Should every baby have their Genome sequenced?

Annie Janvier, John Lantos and I have just published an article about Next Generation Sequencing (Janvier A, et al. Next generation sequencing in neonatology: what does it mean for the next generation? Hum Genet. 2022), which is a common way of referring to rapid whole genome or whole exome sequencing. We hang the discussion on 3 cases from the NICU at my hospital, which all had certain similarities, they were term newborn infants with unexplained refractory seizures. In each case rapid next generation sequencing (NGS) was organised, and took 5 to 7 days to have a result. We did not have access to ultra-rapid sequencing, which, in some publications, can have a turn around time of about 72 hours. In all 3 of our case histories the NGS gave a result of compound heterozygosity of probably pathogenic abnormalities affecting a likely responsible gene.

Our discussion is focused on the following considerations: 1. A small minority of NICU patients have uncertain diagnoses; 2. among babies with uncertain diagnoses, a minority have a diagnostic finding on NGS; 3. among babies with a diagnostic finding, a minority have an impact of NGS on their therapy; 4. among babies with an impact of NGS, a minority have a therapeutic intervention that will improve their condition. Which might all sound like we are Luddites fighting against the inevitable, but each statement is based on evidence from the literature.

  1. Most babies are in the NICU because of prematurity, sepsis, asphyxia or major congenital anomalies. Only the last of those are sometimes monogenic, as well as some of the remaining infants with, for example, unexplained hypotonia or seizures or multiple minor anomalies. In large published cohorts it is often not clear what the denominator was, in one study from the Netherlands, NGS was considered appropriate in 2% of babies admitted to the NICU.
  2. The proportion of babies with a positive, possibly diagnostic, finding on NGS, among those considered for testing, is between 19% and 51%. It will obviously depend on the threshold for testing, if testing is applied more widely the proportion with a possibly diagnostic finding will fall. But the proportion with incidental findings will be stable.
  3. In how many babies does a diagnostic finding have a useful impact on their clinical management? This question was the hardest to answer from our literature review, as the reported impacts on management, and how they were defined were often unclear. Very often, the purported benefits were very questionable such as “referral to an endocrinologist” or “prescription of salbutamol”. Some of the rationales smacked of genetic determinism, for example a case where a supraglottoplasty was avoided because the precise variant associated with the infant’s CHARGE syndrome was discovered. I don’t know about you, but I wouldn’t have a supraglottoplasty performed, or not, based on the genetic rearrangement, but on whether that individual child had airway obstruction likely to be improved by surgery. Two infants with identical genetic abnormalities may have very different phenotypes, which has been shown many times, even in cases of mono-zygotic twins with CHARGE.
  4. Among those with a medically actionable genetic abnormality, it is an even smaller proportion who have a condition for which specifically tailored or curative treatment exists for the condition diagnosed. We found, for example, cases in the reported cohorts of Dravet syndrome and of hyperoxaluria where therapy was changed after NGS, but even those specific examples are cases where other children have been effectively managed without NGS. Which isn’t to say that there were no benefits of NGS, just that a more rapid diagnosis and tailored therapy should be balanced against the cost implications, and also any potential adverse impacts.

One of the most commonly reported “benefits” of NGS in the NICU is a recognition that a condition is uniformly lethal or refractory to treatment, leading to a redirection of the goals of care, with the suggestion that this can occur more rapidly when there is an NGS result. In contrast, we think that caregivers and families may become unwilling to withdraw life-sustaining interventions without the NGS results, which may well lead to delays in redirection of care, and periods of unnecessary NICU treatment. Unless you have the enormous funding required to perform ultra-rapid NGS on demand, then a delay of at least 5 days is likely; even with ultra-rapid NGS this will likely be 72 hours minimum. As the majority of NGS results do not produce an aetiologic diagnosis, it could well be that the most frequent result of performing NGS is a delay in the withdrawal of life-sustaining interventions.

Very often, in the published case histories that we tried to analyse, it did indeed seem that performing NGS just delayed withdrawal of such interventions when it was clear that it was already something that should be considered. Obviously the brief details in a publication covering multiple cases cannot convey the complexity of the interactions of the medical team and the family, but our own experience, as described in our cases, illustrates that as something that can occur. One of our cases developed an iso-electric EEG during the interval between sending the NGS and receiving the result. We could have, and some families would have requested, waiting until the result was available, our evaluation of the situation was that there were no diagnostic possibilities that could lead to a good outcome and the medical team and parents agreed to redirection of care without the NGS result. In our estimation, that case was actually one where the NGS was helpful, just not in a way that would have been considered in any of the published cohorts. The parents were very relieved that the diagnosis was found, which reduced their feelings of guilt, and allowed them to adapt.

Another of our cases had a very different result, with an NGS finding of a condition that would likely lead to profound intellectual limitations and behavioural problems, for that case the parents stated that knowing the results had seriously adversely impacted their ability to adapt as new parents. The third case had a sort of neutral result, the parents were content to have a diagnosis but it made no difference to them regarding how they wanted their infant treated.

All of the cases in our article had a result from the NGS that was considered to be “probably pathological” affecting genes known to be probably implicated. We selected those cases to make important points for our discussion, but they represent a small minority of NGS results. Much more commonly NGS does not provide a diagnosis. Also very commonly NGS results reveal possibly pathogenic abnormalities, or abnormalities “of uncertain significance”, which may make decision-making more difficult rather than more straightforward. In addition, there are, of course, the incidental findings of abnormalities in other genes that may have clinical significance for unsuspected conditions. About 5% of NGS in children, for example, reveals cancer susceptibility genes, which may be of benefit for the future of the child, but very often the benefit is currently unclear, and balancing adverse impacts have not been considered.

I was surprised recently to see a debate in the BMJ, with pro and con articles regarding the idea of universal whole genome sequencing as a possible new standard for neonatal screening. Even though the pro position did introduce some nuances, and suggested a progressive revealing of results of Whole Genome Sequencing according to which results an independent panel would consider relevant at different ages, it still seemed to me to be motivated by the kind of genetic determinism that I mentioned above. The authors seem to believe that a genetic abnormality equates to the diagnosis of a disease state, and that revealing a diagnosis will improve health outcomes. Let me give you one counter example, discussed by John Lantos in his article The False-negative Phenotype. This is an example for just one genetic anomaly, Krabbe’s disease, in which universal screening in New York state commences with a screen for the metabolic abnormality (low galactocerebrosidase levels), and, among those who are proven to have the biochemical abnormality, then sequences the gene responsible. Ninety percent of babies who are identified as having both the biochemical abnormality and the genetic defect remain asymptomatic. This disease was previously thought to be just about universally lethal, but with screening we now know that is not true. It is also unclear how many babies without the biochemical abnormality have the gene defect; so what should we do when a baby is identified as having the genetic abnormality that causes Krabbe’s disease? There are many other examples (perhaps none so striking) of genetic abnormalities which are thought to be clearly pathogenic being discovered in individuals who do not have the disease thought to be caused by that abnormality, some other examples are discussed by Dr Lantos in that article.

The pro article in the BMJ does not mention that as a concern. They also state that “extensive clinical evidence has shown that screening for genetic diseases saves lives. Research has shown that it can be cost effective”. Those 2 assertions should be challenged, In answer to the first assertion, yes, screening for phenylketonuria saves lives and brain cells, screening for cystic fibrosis improves pulmonary outcomes, many other examples are available, but neither of those examples rely on genetic screening, they actually rely on detecting the presence of the disease, which, I reiterate, is not the same as finding the presence of the genetic anomalies. In support of the second assertion they reference an article which does not support their assertion! The referenced article in question models the cost-effectiveness of informing patients about a series of 56 incidental findings which the College of Medical Genetics in the USA recommend informing patients about if they have genomic testing. What the study actually found was that informing asymptomatic adults about those 56 findings was NOT cost-effective (unless the NGS was very cheap). With universal NGS of asymptomatic babies, of course, every finding will be an “incidental finding”, which will lead to an enormous increase in workload for our genetic counsellors and clinical geneticists. The additional complexity which is added by the fact that huge numbers of genetic variants are of “uncertain pathogenicity” or may be reclassified from being “likely pathogenic” to “likely benign” as more data accumulate, makes the idea of universal sequencing of the whole genome a non-starter.

My recent experience of highly selective NGS has sometimes revealed important diagnoses, and had a benefit for families with a diagnosis. In one case, for example, of an infant with multiple apparently unrelated disorders the diagnosis of MIRAGE syndrome (that I had never heard of) was helpful to stop us searching for other causes. Supportive treatment of each of the problems was organised, and the family were relieved to have an answer. There was, as usual, no specific treatment, but as mentioned that is an extremely rare result of NGS. On the other hand, some families are relieved to hear that the NGS is negative, and that their baby’s problems do not appear to have a genetic cause, that is also a potential benefit.

The message of our article is that the potential and real benefits to some families should not be exaggerated. An appraisal of the value of selective NGS, or of the idea of universal NGS, requires a realistic evaluation of the benefits and also of the adverse impacts on some families. I don’t think NGS will ever be cost effective if you calculate the benefits as QALYs gained, there are so few babies for whom a genetic diagnosis leads to a life prolonging treatment, or a life improving treatment. The very real benefits for some families are much less tangible and impossible to cost. But we must not forget the potential harms also, in order to find ways to minimize them. The advent of truly effective gene therapies (most recently for sickle cell disease) suggests that in the future there may well be a substantial group of conditions which could be treated in presymptomatic babies; that may become another argument for universal NGS screening. Until that happens, and until we figure out how to pay for all the gene therapies that are on their way, I think we should stick to highly selective NGS, and recognize the enormous difficulties in the informed consent process.

About Keith Barrington

I am a neonatologist and clinical researcher at Sainte Justine University Health Center in Montréal
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