ENOrphanet Journal of Rare Diseases | Cost Analysis of Hospitalized Children with Suspected Rare Genetic Diseases: Direct and Indirect Cost Assessment in a Routine Genetic Testing Cohort
Date: February 12, 2026
Classification: Frontiers
Recommend:
This study is the first to systematically evaluate the total healthcare costs of hospitalized children suspected of rare genetic disorders undergoing routine genetic testing in a Canadian context. It reveals significantly higher costs in the neonatal group compared to other age groups, providing critical baseline data for health economic decisions aimed at optimizing rare disease diagnostic pathways.
Literature Overview
This paper, 'Cost analysis of hospitalized children suspected of rare genetic diseases,' published in the Orphanet Journal of Rare Diseases, reviews and summarizes the medical cost structure during the first hospitalization of pediatric patients receiving routine genetic testing (CGT) at a Canadian tertiary pediatric hospital. Based on retrospective data from 223 patients, the study uses the hospital's internal cost database (CPSS) for cost accounting, focusing on direct and indirect cost components, length of stay, and clinical outcomes, with stratification by age, sex, and number of tests. The research reveals that hospitalization costs for children suspected of rare genetic disorders are substantially higher than those of the general pediatric population, particularly among neonates. This work fills a research gap in Canada regarding the economic burden of hospitalization for rare diseases and provides a historical benchmark for future evaluations of the health economic value of whole-exome or whole-genome sequencing.Background Knowledge
Rare Genetic Disorders (RGDs) are a group of diseases caused by gene mutations, with an overall incidence of approximately 1–2% of live births, and are a major cause of hospitalization and mortality in infants and young children. Due to high phenotypic heterogeneity and lack of specific clinical markers, diagnosis often follows a 'diagnostic odyssey,' leading to prolonged hospitalizations, multiple rounds of testing, and high healthcare expenditures. Current mainstream diagnostic technologies include chromosomal microarray, targeted gene panel sequencing (CGT as used in this study), whole-exome sequencing (ES), and whole-genome sequencing (GS). Although next-generation sequencing (NGS) technologies demonstrate higher diagnostic yields, their adoption in Canada remains limited by insurance coverage and cost-effectiveness debates. Previous studies have largely focused on the U.S. or specific diseases, lacking comprehensive assessments of hospitalization costs within Canada’s public healthcare system. This study’s innovation lies in using real-world data to quantify the economic burden of the CGT cohort, offering empirical support for policymakers and healthcare institutions to optimize rare disease screening strategies. Its significance lies in establishing a cost baseline for the CGT era, enabling future comparisons of the cost-saving potential of newer sequencing technologies.
Research Methods and Experiment
This study is a single-center, retrospective cohort study based on medical records. Data were collected from pediatric patients hospitalized at CHU Sainte-Justine in Montreal between January 2021 and November 2022 who underwent routine genetic testing (CGT). Inclusion criteria included age under 18 and receiving CGT during hospitalization; non-residents of Quebec were excluded. A total of 223 patients were included. Hospitalization costs were extracted from the hospital’s internal CPSS (Coût par Parcours de Soins et Services) cost database, covering direct costs (e.g., medications, laboratory tests, clinical care) and indirect costs (e.g., hospital overhead). The study used a non-parametric bootstrap method (10,000 iterations) to calculate 95% confidence intervals for average costs, with stratified analyses by age, sex, and number of CGT tests. All costs were adjusted to 2023 Canadian dollars (CAD).Key Findings and Insights
Research Implications and Outlook
This study is the first to systematically quantify the hospitalization-related economic burden of children suspected of rare genetic disorders within Canada’s public healthcare system, revealing the high costs associated with current CGT strategies, especially in neonatal intensive care settings. The findings underscore the potential value of rapid diagnosis in reducing hospital stays and healthcare expenditures. As whole-exome/genome sequencing (ES/GS) becomes increasingly available in Canada, future research must evaluate whether these new technologies can reduce costs by shortening the diagnostic journey, minimizing unnecessary testing, and reducing hospitalization duration. The cost data provided in this study can serve as a baseline for future health technology assessments (HTA), enabling modeling and comparison of the long-term cost-effectiveness of different diagnostic strategies.
Conclusion
This study systematically evaluates the hospitalization costs of children undergoing routine genetic testing (CGT) for suspected rare genetic disorders at a Canadian tertiary pediatric hospital. The results show that the average hospitalization cost reaches CAD 170,000—over 30 times higher than that of typical pediatric admissions—with significantly higher costs and mortality rates observed in neonates. Clinical care, pharmacy, and laboratory testing are the primary cost drivers, and patients undergoing multiple CGT tests incur substantially higher expenses. The study highlights issues of time delays and economic burden in the current diagnostic process, providing key empirical support for optimizing rare disease diagnostic pathways. Although focused on the CGT era, these findings establish an important baseline for evaluating the cost-effectiveness of emerging technologies such as whole-exome or whole-genome sequencing. Promoting rapid and precise genomic diagnosis may not only improve patient outcomes but also reduce overall healthcare spending in the long term. This study fills a critical gap in rare disease health economics in Canada and offers valuable insights for healthcare policy and resource allocation.
