status, copy-number variation, and RNA sequencing expression, were also inputted into the model to measure and explain relative risk of cancer death.
The scientists “evaluated the model’s efficacy by feeding it data sets from 14 cancer types as well as patient histology and genomic data. Results demonstrated that the models yielded more accurate patient outcome predictions than those incorporating only single sources of information,” states a Brigham press release.
“This work sets the stage for larger healthcare AI studies that combine data from multiple sources,” said Faisal Mahmood, PhD, Associate Professor, Division of Computational Pathology, Brigham and Women’s Hospital; and Associate Member, Cancer Program, Broad Institute of MIT and Harvard, in the press release. “In a broader sense, our findings emphasize a need for building computational pathology prognostic models with much larger datasets and downstream clinical trials to establish utility.”
Future Prognostics Based on Multiple Data Sources
The Brigham researchers also generated a research tool they dubbed the Pathology-omics Research Platform for Integrative Survival Estimation (PORPOISE). This tool serves as an interactive platform that can yield prognostic markers detected by the algorithm for thousands of patients across various cancer types.
The researchers believe their algorithm reveals another role for AI technology in medical care, but that more research is needed before their model can be implemented clinically. Larger data sets will have to be examined and the researchers plan to use more types of patient information, such as radiology scans, family histories, and electronic medical records in future tests of their AI technology.
“Future work will focus on developing more focused prognostic models by curating larger multimodal datasets for individual disease models, adapting models to large independent multimodal test cohorts, and using multimodal deep learning for predicting response and resistance to treatment,” the Cancer Cell paper states.
“As research advances in sequencing technologies, such as single-cell RNA-seq, mass cytometry, and spatial transcriptomics, these technologies continue to mature and gain clinical penetrance, in combination with whole-slide imaging, and our approach to understanding molecular biology will become increasingly spatially resolved and multimodal,” the researchers concluded.
Anatomic pathologists may find the Brigham and Women’s Hospital research team’s findings intriguing. An AI tool that integrates data from disparate sources, analyzes that information, and provides useful insights, could one day help them provide more accurate cancer prognoses and improve the care of their patients.
Clinical laboratories and pathology groups can benefit from knowing how genetic testing is being used for other than medical testing purposes
It is useful for pathologists and clinical laboratory managers to be aware of the different ways genetic testing and DNA sequencing is being conducted. That’s because a genetic test for one purpose—such as identifying an individual’s relatives and connection to a region or a cultural group—might generate data that could become part of that person’s medical care.
Thus, an ongoing genetic study in South Africa highlighting the issue of so-called “helicopter research” will be informative for Dark Daily’s readers.
Also known as “neo-colonial science,” helicopter research describes when scientists from wealthy countries perform research in lower-income countries in ways that may be deemed exploitative or disrespectful to local populations.
“Scientists conduct helicopter research when they collect data from developing countries and marginalized communities with little to no involvement from local researchers and community members,” wrote researchers Dana Al-Hindi, and Brenna Henn PhD, in an article for The Conversation. “Helicopter research also occurs when researchers take data out of the country they collected it from without either providing benefit to or sharing the results with the community.”
In an article for The Conversation, UC Davis researchers Brenna Henn, PhD (left), and Dana Al-Hindi (right), wrote, “While we have learned a great deal from these communities, we have been unable to fulfill a common request: providing them their individual genetic ancestry result. In our attempts to overcome the logistical challenges of providing this information, we’ve grappled with the common question of how to ensure an equitable balance of benefits between researchers and the community they study. What we’ve found is that there is no easy answer.” Clinical laboratories will want to remember the term “Helicopter Research” in relation to these types of studies. (Photos copyright: UC Davis/The Conversation.)
The South Africa study, conducted over the past 12 years, aims to use genetic data “to help unravel the history and prehistory of southern Africans and their relationship to populations around the world,” the authors wrote in The Conversation.
The researchers have been using the genetic data to trace the ancestry of indigenous Khoekhoe and San peoples in South Africa as well as other populations that self-identify as “Colored.”
“Early European colonizers initially used this term to refer to indigenous Khoekhoe and San groups long before it was codified by the apartheid government in 1948,” the researchers wrote. “It persists today as an ethnic category, broadly encompassing Khoe-San groups, various East African, Indian, and Southeast Asian populations brought by the slave trade, and people of mixed ancestry.”
Challenges Sharing Genetic Data with Study Participants
Participants in the study have asked to see their personal genetic ancestry results, but the researchers noted several challenges, including local restrictions and the difficulty of presenting complex data in “an accessible and digestible form.” So, the researchers partnered with consumer-focused genetic testing company 23andMe (NASDAQ:ME).
23andMe provided additional funding for the research, assisted the researchers in community outreach, and “expanded our ability to ‘capacity-build’—that is, to make sure that the knowledge and skills we gain are shared with local institutions,” Henn and Al-Hindi wrote in The Conversation. They added that they are still dealing with questions about whether their efforts to provide equitable benefits are sufficient.
“Our research team, local collaborators, and 23andMe are all concerned about how to best address the risk of helicopter research, coercion, and any unknown risks that may arise from disclosing personal ancestry results,” they wrote.
Cape Town Statement on Fostering Research Integrity
The issue of helicopter research was a major focus at the 7th World Conference on Research Integrity (WCRI), held May 29-June 1 in Cape Town, South Africa. It was the first WCRI to be held in Africa and adopted the theme “Fostering Research Integrity in an Unequal World.”
One outcome of the conference will be an effort to produce what is known as the Cape Town Statement on Fostering Research Integrity. The statement will “highlight the importance of fairness in international research partnerships,” noted Research Professional News.
The statement “compels institutions and researchers alike to act on their responsibilities to promote equity, diversity, and fairness in research partnerships,” conference speaker Retha Visagie, DCur, told the publication. She leads the Research Integrity Office at the University of South Africa.
Conference co-chair Lyn Horn, PhD, director the Office of Research Integrity at the University of Cape Town, told the publication that it could take up to a year before a draft of the statement is ready for comment.
One overarching goal will be to “demonstrate why inequity and unfair practices in research collaborations and contexts is a research integrity (RI) matter,” the authors wrote. “Second it must identify some key values or principles and action guides that will address the issue of equity and fairness in research within the context of the complete research life cycle from research agenda setting and call to proposal development, through grant application, allocation and management of funding, data production, analysis, management and sharing, to outputs, translation, and evaluation.”
Another conference speaker, Francis Kombe PhD, told attendees the statement will offer guidance specifically to institutions such as universities, journals, and funding organizations, the journal Science reported. That stands in contrast to earlier statements on helicopter research, which were geared more toward individuals and small groups.
How any of this will impact clinical laboratories and pathology groups remains unclear. Nevertheless, it is worthwhile knowing how gene sequencing is being used by researchers for purposes other than to guide diagnoses and treatment of patients.
