Genomics is no longer the future of medicine—it is already here. Advances in next-generation sequencing (NGS) and bioinformatics have transformed how clinicians can diagnose and manage patients across multiple specialties. Yet many hospitals continue to treat genomic testing as an optional or external service, resulting in delays, repeated hospitalizations, and mounting costs.
The central thesis is clear: delays in adopting genomic testing cost hospitals more than the upfront investment in rapid genomic solutions. The consequences are not only clinical but also economic and organizational. This article examines the current landscape of genomic medicine in hospitals, including the hidden costs of waiting, the measurable return on investment (ROI), real-world clinical use cases, barriers and solutions, and ultimately, why the time to act is now.
Current Landscape in Hospitals
In many hospitals, genetic testing is managed in an ad hoc way. When a clinician suspects a hereditary disorder, samples are often shipped to outside reference laboratories. While technically feasible, this approach leads to long turnaround times and fragmented care (Glaubitz et al., 2025).
On average, patients with rare diseases take 5–7 years to receive a molecular diagnosis, during which time they generate data relative to the “diagnostic odyssey.” They endure returning hospitalizations, uncomfortable procedures, and futile treatments while on this journey (EveryLife Foundation, May 2017). Loss of income and reputation is a double hit on hospitals.
Indeed, the diagnostic yield of exome sequencing in infants presenting with suspected monogenic disorder is highly likely to be higher than “usual care” if sequencing can be integrated early in the clinical pathway (Stark et al., 2016). In a subsequent study, early genomic testing not only increased the probability of optimal-based treatments but also decreased the number of procedures that were unnecessary, thereby proving to be cost-effective (Stark et al., 2019).
The Hidden Costs of Waiting
Direct Costs
One of the largest burdens comes from prolonged hospitalizations. Critically ill infants in NICUs without a genetic diagnosis often remain in intensive care for significantly longer periods. Studies have shown that rapid genome sequencing shortens NICU stays and prevents invasive procedures (Farnaes et al., 2018). Repeated imaging, biopsies, and metabolic tests, while essential in the absence of a clear diagnosis, can cost tens of thousands of dollars per patient (Tan et al., 2017).
Unnecessary medications represent another direct cost. Without a genetic diagnosis, patients are frequently treated empirically, sometimes with drugs later proven ineffective or even contraindicated. In epilepsy, for example, sodium channel blockers can worsen seizures in patients with SCN1A mutations; yet these drugs are often prescribed before a genetic test confirms the contraindication (Schwarze et al., 2018).
Indirect Costs
Hospitals also face less visible but equally damaging costs.
- Missed or delayed diagnoses increase the risk of litigation and malpractice claims (Phillips et al., 2018).
- Families who endure years without answers often lose trust in the institution, harming reputation and patient loyalty.
- Staff resources are wasted chasing test results from external laboratories, contributing to burnout among clinicians and administrators.
Missed Revenue
Hospitals are also missing out on potential revenue when they don’t have their own in-house genomics technology. They could be frozen out of clinical trials that depend on rapid molecular diagnoses, losing funding and status. Hospitals that do not have genomic capabilities would be unable to brand themselves as rare disease or precision oncology referral centers, leading to loss in patient traffic that could boost both their balance sheets and reputation (Kang, 2022).
The ROI of Genomics
Economic ROI
Cost-effectiveness analyses consistently demonstrate net savings. In the California-based Project Baby Bear, sequencing costs of $1.7 million were outweighed by a reduction in healthcare costs, saving $2.5 million, much of which was related to shortened lengths of hospital stays and reduced inappropriate testing (Rady Children’s Institute for Genomic Medicine, 2020).
Another multicenter study demonstrated the cost-effectiveness of genome sequencing as the first-line test for critically ill pediatrics when compared to serial standard testing (Regier et al., 2024).
Strategic ROI
Hospitals that make investments in genomics are more likely to draw:
- referrals;
- research;
- grant opportunities.
Being perceived as an innovation leader helps in the recruitment of clinicians and researchers. The cost for genomics is percolating down with time, and indeed this can only be achieved when tested at scale not in pilots (Stark et al., 2019).
Neonatal Intensive Care
Rapid whole-genome sequencing has transformed care in NICUs. Among the critically ill newborns, sequencing shortened the length of hospital stay, spared invasive tests, and provided life-altering diagnoses (Farnaes et al., 2018).
Oncology
In the field of oncology, germline testing reveals hereditary cancer syndromes and informs patient care and family counseling. The ability to identify carriers of BRCA or Lynch syndrome early in life allows for inexpensive surveillance and prevention that decreases lifelong costs and morbidity (Tan et al., 2017).
Cardiology
Cardiology genetic testing identifies patients with channelopathies and inherited cardiomyopathy. This will then allow directed management, notably defibrillator implantation when indicated, thus avoiding both sudden deaths and unnecessary expenditures (Schwarze et al., 2018).
Neurology
Rapid sequencing in pediatric neurology is particularly relevant for locating treatable epileptic encephalopathies and potentially exposes patients to precision treatments instead of contraindicated medications. It not only produces better results but also cuts long-term hospitalization expenses (Phillips et al., 2018).
Barriers for Hospitals And How to Overcome Them
Cost of Sequencing
There’s an investment required in sequencing and analysis, but the prices are falling very quickly. Hospitals can begin by contracting or partnering with specialty genomic centers. AI-based interpretation tools also contribute to cost-saving and manpower reduction (Kang, 2022).
Expertise Gaps
As clinicians and laboratory professionals increasingly engage with genomic data, the interpretation of complex genetic findings often requires specialized expertise in genetics and bioinformatics. These skills may not yet be widely available within most hospital settings, where teams can face challenges in efficiently processing and contextualizing large-scale sequencing results.
Given the rapid evolution of sequencing technologies and variant interpretation guidelines, even experienced professionals benefit from dedicated resources and support tools. To strengthen clinical genomics implementation, potential approaches include:
- shared service models;
- partnerships with academic or reference centers;
- formal training opportunities for current staff (Stark et al., 2016).
Complementing these efforts, bioinformatics interpretation platforms that systematically organize and annotate genetic data can help bridge the gap—providing clinicians with accessible, standardized insights that enhance the accuracy and efficiency of genomic decision-making.
Integration with EMR/LIS
Genomic information needs to be integrated into electronic health records to become actionable. Standards such as HL7 FHIR2 should be embraced by institutions, which may build a staged approach to integration, beginning with PDF reports, for example, and progressing towards structured variant data (Phillips et al., 2018).
Reimbursement and Policy
Payers are still skeptical, but real-world evidence is forcing changes in the reimbursement landscape. Hospitals that pilot genomic programs and report out data will have the most leverage in reimbursement negotiations (Regier et al., 2024).
Why Act Now
Globally, leading hospitals are already implementing genomic medicine, making it a standard expectation rather than a premium service. Patients increasingly demand personalized approaches, and delaying adoption risks losing both patients and prestige (EveryLife Foundation, 2023). Moreover, the longer institutions wait, the more they spend on inefficient diagnostic odysseys. Early adopters will also benefit most from falling sequencing costs and growing reimbursement support (Schwarze et al., 2018).
Conclusion
Genomics is here, and the evidence is overwhelming: hospitals that invest now will save money, improve outcomes, and gain strategic advantage. Continuing to delay adoption is not neutral but costly. The real choice facing hospital leadership is whether to lead or lag.
Hospitals that implement genomic diagnostics today will lead tomorrow in both outcomes and economics.
References
- EveryLife Foundation. (2023). The cost of delayed diagnosis in rare disease: Early diagnosis could save $500,000 per patient. EveryLife Foundation.
- Farnaes, L., Hildreth, A., Sweeney, N. M., Clark, M. M., Chowdhury, S., Nahas, S., Cakici, J. A., Benson, W., Kaplan, R. H., Kronick, R., & Dimmock, D. P. (2018). Rapid whole-genome sequencing decreases infant morbidity and cost of hospitalization. NPJ Genomic Medicine, 3, 10.
- Glaubitz, R., et al. (2025). The cost of the diagnostic odyssey of patients with suspected rare diseases. Orphanet Journal of Rare Diseases, 20(1).
- Kang, D. Y. (2022). Whole genome sequencing will reduce the cost of diagnostics. Gene Therapy & Molecular Biology Perspectives.
- Phillips, K. A., Douglas, M. P., & Marshall, D. A. (2018). Assessing the value of next-generation sequencing. Value in Health, 21(9), 920–924.
- Rady Children’s Institute for Genomic Medicine. (2020). Genomic sequencing for infants in intensive care yields life-changing benefits. Rady Genomics.
- Regier, D. A., et al. (2024). Real-world diagnostic outcomes and cost-effectiveness of genome sequencing. Genetics in Medicine, 26(1), 45–53.
- Schwarze, K., Buchanan, J., Taylor, J. C., & Wordsworth, S. (2018). Are whole-exome and whole-genome sequencing approaches cost-effective? A systematic review of the literature. Genetics in Medicine, 20(10), 1122–1130.
- Stark, Z., Schofield, D., Martyn, M., Rynehart, L., Shrestha, R., Alam, K., Lunke, S., Tan, T. Y., Gaff, C. L., & White, S. M. (2019). Does genomic sequencing early in the diagnostic trajectory make a difference? A follow-up study of clinical outcomes and cost-effectiveness. Genetics in Medicine, 21(2), 516–523.
- Stark, Z., Tan, T. Y., Chong, B., Brett, G. R., Yap, P., Walsh, M., Yeung, A., Peters, H., McGillivray, G., & White, S. M. (2016). A prospective evaluation of whole-exome sequencing as a first-tier molecular test in infants with suspected monogenic disorders. Genetics in Medicine, 18(11), 1090–1096.
- Tan, T. Y., Dillon, O. J., Stark, Z., Schofield, D., Alam, K., Shrestha, R., Chong, B., Phelan, D., Brett, G. R., & White, S. M. (2017). Diagnostic impact and cost-effectiveness of whole-exome sequencing in children with suspected monogenic disorders. European Journal of Human Genetics, 25(6), 662–670.