It is over 2 years since I posted about this issue, in the meantime there have been a number of new initiatives, and several review articles and opinion pieces. Including a JAMA, “research of the year” article”.
I was triggered to return to this issue by a recent example of such an editorial which claimed that universal neonatal genome sequencing (UNGS) “pilot programmes like the Generation Study by Genomics England, which showed that whole-genome sequencing could identify rare, treatable conditions in about one in every 200 babies.” (Of note there is no author given for this editorial, perhaps it was generated by AI, interestingly a letter from a genomics researcher in the UK, in response to a letter to the editor, actually quotes this editorial as if it were reliable data from the project!)
This sounded to me to be a bit higher than previous estimates I have seen. Sometimes the supposed advantages of a Whole Genome Sequence have been dramatically overstated, for example, counting “referral to a pulmonologist” in the accumulated sum of benefits of screening. For large numbers of WGS performed in the NICU in sick infants, when there is actually a diagnostic result, the consequence has been redirection of care to comfort/palliative care, and sometimes the delay, waiting for the result, leads to a delay in redirection of care, when it could have been performed sooner without the WGS. For UNGS on the other hand, we really want to detect conditions in a pre-symptomatic phase which are amenable to intervention, and for which intervention improves outcomes, either survival, illness, or quality of life.
We also want to avoid false positives, that is detection of genetic variants that are abnormal, and associated with a disease, but do not cause the disease in that individual. The case of Krabbe’s disease, screened for in New York state, comes to mind. In nearly 2 million screens, positive results occurred in 620, of whom 346 had the genetic abnormality. Only 5 of them actually turned out to have infantile Krabbe’s disease, a PPV of only 1.4% for the disease among those who had the abnormal gene.
I decided to do my usual, and verify the source of the “treatable diagnosis in 1/200”, statement, and it seems that the authors (or the AI) have severely misinterpreted the results from Genomics England. That reference noted that, in the proposed 100,000 neonatal genomes they are accumulating, they are searching for a list of 200 different diagnoses, which they have selected as being candidates based on 4 principles. The principles are (a variation on the Wilson and Jungner criteria, which were modified to apply specifically to genetic screening): that a known gene is responsible for a disease; that the gene variant usually causes an important condition; that the condition is treatable when found on screening; and that all persons have access to treatment equitably. Which are principles that I think we can all agree with.
Other publications from Genomics England state that “fewer than 10% of rare genetic conditions have a treatment that is effective in improving patient outcomes”. (That isn’t referring to the conditions in their screening list, but in general). Of course, for several of the more common treatable conditions, universal neonatal screening is already in place (PKU, cystic fibrosis). What is the additional yield of treatable diagnoses, compared to standard screening? Surely that is the most important question, but I have had a lot of difficulty finding an answer. That is partly because standard screening is not standard around the world, but extremely variable, and the list of genetic conditions included as the targets in each program is extremely variable.
The various pilot studies, and there are now many, are also extremely variable, and have a diagnostic yield which is very variable, depending on which conditions are included, and usually do not state how many of them are actually treatable. Indeed there are over 30 current research programs into UNGS, as well 8 commercial bodies offering NGS if you pay for it (shown with the + symbol in the figure).

Of course, there may be benefits of a diagnosis, without an actual “treatment” as such. In one pilot, from Belgium, the largest diagnostic group, by far, was G6PD deficiency, which accounted for almost 50% of the positive UNGS results. That was a modestly sized study (about 3,900 babies included) with a diagnostic result in 71 cases, 44 of which were G6PD deficiency. The remainder were a variety of diagnoses with a variety of actions that were required. Four cases of CF, for example, 2 of biotinidase deficiency requiring biotin supplementation, and 2 of haemophilia with mild reductions in Factor VIII levels requiring intervention if they need surgery. There were several diagnoses that required enhanced specific surveillance in the future (cardiomyopathy variants for example).
The diagnosis of G6PD deficiency may indeed be a real benefit to the patient, who can avoid triggering factors for life, so I would count that as a potential benefit of UNGS; many screening programs, including in Quebec where I live, do not currently include G6PD. Indeed there are published standards which include the regulations in New York State where “public health law was amended to include quantitative diagnostic G6PD deficiency testing for infants with hemolytic anemia, hemolytic jaundice, early-onset increasing neonatal jaundice persisting beyond the first week of life (bilirubin >40th percentile for age in hours), admitted to hospital for jaundice following discharge, or familial or population risk for G6PD deficiency. G6PD testing is performed as a hospital diagnostic test, not by dried blood spot testing”. Does the detection of G6PD deficiency, by UNGS, confer an additional, measurable benefit to the infant, over such an aggressive case finding policy as that in New York?
One of the “publications of the year” in the JAMA group of journals, was the description of the GUARDIAN pilot of 4000 UNGS results. That study found 120 true positive results in the infants, of which 110 would not have been detected by traditional neonatal screening, 92 of those were G6PD deficiency. The remaining 18 infants include 1 with a fatty acid disorder (MCAD) 1 with achondroplasia (surely, a good physical exam would have picked this up) 1 with hypochondroplasia, 1 with Wilson’s disease, and 2 with prolonged QT. This study used a list of 156 “actionable conditions”, and there was a subgroup of infants whose parents consented to expanded testing including a further 99 conditions which were developmental disorders with an increased seizure risk. Among the infants who had that expanded testing they found a variety of disorders, total n=6, including, for example, 2 with different genes linked with Rett syndrome.
The large number of studies in progress is an indication of the uncertainty of the benefits. I also am very concerned about the potential for abuse in the future, with every infant’s genome sequenced in a database somewhere. My provincial government has just imposed a law which allows government officials access to everyone’s medical record. Ostensibly this is to improve co-ordination and access, but it is a serious intrusion into the confidentiality of medical records, and is being strongly contested by medical organisations here. Once everyone’s genome is recorded in a database, the potential for abuse is enormous.
The largest array of genes being screened for appears to be in BabySeq, with over 4000 genes in their list. Before instituting such a program as the universal norm, we have to be certain that the benefits, for the small number of infants who are detected by UNGS over and above the regular neonatal screening programs, outweigh the possible risks. A first step would be to determine whether detecting G6PD deficiency in asymptomatic infants actually improves their outcomes in some measurable way. The second step would be to analyse the outcomes of the 0.5% of babies who have another diagnosis, some of whom require follow-up, and some require a preventative intervention.
Most of the large programs around the world seem to be taking such a cautious approach. I am unsure if the commercial programs, whose primary motivation is profit, are quite as reasonable.





























