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Tufts Medicine Study Shows Rapid Whole Genome Sequencing Highly Successful at Screening Newborns for Cancer in Children’s Hospitals

Mar 22, 2024 | Laboratory News, Laboratory Testing, Molecular Diagnostics, Genetic Testing, Whole Gene Sequencing, Precision Medicine

Pathologists and clinical laboratories have an opportunity to help create newborn rWGS programs in their parent hospitals and health systems

Diagnosing disease in infants is particularly difficult using typical clinical laboratory testing and modalities. Thus, the use of rapid Whole Genome Sequencing (rWGS) is gaining acceptance when such a procedure is deemed “medically appropriate” based on the child’s symptoms.

In “Whole Genome Sequencing for Newborns Gains Favor,” Robert Michel, Editor-in-Chief of Dark Daily’s sister publication The Dark Report wrote, “Evidence is swiftly accumulating that use of rapid Whole Genome Sequencing for certain children in NICUs can enable diagnostic insights that guide effective interventions. Further, these pilot rWGS programs in children’s hospitals are showing a solid return on investment because of improved care. It is predicted that more hospitals may soon offer rWGS.”

Michel’s prediction is backed up by a recent study published in JAMA Network titled, “Rapid Whole-Genomic Sequencing and a Targeted Neonatal Gene Panel in Infants with a Suspected Genetic Disorder.”

Conducted at Tufts Medical Center in Boston, the researchers found that “Whole genome tests are nearly twice as good as narrower tests at unearthing genetic abnormalities that can cause disease in infants—the study found 49% of abnormalities, compared to 27% with more commonly used tests targeting particular types of genetic diseases,” the Associate Press reported.

The AP story follows the medical journey of a now 4-year-old who was diagnosed with a rare bleeding disorder. The nearly fatal condition was only caught because broad genetic testing found she suffered from factor XIII deficiency, a blood disorder characterized by the inability to clot properly.

“I’ve been doing clinical trials of babies for over 40 years,” neonatologist Jonathan Davis, MD (above), Chief, Division of Newborn Medicine at Tufts Children’s Hospital at Tufts Medical Center and Professor of Pediatrics, Tufts University School of Medicine, told the AP. “It’s not often that you can do something that you feel is going to really change the world and change clinical practice for everyone.” Clinical laboratories that work with oncologists to treat children suffering from cancer will understand Davis’ enthusiasm. (Photo copyright: Tufts Medicine.)

Incorporating Rapid Whole Genome Sequencing into Infant Care

Genetic diseases are responsible for 41% of infant deaths, according to a Rady Children’s Institute press release, which goes on to say the usage of rWGS may significantly improve the odds for infants born with genetic disorders.

“Broad use of genomic sequencing during the first year of life could have a much greater impact on infant mortality than was recognized hitherto,” said Stephen Kingsmore MD, President/CEO, Rady Children’s Institute for Genomic Medicine, which was one of the additional study sites for the Tufts Medicine researchers.

Genetic testing is already used to predict infant health outcomes, but the Tufts study highlights further developments that could improve the process. Prenatal genetic testing can be utilized both through carrier testing to determine any potential genetic red flags in the parents, and during prenatal screening and diagnostic testing of the fetus.

When an infant presents symptoms after birth, rWGS can then be implemented to cast a broad net to determine the best course of treatment.

According to ScienceDaily, the Tufts study found rWGS “to be nearly twice as effective as a targeted gene sequencing test at identifying abnormalities responsible for genetic disorders in newborns and infants.”

However, the rWGS tests took an average of six days to come back, whereas the targeted tests took only four days, ScienceDaily reported. Also, there is not full consensus on whether a certain gene abnormality is actually the cause of a specific genetic disorder.

“Many neonatologists and geneticists use genome sequencing panels, but it’s clear there are a variety of different approaches and a lack of consensus among geneticists on the causes of a specific patient’s medical disorder,” Jill Maron, MD, Vice Chair of Pediatric Research, Tufts Medical Center, and a co-principal investigator of the Tufts study, told Science Daily.

rWGS Costs versus Return on Investment

Some also question the upfront cost of genetic testing. It can be high, but it’s coming down and Maron stresses the importance of the tests.

“Genome sequencing can be costly, but in this targeted, at-risk population, it proves to be highly informative. We are supportive of ongoing efforts to see these tests covered by insurance,” she told ScienceDaily.

Each of the doctors associated with the Tufts study emphasized the importance of this testing and the good that can be done for this vulnerable group. The potential value to the children, they say, far outweighs the drawbacks of the testing.

“This study provides further evidence that genetic disorders are common among newborns and infants,” Kingsmore told ScienceDaily, “The findings strengthen support for early diagnosis by rapid genomic sequencing, allowing for the use of precision medicine to better care for this vulnerable patient population.”

For clinical laboratories, there is also good news about reimbursement for rWGS. In a story published last fall KFF Health News wrote, “Since 2021, eight state Medicaid programs have added rapid whole-genome sequencing to their coverage or will soon cover it, according to GeneDX, a provider of the test. That includes Florida … The test is also under consideration for coverage in Georgia, Massachusetts, New York, and North Carolina, according to the nonprofit Rady Children’s Institute for Genomic Medicine, another major provider of the test.”

“Collectively, these developments are encouraging children’s hospitals, academic centers, and tertiary care centers to look at establishing their own rWGS programs,” wrote Michel in The Dark Report. “In settings where this is appropriate, hospital and health system-based clinical laboratories have an opportunity to take an active role in helping jump start a newborn rWGS program in their institutions.”

Pathologists should continue to monitor rWGS, as well as prenatal and carrier testing, to have a full awareness of its growing use in infant and young child cancer screening.

—Ashley Croce

Related Information:

Rapid Whole-Genomic Sequencing and a Targeted Neonatal Gene Panel in Infants with a Suspected Genetic Disorder

A Broad Genetic Test Saved One Newborn’s Life. Research Suggests it Could Help Millions of Others

Whole Genome Sequencing for Newborns Gains Favor

Study Finds Association of Genetic Disease and Infant Mortality Higher than Previously Recognized: 41% of Infant Deaths Associated with Genetic Diseases

Prenatal Genetic Screening Tests

Genome Sequencing Highly Effective at Diagnosing Genetic Disorders in Newborns and Infants

Rapid Genome Sequencing for Diagnosing Critically Ill Infants and Children: From Evidence to Equitable Implementation

Rapid Whole Genome Sequencing Has Clinical Utility in Children in the Pediatric Intensive Care Unit

Kaufman Hall Report Says Hospitals Saw Less Inpatients and Outpatients during Summer as Bad Debt and Charity Care Rose

Sep 20, 2023 | Laboratory News, Laboratory Resources, Laboratory Testing, Management & Operations

As a result, health system-based clinical laboratories likely saw a decline in test orders as well a decrease in outreach revenue

Bad financial news continues in the hospital industry. According to an August 2023 National Hospital Flash Report from consulting firm Kaufman Hall, hospitals’ financial performance deteriorated in July, partly due to declines in inpatient and outpatient volumes and rising bad debt and charity care.

The implication from these findings is that hospital-based clinical laboratories saw a drop in test volume and any lab revenue associated with inpatient testing.

In an analysis of data from more than 1,300 hospitals, Kaufman Hall noted a dip in hospitals’ median calendar year-to-date operating margin from 1.4% in June down to 1.3% in July. The data also showed “a greater pullback in volume on the outpatient side, which may be attributed to patients choosing not to pursue elective procedures during the summer,” a Kaufman Hall news release stated.

Kaufman Hall’s National Hospital Flash Report by Erik Swanson, Senior Vice President, Data and Analytics, and Brian Pisarsky, Senior Vice President, Strategic and Financial Planning, is an analysis of actual and budget data—sampled from Syntellis Performance Solutions—which is representative of hospitals of various sizes and areas in the US.

“It’s clear that today’s challenging financial environment is here to stay, and hospital leaders must be proactive in seeking out opportunities to refine their operations and remain competitive,” said Erik Swanson, Senior Vice President, Data and Analytics, Kaufman Hall, in a news release. Clinical laboratory leaders would be wise to follow the same advice. (Photo copyright: Kaufman Hall.)

Expenses Declined, Bad Debt and Charity Care Rose

Here are other national data Kaufman Hall reported for July 2023 as compared to June 2023:

Adjusted discharges per calendar day dropped 7%.
Operating room minutes per calendar day declined 13%.
Emergency department visits per calendar day fell 1%.
Bad debt and charity care as a percentage of hospitals’ gross operating revenue was up 7%.
Purchased service expense per adjusted discharge was down 3%.
Labor expense per adjusted discharge also fell 3%.

Even though expenses slightly declined during July, patient volume decreases “pulled down” the margins, Healthcare Innovation reported, which called the report “a gloomy one.”

Also, the uptick in bad debt and charity care while volumes decreased created a “difficult situation for hospitals,” Medical Economics observed.

Here are the report’s “key takeaways,” according to Kaufman Hall:

All volume indicators were down, but operating margins were still better than 2022.
Outpatient volume decreased more than inpatient, possibly due to patients choosing not to have elective procedures during the summer.
The decline in expenses was “not enough to offset revenue losses,” and inflation will continue to take its toll on labor expenses.
Medicaid has been “disenrolling” members in 30 states during June and July, and bad debt and charity care have increased.

The report also called out need for improvement in providers’ discharge of patients to skilled nursing facilities. “Hospitals that prioritize care transitions to skilled nursing facilities are performing better than institutions [that] do not,” Swanson said in the news release.

“Identifying steps that can ensure a smooth transition, such as obtaining pre-authorizations and planning discharge early, will help organizations reduce expenses and improve patients’ experience,” he continued.

For Hospitals, 2023 Not as Bad as 2022

MedCity News pointed out that though July’s operating margin index decline followed four months of growth, hospitals are still way ahead of 2022 performance when median operating margins were -0.98% in July 2022.

Still, it appears hospitals are struggling to secure financial footing after 2022, an overall bad financial year for the hospital industry.

In “Tough Times Ahead for Hospitals and Their Labs,” Dark Daily’s sister publication The Dark Report referenced a Fall 2022 Current State of Hospital Finances Report, prepared by Kaufman Hall for the American Hospital Association. The report noted that “under an optimistic scenario, hospitals would lose $53 billion in revenue [in 2022]. The loss would primarily come from a $27 billion decline in outpatient revenue and $17 billion for inpatient as well as $9 billion in emergency department revenue.”

More recently, a 2023 Becker’s Hospital CFO Report compiled a list of 81 hospitals that had cut jobs since the start of the year in response to “financial and operational challenges.”

Included was Tufts Medicine in Burlington, Massachusetts. In August, the hospital “eliminated hundreds of jobs” in an outsourcing of lab outreach services to Labcorp. The Becker’s report noted that “[Tufts] said it will work with Labcorp to have the majority of affected employees transition to a similar position with Labcorp.”

Tips for Clinical Lab Financial Viability

Medical laboratory leaders need to help ensure financial health of their labs as well as quality and efficiency of services. Advice from Kaufman Hall may be applicable.

The report writers advised providers to secure payer authorizations before a “patient comes in the door.” For clinical labs, this is comparable to the need to secure insurance company authorizations for expensive genetic tests before samples are taken and tests performed.

Another tip from Kaufman Hall is to “collect and use data to inform process improvement” and “make change.” Along those lines, medical laboratories could leverage patient data to guide launch of new services, entry to markets, workflow improvement, and costs reduction.

—Donna Marie Pocius

Related Information:

National Hospital Flash Report: August 2023

Patient Volume and Revenue Decline in July, Challenging Hospitals’ Performance

Kaufman Hall: Hospital Margins Dented by Falling Patient Volume

Hospital Finances Decline in July

Hospitals’ Operating Margins Fell in July after Four Months of Growth

Clinical Laboratory Trends: Tough Times Ahead for Hospitals and Their Labs 81 Hospitals, Health Systems Cutting Jobs