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WGS or WES? First-Tier Whole-Genome Sequencing Emerges as Cost-Effective Solution for Pediatric Genetic Diagnoses

TAIPEI, TAIWAN, Jan 31, 2024- A recent economic study by a team from Italy and the UK found that first-line whole-genome sequencing (WGS) is a cost-effective way to diagnose suspected genetic conditions in pediatric patients. Lead author Mario Cesare Nurchis, a researcher at the Catholic University of the Sacred Heart in Rome, and his team utilized an economic modeling approach to evaluate the diagnostic yields and cost-effectiveness of various genetic testing approaches.

The study incorporated hospital data and published analyses on clinical management and cost assessments. The researchers examined 870 pediatric cases from 2015 to 2022 and compared standard-of-care genetic testing, first- and second-tier whole-exome sequencing (WES), and second-tier WGS. They found that using first-tier WGS is a cost-effective way to diagnose suspected genetic conditions in children. The researchers highlighted that these factors guided the selection of WES or WGS analyses based on the clinical spectrum and previous testing results.

While standard-of-care genetic testing demonstrated the lowest cost, it yielded fewer diagnoses compared to WGS- or WES-based approaches. The study indicated that while the initial cost of first-line WGS may increase, the long-term benefits include cost-effectiveness and more accurate diagnoses. The findings hinted at the potential for minimizing diagnostic delays and facilitating the timely implementation of appropriate treatments through the broader use of WGS.

By studying costs and diagnostic results with specialized algorithms, researchers think that using first-tier WGS might be a cost-effective choice compared to other testing methods. Assuming a "willingness-to-pay" threshold of $32,625 and $54,375 per diagnosis, WGS emerged as a viable option.

However, the investigators acknowledged certain limitations, such as the focus on cost-effectiveness in relation to clinical outcomes rather than quality-adjusted life year measurements. The study didn't explore the possible diagnostic advantages of reanalyzing current WES data. It also didn't look into the costs related to storing data or interpreting noncoding variants found by WGS.

Despite these limitations, the authors championed WGS over WES as a first-tier diagnostic strategy, especially for children with suspected rare diseases. They called for policy changes at the National Health Service in Italy, highlighting the importance of adopting efficient WGS with additional clinical and economic evidence.

The study underscores the increasing imperative of incorporating genetic/genomic testing, particularly WGS, into pediatric care, given the documented diagnostic value and the evolving landscape of payer coverage.


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