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).

Children’s Hospitals Collaborate Using Genomic Medicine to Change Pediatric Care

**Sanford Children’s Genomic Medicine Consortium ** SIOUX FALLS, S.D. — Seven children’s hospitals across the United States are collaborating to rapidly integrate genetics and genomics into primary and specialty pediatric care.

The mission of the Sanford Children’s Genomic Medicine Consortium is to work together on innovative clinical program development, advocacy for children, cutting-edge research and educational programs for the future of genomic medicine.

The seven member hospitals include: Sanford Children’s (Sioux Falls and Fargo), Children’s Minnesota (Minneapolis and St. Paul), Children’s Hospital Colorado (Aurora), Children’s Hospital Los Angeles, Rady Children’s Institute for Genomic Medicine and Rady Children’s Hospital – San Diego, Banner Children’s at Diamond Children’s Medical Center (Tucson) and Nicklaus Children’s Hospital (Miami).

Sanford Health has provided $500,000 in seed funding for Consortium projects over the next year.

The initial projects funded by the Consortium include a study of rapid whole genomic sequencing in critically ill newborn infants, and a study evaluating the routine use of an extensive, pediatric-focused, next generation sequencing panel in the diagnosis of childhood cancers.

Genetic diseases are a leading cause of morbidity and mortality in infants in Neonatal and Pediatric Intensive Care Units (NICU, PICU). These children often undergo an extensive and expensive diagnostic process that may not lead to a final diagnosis. Stephen Kingsmore, M.D., D.Sc., president and CEO of Rady Children’s Institute of Genomic Medicine (RCIGM) is leading rapid whole genomic sequencing in critically ill newborn infants to determine the complete DNA sequence of a child’s genome at one time to identify the risk of genetic diseases. Currently, the average turn-around time for sequencing to diagnosis by the RCIGM team is under a week. That is significantly faster than the common timetable for this type of work, which can take weeks to complete.

“The future of pediatric medicine is being transformed by the ability to rapidly decode the genomes of the most fragile newborns to deliver exact diagnoses and targeted treatment,” said Kingsmore.

Pediatric cancers have different genetic origins compared with adult cancers. Current panels for detecting the genetic origins of a tumor primarily focus on adult cancers. OncoKidsSM developed at Children’s Hospital Los Angeles, is specifically formulated to detect the genomic alterations of pediatric cancers including leukemias, lymphomas, bone, soft tissue and brain tumors.

“The ability to identify the precise underlying genomic alterations in individual tumors with OncoKidsSM allows us to personalize care and innovate how we treat children with cancer,” said Alexander R. Judkins, M.D., Pathologist-in-Chief and Executive Director of the Center for Personalized Medicine (CPM) at Children’s Hospital Los Angeles.

Extending precision medicine to children’s health through this Consortium is inspired by the vision of Denny Sanford. In 2014, the health care philanthropist gave $125 million to Sanford Health to create Sanford Imagenetics, the first program in the nation to embed the latest in genomic medicine with primary care.

“I am thankful to each member for their participation in the Sanford Children’s Genomic Medicine Consortium,” said Gene Hoyme, M.D., Medical Director, Sanford Children’s Genomic Medicine Consortium. “So much can be gained for the care of children through the collaboration of these hospitals.”

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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