Evaluating whole genome sequencing for rare diseases in newborn screening: evidence synthesis from a series of systematic reviews
Authors: Freeman Karoline , Dinnes Jacqueline , Shinkins Bethany , Clark Corinna , Kander Inès , Scandrett Katie , Chockalingam Shivashri , Osman Aziza , Dracup Naila , Court Rachel , Butt Furqan , Visintin Cristina , Bonham James R , Elliman David , Shortland Graham , Mackie Anne , Miedzybrodzka Zosia , Morgan Sian , Boardman Felicity , Takwoingi Yemisi , Taylor-Phillips Sian 
Published: September 2024

Background

Assessment of newborn screening using whole genome sequencing (WGS) presents considerable challenges for policy advisors, not least given the logistics of simultaneously evaluating the evidence for 200 rare genetic conditions. The ‘genotype first’ approach has the potential for harms, and benefits are uncertain.

Objective

To assess different approaches to evaluating WGS for newborn screening to inform the development of a robust method for informing policy decisions.

Methods

We undertook ‘traditional’ reviews of five conditions using standard systematic review methods (considering gene penetrance, expressivity, and prevalence, the accuracy and effectiveness of WGS, and effect of earlier treatment) (search inception to November 2023), evaluated the NIH Clinical Genome Resource (ClinGen) for evidence on the five conditions, reviewed genomic studies of paediatric screening cohorts reporting penetrance for pathogenic variants (search inception to February 2024) and undertook a methodological review of economic evaluations of WGS/ whole exome sequencing (WES) (search inception to January 2024). We explored public views on evaluating WGS.

Data sources

MEDLINE (Ovid), Embase (Ovid), Web of Science, Science Citation Index (via Clarivate), the Cochrane Library (via Wiley), CEA registry and Econlit.

Actionability reports and scores were downloaded from the ClinGen website on 30thApril 2024.

Results

The traditional review approach identified 221 studies that either reported on the genetic spectrum of individuals with the five conditions or provided limited evidence about the benefits of earlier treatment. No evidence about penetrance and expressivity or the accuracy or effectiveness of WGS in newborns was identified. ClinGen reviews were available for four of the five conditions. The ClinGen ‘actionability’ ratings for all four conditions disagreed with the findings of our traditional reviews. Our review of 14 genomic studies of newborn screening cohorts found insufficient information to allow individual highly penetrant pathogenic variants for any condition to be identified for consideration in a screening programme. None of the 86 economic evaluations of WGS or WES were set in a screening context. Some micro-costing studies are available that could help understand the resource use and costs associated with WGS. Following a series of PPI meetings, attendees appreciated the uncertainties of WGS and suggested that a wider stakeholder perspective was needed to inform policy decisions.

Limitations

Although we only examined five conditions in depth, the consistency in lack of data suggests our conclusions are robust.

Conclusions

The traditional systematic review approach for evaluating WGS of newborns identified a paucity of high-quality evidence. Extending the review to all 200 conditions is not feasible and is unlikely to yield the level of evidence required by policy advisors. The use of existing genome resources and review of genomic studies of newborn screening cohorts were not found to be viable alternatives. The cost-effectiveness of WGS in a newborn screening context is unknown.

Future work

Large-scale collaborative research is required to evaluate the short- and long-term harms, benefits and economic implications of WGS for screening newborns. We propose a staged approach to evaluation considering only conditions with pathogenic variants with very high penetrance to minimise harm from overdiagnosis.

Study registration

The protocol for this study is registered on PROSPERO: CRD42023475529

Funding details

This study/project is funded by the NIHR Evidence Synthesis Programme (ESG_HTA_NIHR159928). The views expressed are those of the author(s) and not necessarily those of the NIHR or the Department of Health and Social Care.