Rapid whole genome sequencing improves diagnosis in critically ill infants on a national scale
Vienna, Austria: 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. But whole genome sequencing1 (WGS), carried out rapidly, can provide an accurate diagnosis and therefore lead to improvements in their clinical care. Results from an Australian study of such a use of WGS presented to the annual conference of the European Society of Human Genetics today (Sunday) show how the integration of genomic, transcriptomic2,and functional3 data can accelerate rare disease diagnosis on a national scale.
“The evidence of diagnostic, clinical, and family benefit of rapid genomic testing in critically ill children is overwhelming. This type of testing should become the standard of care for these patients,” says the presenter, Professor Zornitza Stark, clinical geneticist at the Victorian Clinical Genetics Services and Australian Genomics. “And rapid genomic diagnosis programmes should continue to drive improvement, innovation, and discovery more broadly.”
The researchers carried out nationwide ultra-rapid WGS in 290 critically ill paediatric patients with rare disease between January 2020 and January 2022. They aimed to have diagnoses in less than five days. “We wanted the programme to serve as an exemplar of how genomics can improve diagnostic and clinical outcomes in paediatric disease in real time,” says Prof Stark. “We have now incorporated RNA sequencing and, through close collaboration with clinicians and researchers, optimised the use of functional data to secure additional diagnoses.”
Ultra-rapid WGS resulted in a diagnosis in 136 patients, with an average time to diagnosis of just under three days. Of the 154 patients who were not diagnosed by standard WGS analysis, RNA sequencing, functional assays and other tests led to an additional 20 diagnoses. New disease-causing genes were also identified through international matchmaking efforts, and studies are underway to find further diagnoses.
Although the cost of genomic testing remains high compared with other diagnostic investigations, particularly when delivering results in rapid turnaround times, its use provides substantial savings to healthcare systems in the longer term. Complex, time-critical tests such as ultra-rapid WGS are best delivered by a multi-disciplinary team, and that means that both capacity and capability in the clinical and laboratory genetics workforce need to be grown, says Prof Stark.
“Our approach can serve as a model in other healthcare systems, although it will need to be adapted to local circumstances and to evolve over time. For example, Australia has a very geographically dispersed population, which is relatively small compared to the land area. It made sense for us to have a central sequencing laboratory for this study, with a lot of attention paid to sample transport logistics and to including local teams in analysis through virtual meetings. Different models will be needed in countries with high population density.
“Undoubtedly, there are also adults with rare diseases who would have benefited from ultra-rapid genomic diagnosis but were excluded from the study,” Prof Stark says. Clinical genetics services have traditionally been much more involved in providing consultation in neonatal and paediatric intensive care units, facilitating the identification of patients who would benefit from rapid genomic testing, so raising awareness of genomics in the adult intensive care setting will be a challenge in extending access.
Ethical questions are involved too, especially around consent. Families are overwhelmed and distressed when their child is critically ill, so how to best facilitate informed consent is a problem? Indeed, is consent always necessary? Can it be withheld? How should the diagnosis of a genetic condition influence decisions by treating clinicians and by families? Is rapid genomic testing a fair use of resources? All these are important and difficult questions.
”There are still many challenges to be faced, not least finding a way to quickly transition succcessful research programmes into the clinical setting, but we believe our work has shown that ultra-rapid WGS has diagnostic, clinical, and economic benefit on a national level,” says Prof Stark. ”We hope that our approach will soon become part of mainstream diagnostic practice not just in Australia, but also further afield.”
Professor Alexandre Reymond, chair of the conference, said: ”Our Australian colleagues are showing us the path forward on how a multidisciplinary approach that swiftly incorporates genomic data could become general practice to better serve critically-ill newborns.”
1.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.
2. RNA sequencing (‘transcriptomic’) looks at the full range of mRNA molecules expressed by an organism. By looking at the whole transcriptome, researchers can determine gene expression.
3. Functional genomics focuses on the dynamic aspects, e.g., how proteins work, as opposed to the static aspects of the genome such as DNA sequence.
Abstract C11.6: Rapid rare disease diagnosis on a national scale: an integrated multi-omic approach
Incidental findings in genomics: how does their utility balance with their psychological effect on patients?
Vienna, Austria: As the cost of genome and exome1 sequencing falls, its use in characterising rare diseases and personalising cancer treatment, for example, is becoming far more frequent. But such analyses may throw up findings unrelated to the condition for which it has been requested. What to do with these secondary findings (SFs) or incidental findings (IFs) is problematic. Should they be reported to the patient and in what circumstances? How should clinical geneticists deal with the perhaps unnecessary worry that they may cause?
At the annual conference of the European Society of Human Genetics today (Saturday), Ms Estela Carrasco, MSc, a PhD student and genetic counsellor at the Vall d’Hebron Hospital, Barcelona, Spain, will describe how she and colleagues set out to look at the prevalence of SF/IFs in cancer susceptibility genes (CSGs) in patients who had undergone exome sequencing because of rare diseases not related to cancer, and to identify CSGs with a potential clinical actionability that were unrelated to the purpose of the primary analysis. They then evaluated the psychological impact of disclosing SF/IFs to patients and their relatives compared with a cohort who underwent testing because of their family cancer history. They analysed exomes from 533 patients who were examined for non-cancer indications and followed up by examining the psychological impact of the disclosure of the SF/IFs to these patients two to six months after delivery of the results.
“We found SF/IFs pathogenic (potentially disease-causing) variants in CSGs in 2% of patients who had undergone exome testing for reasons unrelated to cancer predisposition,” Ms Carrasco says. “This enabled us to carry out predictive testing in 42 relatives, 18 of whom carried CSGs.”
The psychological impact was higher in those where the variant was identified as an incidental finding, but this needs to be balanced against the advantage of early detection and the preventive strategies that could be introduced in families who had no prior cancer diagnosis, the researchers say. “Although a 2% rate of SF/IFs may not sound very high, it is notable. And genetic counselling can help both in the communication of the results and to help patients and their families adapt to the newly discovered genetic condition,” says Ms Carrasco.
The researchers intend to continue to investigate new ways of delivering genetic test results to patients; for example, the impact of separating the time at which the primary findings are disclosed from the secondary findings. “We believe that being able to demonstrate clinical actionability of the secondary findings is reassuring to patients.”
Out of the 29 carriers identified (11 index cases and 18 relatives), 20 enrolled for further surveillance. The researchers were able to identity three paragangliomas (a type of neuro-endocrine tumour), and one early breast cancer in a 74 year-old woman with a BRCA2 variant who had finished the population-based breast cancer screening. One relative in the BRCA2 family with metastatic prostate cancer was given target therapy after his BRCA2 status was revealed.
Particular problems arise in the case of children, however. “The principle of a child’s autonomy may be lost if disclosure is made before an appropriate age, so healthcare professionals should be cautious when exome sequencing analysis is requested in minors,” says Ms Carrasco. “On the other hand, disclosing these results could generate an indirect benefit for these children because it may allow their relatives to adhere to early detection and prevention programmes, thus preserving their health. To achieve this, it is important to report only clinically actionable genes.
“It is important to provide an adequate counseling to individuals undergoing exome sequencing, or in case of children to their parents or guardians, in order to make sure that all the potential medical applications of genetic testing are understood. And, on the professional front, in cases where exome sequencing is requested by clinicians who have little training in the delivery of information about SF/IFs, genetic counsellors and clinical geneticists should form part of the multidisciplinary team providing care.”
Professor Alexandre Reymond, chair of the conference, said: “Contrary to radiologists, whose incidental findings mean there is a tumour, geneticists’ incidental discoveries are often predictive in nature. While this should not prevent us from acting on an actionable finding, this requires dedicated and specifically trained personnel to ensure that all the information provided to patients and their families is clear, comprehensible, and understood.”
1The exome is made up of all the exons in the genome. These are the DNA sequences that code for protein and are therefore the functional part of the genome.
Abstract C02.5 Coping with incidental findings in cancer susceptibility genes after exome sequencing in paediatric patients
Thalidomide is an effective treatment for abnormal blood vessel formations
Vienna, Austria: The same properties that caused birth defects when it was given to pregnant women, the inhibition of blood vessel formation (anti-angiogenesis), have led to an interest in thalidomide’s therapeutic utility in other fields. At the annual conference of the European Society for Human Genetics on Sunday, Professor Miikka Vikkula, from the de Duve Institute, Université catholique de Louvain, Brussels, Belgium, will present results from a study of the use of thalidomide in patients with severe arteriovenous malformations (AVMs). These results, published today (Friday) in Nature Cardiovascular Research1, show a striking reduction in symptoms and a subsequent improvement of quality of life.
AVMs are abnormal tangles of the blood vessels connecting arteries and veins that alter normal blood flow. They are very painful, and cause bleeding and deformation of the affected body part as well as cardiac problems. Usually congenital, they are often only noticeable in adolescence or adulthood as the person grows. Treatment of severe cases is usually through surgery or embolisation (the injection of an agent that destroys the blood vessels locally, thus inducing scarred tissue), though this is rarely totally effective and can make matters worse.
Some people with AVMs can live relatively normal lives, but even in less severe cases there is always the risk that the abnormal tangles of blood vessels can burst and may cause a stroke when in the brain. About one in every hundred AVM patients suffers a stroke each year.
“Our group has been studying the causes of vascular abnormalities for 30 years,” says Prof Vikkula. “We have identified several genetic causes and have been able to show that certain mutations activate the signalling inside the blood vessel wall -cells and this promotes the abnormal formation of blood vessels (angiogenesis). This led us to wonder about the possibility of using thalidomide to inhibit abnormal blood vessel formation.”
After showing that a vascular malformation could be corrected in a mouse model, Professor Laurence Boon from the Centre for Vascular Anomalies at Saint Luc University Hospital, Brussels, who has been working in collaboration with Prof Vikkula for 30 years, recruited 18 patients with AVMs to a study of the use of thalidomide in their condition. They were aged between 19 – 70 and all had severe malformations that could not be treated by conventional approaches. Patients had to agree to use contraception for at least four weeks before starting thalidomide and to continue for four weeks after the cessation of treatment. Since thalidomide is present in semen, men also had to agree to use condoms during sex.
Patients received either 50mg, 100mg or 200mg of thalidomide per day for between two and 52 months. Eight AVMs were stable after a mean thalidomide cessation of 54 months, and four recurred after a mean duration of 11.5 months. Combined treatment with embolisation, where arteries or veins within the AVM are blocked by an agent that destroys vascular wall cells, allowed the thalidomide dose to be reduced to 50mg per day in five patients. Reducing the dose where possible was important, says Prof Vikkula, because a higher dose was associated with side effects, particularly tiredness and peripheral neuropathy, damage to the nerves located outside the brain and spinal cord that causes weakness and numbness, particularly in the hands and feet.
“All the patients experienced a rapid reduction of pain, together with cessation of bleeding and the healing of ulcers where these were present,” says Prof Vikkula. “The three patients with cardiac failure also saw their problems resolved, and one AVM appeared to be completely cured after 19 months of thalidomide and an eight-year follow-up.
“We know that thalidomide acts through vascular endothelial growth factor (VEGF) a signalling protein that promotes the growth of new blood vessels. VEGF levels are high in vascular abnormalities such as AVMs and is therefore likely that thalidomide reduces signalling via the angiogenesis-promoting pathways. Although our study is only small, the results are convincing, and we hope that they will be confirmed by larger trials.”
A further advantage of the use of thalidomide in the treatment of AVMs is one of cost. Two other drugs, recently developed for use in oncology, and being tested to treat AVMs, cost up to twelve times as much, as well as having numerous side effects.
“We had hypothesised that thalidomide should work in these patients, so our results did not come as a surprise, but it was great to have clinical confirmation that we were right,” Prof Vikkula concludes. “In our view, this is a breakthrough finding and provides a solid basis for the development of molecular treatments for AVMs.”
Professor Alexandre Reymond, chair of the conference, said: “This study shows not only the healthcare and economic benefits of repurposing drugs - even the most maligned - but also how genetic research can lead to real breakthroughs in therapies for difficult to treat, distressing conditions.”
1. DOI : 10.1038/s44161-022-00080-2
Abstract no. C11.3: Thalidomide is an Efficient Treatment for Symptomatic and/or Life-Threatening Arteriovenous Malformations