Not the first smart diaper to come along, but consumers seem unready for diapers that can flag urinary tract infections and other biomarkers usually tested by clinical laboratories
Will wonders never cease? For centuries, parents had only their own senses to determine when infants needed diaper changing. Today, however, caregivers can rely on “smart diapers” to send alerts when a diaper is soiled. Crying, smelly babies may no longer be the gold standard in diaper management. But are smart diapers practical?
The sensor array is “so cheap and simple” it “could clear the way for wearable, self-powered health monitors for use not only in ‘smart diapers’ but also to predict major health concerns like cardiac arrest and pneumonia,” a Penn State new release noted.
However, clinical laboratory managers following similar developments probably know that this is not the first scientific effort to develop a smart diaper that uses some type of sensor to detect a biomarker and issue an alert to the wearer or caregivers.
“Our team has been focused on developing devices that can capture vital information for human health,” said Huanyu “Larry” Cheng, PhD (above), the James L. Henderson, Jr. Memorial Associate Professor of Engineering Science and Mechanics at Penn State in a news release. “The goal is early prediction for disease conditions and health situations, to spot problems before it is too late.” This is yet another example of how researchers are working to take more testing out of clinical laboratories and offer unique assays that can be used as wearables—whether as a diaper, a skin patch, or a smart watch. (Photo copyright: Penn State University.)
This Smart Diaper Is as Simple to Use as Paper and Pencil
The Penn State sensor array takes advantage of how paper naturally reacts to wetness and utilizes the graphite in pencil marking to interact with the water molecules and sodium chloride.
Once the water molecules are absorbed by the paper, the sodium chloride solution becomes ionized and electrons start to stream towards the graphite. This movement sets off the sensor, which is extremely sensitive to humidity. According to the study, the sensor can provide accurate readings over a wide range of humidity levels, from 5.6% to 90%.
“We wanted to develop something low-cost that people would understand how to make and use, and you can’t get more accessible than pencil and paper,” said Li Yang, PhD, a professor in the School of Artificial Intelligence at China’s Hebei University of Technology and one of the authors of the study, in the Penn State news release.
“You don’t need to have some piece of multi-million-dollar equipment for fabrication. You just need to be able to draw within the lines of a pre-drawn electrode on a treated piece of paper. It can be done simply and quickly.”
The diaper is connected to a tiny lithium battery. When the sensor recognizes an increase in humidity the battery powers transmission of the change to a smartphone via Bluetooth technology. This notification informs caregivers that it is time to change the diaper.
“That application was actually born out of personal experience,” explained Huanyu “Larry” Cheng, PhD, James L. Henderson, Jr. Memorial Associate Professor of Engineering Science and Mechanics at Penn State, one of the authors of the study and father to two young children. “There’s no easy way to know how wet is wet, and that information could be really valuable for parents. The sensor can provide data in the short-term, to alert for diaper changes, but also in the long-term, to show patterns that can inform parents about the overall health of their child.”
Do Consumers Want Smart Diapers?
Research into such wearable sensors has been gaining momentum in the scientific community as a novel way to detect and deal with several medical conditions. The Penn State team hopes that devices such as their smart diaper can be used in the future to alert caregivers about the overall health of their children and clients.
“Our team has been focused on developing devices that can capture vital information for human health,” Cheng said. “The goal is early prediction for disease conditions and health situations, to spot problems before it is too late.”
Previous research teams have had similar smart diaper goals.
However, these types of products have yet to gain significant popularity with consumers. Regardless, sales projections for smart diapers remain positive.
According to a MarketsandMarkets report, the smart diaper market, estimated to be $646 million (US) in 2021, is expected to surpass $1.5 billion by 2026. The demand for smart diapers, the report notes, is increasing due to:
Growing elderly populations,
Rising disposable incomes,
Increasing personal hygiene awareness,
Growing populations in emerging countries, and
Expanding preference for advanced technology when it comes to health.
So, it’s uncertain if consumers are now ready for a device in their baby’s diaper telling them it’s time for a change. Regardless, researchers will likely continue developing tools that combine new diagnostics with existing products to help people better understand and monitor their health and the health of their loved ones.
Meanwhile, clinical laboratory managers and pathologists can remain on the alert for future published studies and press releases announcing new wearable items containing sensors, such as smart diapers. The unanswered question is whether both consumers and healthcare professionals will consider these novel inventions useful devices in the care of young and old alike.
Another study in the United Kingdom that also used genomic analysis to understand drug-resistant Shigella produced findings that may be useful for microbiologists and medical laboratory scientists
From the onset of an infectious disease outbreak, public health officials, microbiologists, and clinical laboratory managers find it valuable to trace the origin of the spread back to the “index case” or “patient zero”—the first documented patient in the disease epidemic. Given the decreased cost of genomic analysis and improved accuracy of gene sequencing, infectious disease researchers are finding that task easier and faster than ever.
One recent example is a genomic study conducted at University of Washington (UW) in Seattle that enabled researchers to “retrace” the origin and spread of a “multidrug-resistant Shigellosis outbreak” from 2017 to 2022. “The aim of the study was to better understand the community transmission of Shigella and spread of antimicrobial resistance in our population, and to treat these multi-drug resistant infections more effectively,” the UW scientists stated in a new release.
Shigellosis (aka, bacillary dysentery) is a highly contagious disease of the intestines that can lead to hospitalization. Symptoms include fever, stomach cramps, diarrhea, dysentery, and dehydration.
“Additional analysis of the gut pathogen and its transmission patterns helped direct approaches to testing, treatment, and public health responses,” the UW news release states.
Usually prevalent in countries with public health and sanitation limitations, the “opportunistic” Shigella pathogen is now being seen in high-income countries as well, UW reported.
“You can’t really expect an infectious disease to remain confined to a specific at-risk population. [Shigella infections are] very much an emerging threat and something where our public health tools and therapeutic tools have significant limitations,” infectious disease specialist Ferric Fang, MD (above) told CIDRAP News. Fang is a UW professor of Microbiology and Clinical Laboratory Medicine and a corresponding author of the UW study. (Photo copyright: University of Washington.)
Generally, Shigella infects children, travelers, and men who have sex with men (MSM), the CDC noted.
The UW researchers were motivated to study Shigella when they noticed an uptick in drug-resistant shigellosis cases in Seattle’s homeless population in 2020 at the beginning of the COVID-19 pandemic, Center for Infectious Disease Research and Policy News (CIDRAP News) reported.
“Especially during the pandemic, a lot of public facilities were closed that homeless people were used to using,” infectious disease specialist Ferric Fang, MD, told CIDRAP News. Fang is Professor of Microbiology and Laboratory Medicine at University of Washington and corresponding author of the UW study.
The researchers studied 171 cases of Shigella identified from 2017 to 2022 by clinical laboratories at Harborview Medical Center and UW Medical Center in Seattle. According to CIDRAP News, the UW researchers found that:
46% were men who have sex with men (MSM).
51% were people experiencing homelessness (PEH).
Fifty-six patients were admitted to the hospital, with eight to an intensive care unit.
51% of isolates were multi-drug resistant (MDR).
Whole-Genome Sequencing Reveals Origin
The UW scientists characterized the stool samples of Shigella isolates by species identification, phenotypic susceptibility testing, and whole-genome sequencing, according to their Lancet Infectious Diseases paper. The paper also noted that 143 patients received antimicrobial therapy, and 70% of them benefited from the treatment for the Shigella infection.
Whole-genome sequencing revealed that two strains of Shigella (S. flexneri and S. sonnei) appeared first in Seattle’s MSM population before infecting the PEM population.
The genomic analysis found the outbreak of drug-resistant Shigella had international links as well, according to CIDRAP News:
One S. flexneri isolate was associated with a multi-drug resistant (MDR) strain from China, and
S. sonnei isolates resembled a strain characteristic of a current outbreak of MDR Shigella in England.
“The most prevalent lineage in Seattle was probably introduced to Washington State via international travel, with subsequent domestic transmission between at-risk groups,” the researchers wrote.
“Genomic analysis elucidated not only outbreak origin, but directed optimal approaches to testing, treatment, and public health response. Rapid diagnostics combined with detailed knowledge of local epidemiology can enable high rates of appropriate empirical therapy even in multidrug-resistant infection,” they continued.
UK Shigella Study Also Uses Genomics
Another study based in the United Kingdom (UK) used genomic analysis to investigate a Shigella outbreak as well.
Motivated by a UK Health Security Agency report of an increase in drug-resistance to common strains since 2021, the UK researchers studied Shigella cases from September 2015 to June 2022.
According to a paper they published in Lancet Infectious Diseases, the UK researchers “reported an increase in cases of sexually transmitted S. flexneri harboring blaCTX-M-27 (an antibiotic-resistant gene) in England, which is known to confer resistance to third-generation cephalosporins (antibiotics),” the researchers wrote.
Their analysis of plasmids (DNA with genes having antibiotic resistance) revealed a link in two drug-resistant Shigella strains at the same time, CIDRAP News explained.
“Our study reveals a worsening outlook regarding antimicrobial-resistant Shigella strains among MSM and highlights the value of continued integration of genomic analysis into surveillance and research,” the UK-based scientists wrote.
Current challenges associated with Shigella, especially as it evades treatment, may continue to demand attention from microbiologists, clinical laboratory scientists, and infectious disease specialists. Fortunately, use of genomic analysis—due to its ongoing improvements that have lowered cost and improved accuracy—has made it possible for public health researchers to better track the origins of disease outbreak and spread.
But even though the College of American Pathologists (CAP) and nine other organizations signed a December 12 stakeholder letter to leaders of key House and Senate committees urging passage of legislation that would enable some regulation of LDTs, the VALID Act was ultimately omitted from the year-end omnibus spending bill (H.R. 2617).
That may be due to pressure from organizations representing clinical laboratories and pathologists which lobbied hard against the bill.
Responding to criticism of its stance on FDA oversight of LDTs, in a May 2022 open letter posted on the organization’s website, anatomic pathologist and CAP president Emily Volk, MD, said “we at the CAP have an honest difference of opinion with some other respected laboratory organizations. … We believe the VALID Act is the only viable piece of legislation addressing the LDT issue. … the VALID Act contains many provisions that are similar to policy the CAP has advocated for regarding the regulation of laboratory tests since 2009. Importantly, the current version includes explicit protections for pathologists and our ability to practice medicine without infringement from the Food and Drug Administration (FDA).” (Photo copyright: College of American Pathologists.)
Organizations on Both Sides Brought Pressure to Bear on Legislators
The AAMC and AMP were especially influential, Bucshon told ProPublica. In addition to spending hefty sums on lobbying, AMP urged its members to contact legislators directly and provided talking points, ProPublica reported.
“The academic medical centers and big medical centers are in every state,” Bucshon said. As major employers in many locales, they have “a pretty big voice,” he added.
Discussing CAP’s reasoning behind its support of the VALID Act in a May 26 open letter and podcast, CAP president Emily Volk, MD, said the Valid Act “creates a risk-based system of oversight utilizing three tiers—low, moderate and high risk—in order to target the attention of the FDA oversight.”
While acknowledging that it had room for improvement, she lauded the bill’s three-tier risk-based system, in which tests deemed to have the greatest risks would receive the highest level of scrutiny.
She also noted that the bill exempts existing LDTs from an FDA premarket review “unless there is a safety concern for patients.” It would also exempt “low-volume tests, modified tests, manual interpretation tests, and humanitarian tests,” she wrote.
In addition, the bill would “direct the FDA not to create regulations that are duplicative of regulation under CLIA,” she noted, and “would require the FDA to conduct public hearings on LDT oversight.”
Pros and Cons of the VALID Act
One concern raised by opponents relates to how the VALID Act addressed user fees paid by clinical laboratories to fund FDA compliance activities. But Volk wrote that any specific fees “would need to be approved by Congress in a future FDA user fee authorization bill after years of public input.”
During the May 2022 podcast, Volk also cast CAP’s support as a matter of recognizing political realities.
“We understand that support for FDA oversight of laboratory-developed tests or IVCTs is present on both sides of the aisle and in both houses of Congress,” she said. “In fact, it enjoys wide support among very influential patient advocacy groups.” These groups “are very sophisticated in their understanding of the issues with laboratory-developed tests, and they do have the ear of Congress. There are many in the laboratory community that believe the VALID Act goes too far, but I can tell you that many of these patient groups don’t believe it goes far enough and are actively pushing for even more restrictive paradigms.”
Also urging passage of the bill were former FDA commissioners Scott Gottlieb, MD, and Mark B. McClellan, MD, PhD. In a Dec. 5 opinion piece for STAT, they noted that “diagnostic technologies have undergone considerable advances in recent decades, owing to innovation in fields like genomics, proteomics, and data science.” However, they wrote, laws governing FDA oversight “have not kept pace,” placing the agency in a position of regulating tests based on where they are made—in a medical laboratory or by a manufacturer—instead of their “distinctive complexity or potential risks.”
In their May 22 letter, opponents of the legislation outlined broad areas of concern. They contended that it would create “an onerous and complex system that would radically alter the way that laboratory testing is regulated to the detriment of patient care.” And even though existing tests would be largely exempted from oversight, “the utility of these tests would diminish over time as the VALID Act puts overly restrictive constraints on how they can be modified.”
CLIA Regulation of LDTs also Under Scrutiny
The provision to avoid duplication with the Clinical Laboratory Improvement Amendments (CLIA) program—which currently has some regulatory oversight of LDTs and IVCTs—is “insufficient,” opponents added, “especially when other aspects of the legislation call for requirements and activities that lead to duplicative and unnecessary regulatory burden.”
Opponents to the VALID Act also argued that the definitions of high-, medium-, and low-risk test categories lacked clarity, stating that “the newly created definition of moderate risk appears to overlap with the definition of high risk.”
The opponents also took issue with the degree of discretion that the bill grants to the US Secretary of Health and Human Services. This will create “an unpredictable regulatory process and ambiguities in the significance of the policy,” they wrote, while urging the Senate committee to “narrow the discretion so that stakeholders may better evaluate and understand the implications of this legislation.”
Decades ago, clinical laboratory researchers were allowed to develop assays in tandem with clinicians that were intended to provide accurate diagnoses, earlier detection of disease, and help guide selection of therapies. Since the 1990s, however, an industry of investor-funded laboratory companies have brought proprietary LDTs to the national market. Many recognize that this falls outside the government’s original intent for encouragement of laboratory-developed tests to begin with.
Coordinating at-home testing for monkeypox may provide opportunities for clinical laboratories to add value for their physician clients
Microbiologists and clinical laboratory managers who oversee medical laboratory tests for monkeypox (aka, mpox) will be interested to learn that, according to the US Centers of Disease Control (CDC), cases per day have dropped into the single digits.
The United States led the world in cases during the 2022-2023 outbreak, according to the most recent CDC statistics. As of February 15, the US has reported 30,193 cases of monkeypox with 32 deaths.
Nevertheless, January 31 was the day that the US public health emergency involving monkeypox officially expired. Data from the World Health Organization shows the number of daily monkeypox cases in most countries around the world is declining, although numbers of cases are still increasing in some South American countries.
The global monkeypox outbreak appears to have slowed considerably, but are we out of the woods?
“There were concerns that there would be ongoing transmission and that ongoing transmission would become endemic in the United States like other STIs: gonorrhea, chlamydia, syphilis. We have not seen that occur,” Jonathan Mermin, MD (above), Director of the National Center for HIV, Viral Hepatitis, STD, and TB Prevention at the CDC, told CNN.”We are now seeing three to four cases a day in the United States, and it continues to decline. And we see the possibility of getting to zero as real.” This decline in monkeypox test corresponds with a similar decline in COVID-19 clinical laboratory testing as well. (Photo Copyright: CDC.)
Untried Vaccine and At-home Testing for Monkeypox
When the monkeypox outbreak began in May of 2022, there were concerns about the US’ level of preparedness for dealing with a second pandemic while also battling COVID-19. But monkeypox was not entirely unknown to the scientific and medical communities.
Monkeypox first appeared in 1958 amongst a colony of monkeys being kept for research. The origin of the disease is not known. According to the CDC, the first reported human case of monkeypox was in 1970. Prior to the 2022 outbreak, most cases were found in central and western African countries. Cases outside of those areas could be traced back to travel from those specific countries.
When cases of monkeypox first appeared in the US, public health officials were concerned about the availability of testing, vaccines, and treatments. As CNN reported, though there was a new vaccine available, its effectiveness against monkeypox had never been tested on humans.
That treatment, known as TPOXX (Tecovirimat), was an antiviral drug approved by the FDA in 2018 to treat smallpox in adults and children, according to an FDA factsheet. The drug was difficult to obtain, and it took until August of 2022 for the federal government to declare monkeypox a public health emergency. That allowed it to deploy emergency funds towards fighting the outbreak.
The demographic found to be at the highest risk of monkeypox infection were men who have sex with other men. According to MedPage Today, “Daskalakis had both pandemic experience as former senior lead on equity in COVID-19 data and engagement for the New York City Department of Health and Mental Hygiene and an ‘in’ with the LGBTQ+ community from his work in HIV prevention and his transparency about being a gay man.”
When comparing monkeypox to HIV, Daskalakis said, “This one [monkeypox], you don’t have to change behaviors for generations; it’s for a few months. Once you build your force field of immunity with vaccines, people can make their own informed decisions about their risk.”
Opportunities for Clinical Laboratories
So, how should clinical laboratories respond if there’s another monkeypox flare up?
Daskalakis advocates for home testing. “People that are going to order home tests are going to be motivated to action in other ways. And so, thinking about HIV home testing, which was the grandparent of COVID-19 home testing, this really shows us how you reach people you’re not going to reach when you have lab-based, provider-only testing … When you look at the HIV home testing data from the CDC, 26% of the people that ordered a home test had never been tested before. That is way higher than what you would expect,” he told MedPage Today.
We are not out of the woods in regard to monkeypox, vigilance is still required. But with existing harm reduction measures in the most vulnerable community, at-home testing and advancements in vaccines could help us keep our numbers as low as possible.
Recent intrusions into the hospitals’ IT systems resulted in blocked medical records including medical laboratory data
Healthcare cyberattacks continue to be a threat that bring potentially costly business consequences for clinical laboratories. Just in the past month, two hospital systems had their health information technology (HIT) systems disrupted due to security incidents. In response, the hospitals’ medical laboratories were forced to switch from digital to paper documentation and, in at least one case, the organization reportedly had difficulty accessing electronic laboratory test results.
At Tallahassee Memorial, an “IT security issue” on Feb. 2 resulted in the organization shutting down its IT systems for 13 days, including at its clinical laboratory. The hospital’s computer network went back online on Feb. 15, according to a news release.
At Atlantic General Hospital, according to an AGH news release, IT personnel discovered a ransomware attack on Jan. 29 that affected the hospital’s central computer system. As a result, the walk-in outpatient laboratory was closed until Feb. 14.
These recent cyberattacks underscore the importance for clinical laboratory leaders to have plans and procedures already in place prior to a disruption in access to critical patient data.
Healthcare cyberattacks can be a “complete blindside for a lot of organizations that think they have protections in place because they bought a product or they developed a policy,” said Ben Denkers (above), Chief Innovation Officer at CynergisTek, an Austin, Texas-based cybersecurity company, in an exclusive interview with The Dark Report. Since clinical laboratory test results make up about 80% of a patient’s medical records, disruption of a hospital’s IT network can be life threatening. (Photo copyright: The Dark Report.)
Laboratory Staff Unable to View Digital Diagnostic Results at Tallahassee Memorial
Though the exact nature of the incident at Tallahassee Memorial HealthCare has not been divulged, hospital officials did report the incident to law enforcement, which suggests a cyberattack had occurred.
Electronic laboratory test results were among the casualties of the IT difficulties at TMH. “Staff have been unable to access digital patient records and lab results because of the shutdown,” a source told CNN.
Attempts by Dark Daily to reach a medical laboratory manager for comment at TMH were unsuccessful. However, in a news release posted online shortly after the cyberattack, the health system advised staff members on dealing with the IT outages.
“Patients and families may notice the switch to paper documentation during registration, admission, or during their care, as our providers will be using paper forms, prescription pads, handwritten notes, or other similar paper methods where they may usually use an electronic process,” the news release stated. “We apologize for any delays this may create. We practice for situations like this, and we are prepared to provide safe, high-quality care to our patients during computer system downtimes.”
Atlantic General Hospital Reports Ransomware Incident to the FBI
At Atlantic General Hospital, the outpatient walk-in laboratory and outpatient imaging department both temporarily closed because of the ransomware attack.
Staff members throughout the hospital were “forced to manually check patients in and out of appointments and record all other information by hand instead of online,” Ocean City Today reported.
The hospital immediately informed the FBI of the ransomware incident and continues to work with an incident response team to determine whether criminals accessed any sensitive data. It was not clear whether the organization ultimately paid a ransom to unlock its systems.
The hospital’s medical laboratory director did not respond to an email from Dark Daily seeking further comment.
Healthcare Cyberattacks Attempt to Gain Access to Data
Therefore, it is critical that clinical laboratory and hospital staff work with their IT counterparts to verify that technology and processes are in place to protect access to patient data.
In “Labs Must Audit Their Cybersecurity Measures,” Ben Denkers, who at that time was Chief Innovation Officer at CynergisTek, a cybersecurity firm based in Austin, Texas, told The Dark Report, “Testing, validating, and auditing whether measures are working as designed is a change of mentality for a lot of organizations.” (If you don’t subscribe to The Dark Report, try our free trial.)
An IT network attack is an attempt by a cybercriminal to gain unauthorized access to devices that contain and exchange data within an organization. Although this information may be on individual devices or on servers, network attacks are often only possible after a hacker enters a system through an endpoint, such as an individual’s email inbox.
“It’s important to understand that while the network server itself might have ultimately been the target, that doesn’t necessarily mean that it was compromised first,” Denkers told The Dark Report. “Phishing is a perfect example of a way an attacker could first gain access to a workstation, and then from there move laterally to a server.”
The final cost of a healthcare cyberattack often exceeds the ransom. Media coverage can lead to an organization’s diminished reputation within the community, and if protected health information (PHI) is accessed by the criminals, a hospital or health system may need to pay for identity theft monitoring for affected patients.
There also are regulatory repercussions that can be costly depending on the circumstances surrounding a cyberattack. For example, on Feb. 2, the US Department of Health and Human Services’ Office for Civil Rights announced a settlement with Banner Health Affiliated Covered Entities (Banner Health), a nonprofit health system headquartered in Phoenix, to resolve a data breach resulting from a hacking incident in 2016. That incident disclosed PHI for 2.81 million patients.
As part of the settlement, Banner Health paid a $1.25 million penalty and will carry out a corrective action plan to protect PHI in the future and resolve any alleged HIPAA violations, according to the HHS Office for Civil Rights.
This hefty penalty is a reminder to pathologists and clinical laboratory managers that—when it comes to cyberattacks—the classic adage “an ounce of prevention is worth a pound of cure” is appropriate advice.
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.
