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Whole Genome and Exome Sequencing are Superior Diagnostic Tests for Children with Suspected Genetic Diseases

First meta-analysis of scientific literature underscores the greater clinical and diagnostic utility of sequencing compared to standard genetic testing

July 9, 2018–Whole Genome Sequencing (WGS) and Whole Exome Sequencing (WES) of children with suspected genetic diseases are more useful than the current first-line test, according to a study published today by the Rady Children’s Institute of Genomic Medicine in the journal npj Genomic Medicine.

The study compared the usefulness of the current most established testing method—
chromosomal microarray (CMA)—to relatively new, more advanced tests: WGS and WES—in detecting the cause of genetic anomalies and guiding medical management of patients.

“What we learned is that WGS and WES offer greater diagnostic and clinical utility than CMA, leading us to conclude that WGS and WES should be considered first-line genomic tests for children with suspected genetic diseases,” said Michelle Clark, PhD, statistical scientist at the Rady Children’s Institute of Genomic Medicine (RCIGM) and the first author of the study.

Genetic diseases are the leading cause of death in infants in North America affecting an estimated four percent of newborns. Rare genetic diseases also account for approximately 15 percent of admissions to children’s hospitals.

Since 2011, Whole Genome and Whole Exome sequencing have been increasingly used for diagnosis of genetic diseases, primarily on an experimental basis as guidelines do not yet exist for their use. In addition, medical insurance reimbursement for is available on a very limited basis for WES but not for WGS. As a consequence, while these tests are more useful, they are not widely available.

The basis for the publication was a thorough, systematic review of scientific literature covering nearly seven years (January 2011 to August 2017). The study, led by RCIGM president and CEO Stephen Kingsmore MD, DSc, analyzed the results of 37 research studies involving more than 20,000 children with suspected diseases and compared the diagnostic and clinical utility of WGS, WES and CMA in these cases.

The Institute team has engineered a Whole Genome Sequencing process to rapidly decode, analyze and interpret the cause of genetic disorders in newborns and children in intensive care in a matter of days.

WGS is a single genetic test that can screen a blood sample for thousands of genetic anomalies and quickly identify the root causes of a child’s condition. As part of their research protocols, the RCIGM team is working to equip clinicians with this critical information to facilitate medical decision making.

Most important, early intervention may avoid unnecessary treatment, invasive surgeries, and reduce hospitalization time, ultimately reducing suffering, bringing down the cost of care and improving quality of life for affected babies and children.

“Our hope is that Whole Genome Sequencing will soon become routine so that all children who need it can have access to this life-saving technology,” said Kingsmore.

Currently, RCIGM is offering rapid Whole Genome Sequencing (rWGS) only through research studies offered to patients at Rady Children’s Hospital-San Diego and children’s hospitals participating in RCIGM’s clinical trials. Among the hospitals collaborating with RCIGM are Children’s Hospital of Orange County, Children’s Minnesota, Colorado Children’s and Nicklaus Children’s Hospital (Miami).

WGS Helps Diagnosis and Reduces Healthcare Costs for Neonates in Intensive Care

European Society of Human Genetics Milan, Italy: Children who are born severely ill or who develop serious illness in the first few weeks of life are often difficult to diagnose, with considerable implications for their short and longer-term care. Whole genome sequencing*carried out quickly has the potential to provide an early diagnosis, and thus improve the clinical care of these infants as well as reducing its cost, the annual conference of the European Society of Human Genetics will hear tomorrow (Sunday).

Dr Shareef A. Nahas, Senior Director, Rady Children’s Institute for Genomic Medicine, San Diego, CA, United States, will report on his team’s study of rapid whole genome sequencing (rWGS) of all inpatient children under one year of age who were nominated for genetic investigation at Rady Children’s Hospital. Rapid WGS is able to return results in 48 to 96 hours, whereas standard genetic testing takes six to eight weeks to provide a result. They then noted subsequent changes in medical care that occurred while the child was still in hospital. Where there was a significant change in care due to a new diagnosis, the cases were reviewed by an independent expert panel who tried to determine what they believed would have happened had the child not received rWGS.

After 12 months of testing, 363 patients had been enrolled in the study and rWGS interpreted in 340 of them. This yielded a diagnosis in 115 cases (about 34%). Diagnosis occurred quickly, on average within 96 hours. Changes in management as a result of diagnosis were identified in 77 patients, or about 67% of those diagnosed. Such changes ranged from specific changes, for example surgical interventions, to guidance in palliative care. Among the first 42 infants diagnosed, rWGS provided over $1.3million in net cost saving over the projected standard care.

“To date, our studies have shown a considerable clinical and economic benefit of sequencing children who were identified by clinicians as being suspected of having a genetic disorder. In the course of the study, one child was spared devastating neurological damage,and one had a significantly reduced risk of death. The net cost savings totalled several hundred thousand dollars, even when we included the cost of analysing the genome of the child and both parents, » says Dr Nahas.

Although many studies have shown that WGS improves the diagnosis if genetic disorders in infants and can lead to beneficial changes in their management, the new research has shown that, by implementing rapid sequencing, cost savings will also ensue. « We are now in a situation where we have a technology that leads to improved diagnosis and improved outcomes but is also not a net burden on healthcare resources. This means that for large healthcare payers, there is not a logical cost barrier to implementing rWGS in neonates suspected to have a genetic disorder. There will need to be further data on who else can benefit from early use of this technology but implementation in the current cohort should not be delayed, » says Dr Nahas.

Currently, the use of WGS among sick neonates is very infrequent across the world, and there are few healthcare systems that have the ability to turn round genetic testing quickly enough to be clinically relevant, the researchers say. This is vital if medical management needs to be changed during the childrens’ hospitalisation. In the course of Dr Nahas’ study, one child was spared devastating neurological damage and another had a significantly reduced risk of death.

« The logic for the use of rWGS in these patients, both diagnostic and economic, is totally convincing. We have demonstrated that early sequencing saves money during admission. We were surprised by the proportion of children who received a change in care during that admission – around 25% of children sequenced and 80% of those diagnosed. This rate is much higher than other published rates for neonates who received WGS. We believe that this difference is due to the fact that the children received results at a much younger age, at a point where medical decisions were yet to be made.

« There is an ethical imperative to act in the best interest of neonates, but implentation will require a concerted effort across all healthcare systems, and this will need to be at government level in Europe. Consistent with many diagnostic tests in the post-natal period, rWGS has the potential to identify conditions associated with lifelong disability or shortened lifespans, » Dr Nahas will conclude.

In a second presentation, Courtney French, PhD, a research associate/bioinformatician at the University of Cambridge, Cambridge, UK, will describe how she and colleagues carried out WGS analyses on 145 severely ill babies and children with an unidentifiable disease. As a result, they were able to identify the cause of disease in more than 15% of cases.

« We have developed a rapid, affordable turnaround pipeline for this sequencing within the UK National Health Service system. This means that we can feed back clinically relevant information to doctors and parents in a timescale that allows care to be affected. Because it is hard to tell from observation alone who will benefit from genomic diagnosis, we think that it should be carried out on all eligible children, rather than doctors deciding on individual cases based on previous clinical knowledge. By comparing the entire DNA sequence in children to that of their parents we can identify quickly the likely cause of disease, » says Dr French.

The researchers are using their current data to investigate how rare genetic diseases present at an earlier stage than they are usually diagnosed in newborns. « Greater numbers of patients will expand our ability to do this, and we hope that our work will serve as a model for expanding the programme to other hospitals and regions, » Dr French will say. « The success of this project will depend on people working together across the health research and healthcare system. The translation of this work to routine care will require significant investment of resources in achieving consent from parents, and in giving information at what is a very stressful time for them. »

Many of the conditions characterised through WGS to date can be treated more effectively once identified. In the Cambridge dataset, several epilepsies that respond better to some medications than others were found. And there were cases where the diagnosis was able to prompt better screening for the clinical consequences of a condition and enabled the creation of a properly focused care plan, for example cardiac surveillance, renal follow up, or dietary advice. Even where there is no effective treatment available, having a diagnosis can provide reassurance to families that all that could be done has been done, and it can also provide useful information to parents when they are considering the most appropriate care for their child in the future.

« We were pleasantly surprised at the enthusiastic welcome parents gave to our study, with more than half of those approached wanting to take part. Despite the complications of getting samples from both parents, as well as their child, we managed to achieve this in 85% of families. We were also surprised at the huge range of clinical conditions we were able to diagnose, and particularly to find that when a child was already known to have learnng disability or developmental delay we were more likely to make a genetic diagnosis. This reflects the enormous increase in genetic knowledge over the last decade; ten years ago we would not have been able to do this even if we had sequenced the genome.

« Genome sequencing is currently rare in newborns and paediatric cases, but our research has shown that it can be extremely effective in providing rapid answers in difficult to diagnose cases. It is also be cost-effective, since it can reduce the time spent as an in-patient. Early diagnosis of neonatal and paediatric disease is not only important in pointing the way to the best care and treatment, but also in reducing anxiety for parents, » Dr French will conclude.

Chair of the ESHG conference, Professor Joris Veltman, Director of the Institute of Genetic Medicine at Newcastle University, Newcastle, United Kingdom, said: “Both these studies confirm the value of genome sequencing to detect the cause of unexplained disease. The study of Nahas shows that this can now even be done within four days, which is very impressive. This greatly increases the practical use of genetics in an acute clinical setting where treatment decisions can now be made based upon this powerful test. Personalised genomic medicine is becoming a reality!”

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*. Whole genome sequencing is the process of determining the complete DNA sequence of an individual, including all the chromosomal DNA and that contained in the mitochondria.

Nahas: Abstract no: CO7.5. Rapid Whole Genome Sequencing Improves Clinical Utility and Cost Effectiveness of Acutely Ill Children admitted to Neonatal Intensive Care Units

French: Abstract no: CO7.4 Next Generation Children Project: Whole genome sequencing for rapid diagnosis of severely ill children in intensive care

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Rapid genome sequencing could revolutionize health care for acutely ill babies

The story of Maverick Coltrin’s medical mystery is gripping: Last October, he was just 6 days old when he stopped eating. Then the seizures came. His tiny arms and legs would stiffen for a few seconds as many as 30 times per hour. Doctors at Rady Children’s Hospital in San Diego tried multiple tests and medications, but nothing revealed what was wrong. When Maverick turned dusty blue, his parents asked, “Do you think he’s going to survive?”

The answer: “We’re doing everything we can.”

“Everything” was about to have a new meaning.

DNA Testing Offers New Hope for Infants with Genetic Disease

Studies suggest that whole-genome sequencing can be done more quickly and cheaply, offering fast diagnoses that can save ailing babies.

While genetic diseases pose the single biggest source of infant mortality in the U.S., many of these disorders are so rare and little understood that an accurate diagnosis can take weeks or months.

RCIGM to Share in $34 million NIH Clinical and Translational Science Award

Forms partnership with Rady Children’s Institute for Genomic Medicine

LA JOLLA, CA – April 30, 2018 – The Scripps Translational Science Institute (STSI) has received over $34 million in renewed funding from the National Institutes of Health’s National Center for Advancing Translational Science (NCATS) to advance medical research and clinical care through genomic and digital technologies. This is the third 5-year Clinical and Translational Science Award (CTSA) to be awarded to STSI, which is part of The Scripps Research Institute (TSRI).

“We are thrilled to have the NIH’s continued support for our efforts to advance individualized medicine, both in care of patients and in training of young physicians and scientists,” says Eric Topol, M.D., who is the principal investigator for the CTSA, director of STSI and an executive vice president at TSRI.

Supported in part by the CTSA since 2008, STSI has been leading the charge to advance health care through the use of genomics, digital medicine and bioinformatics. The CTSA Program supports a national network of academic medical research institutions—known as “hubs”—that work together to improve the translational research process of turning findings from basic science into effective interventions that improve human health.

The new round of funding will provide resources and infrastructure support for STSI to further its mission of applying genomic and digital technologies, coupled with bioinformatics tools to better understand each individual and ultimately render more effective care.

As part of the CTSA, STSI has formed a new partnership with Rady Children’s Institute for Genomic Medicine (RCIGM), a leader in ultra-rapid, whole-genome sequencing programs in acutely ill infants.

“Genomic medicine research programs at STSI and RCIGM synergize significantly, especially as related to the genetics of rare and infectious diseases,” says Stephen Kingsmore, M.D., D.Sc., president and CEO of RCIGM. “We are looking forward to working closely with Dr. Topol’s team to advance the implementation of genomic medicine in our region of southern California and through the national CTSA consortium.”

In addition, the CTSA renewal features a drug discovery collaboration between STSI and another of TSRI’s affiliated institutes, the California Institute for Biomedical Research (Calibr), which focuses on the translation of basic research to new medicines that address unmet medical needs.

“We are thrilled to enable the broader Scripps Research mission by partnering with STSI to engage the CTSA network, bringing to bear drug discovery tools that could enable rapid translation of new therapeutic approaches to patients,” says Matt Tremblay, PhD, chief operating officer of Calibr.

STSI will continue to work with long-standing clinical partner Scripps Health, and with the San Diego Supercomputer Center who provides infrastructure support for a number of big data projects in genomics, digital medicine and informatics.

In addition to supporting research, the CTSA at STSI funds the training of future leaders in translational science through a professional development award that allows for early career clinical researchers to pursue specialized training in translational research. It also supports translational research training for doctoral students at TSRI.

The grant numbers are UL1TR002550, KL2TR002552 and TL1TR002551.

About The Scripps Research Institute
The Scripps Research Institute (TSRI) is one of the world’s largest independent, not-for-profit organizations focusing on research in the biomedical sciences. TSRI is internationally recognized for its contributions to science and health, including its role in laying the foundation for new treatments for cancer, rheumatoid arthritis, hemophilia, and other diseases. An institution that evolved from the Scripps Metabolic Clinic founded by philanthropist Ellen Browning Scripps in 1924, the institute now employs more than 2,500 people on its campuses in La Jolla, CA, and Jupiter, FL, where its renowned scientists—including two Nobel laureates and 20 members of the National Academies of Science, Engineering or Medicine—work toward their next discoveries. The institute’s graduate program, which awards PhD degrees in biology and chemistry, ranks among the top ten of its kind in the nation. In October 2016, TSRI announced a strategic affiliation with the California Institute for Biomedical Research (Calibr), representing a renewed commitment to the discovery and development of new medicines to address unmet medical needs. For more information, see http://www.scripps.edu.

About the Scripps Translational Science Institute
The Scripps Translational Science Institute (STSI) of The Scripps Research Institute focuses on individualized medicine, using the tools of digital medicine and genomics to better understand each person and render more effective healthcare. In 2016, STSI was awarded a grant for over $200M by the National Institutes of Health’s Precision Medicine Initiative to lead the All of Us Research Program’s Participant Center. STSI is further supported, since 2008, by the flagship NIH Clinical and Translational Science Award to promote human health and train future leaders in biomedicine. For more information, visit www.stsiweb.org.

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