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Why sequencing-based biomarkers are reshaping precision medicine

Innovations in sequencing technologies have transformed the whole concept of precision medicine by enabling a deep analysis of genetic and molecular variation. Besides single-gene testing (SGT) such as Sanger sequencing, next-generation sequencing (NGS) offers the opportunity to detect genomic changes and molecular biomarkers simultaneously, enhancing diagnosis, prognosis, and treatment decision-making. At a population level, the risk prediction and early diagnosis of diseases have been made possible by the large-scale genomic studies coupled with longitudinal health data. Furthermore, the timely decision-making in critically ill patients has been achieved in the clinical setting through the rapid sequencing and multi-omics analysis. These strategies represent a paradigm shift to data-driven, integrative precision medicine, in which patient care and treatment delivery are directly influenced by molecular data. Sequencing-based biomarkers offer a more comprehensive insight into the biology of the disease than traditional biomarkers because they allow the measurement of complex interactions between genes, proteins, and metabolites. Also, machine learning (ML) and artificial intelligence (AI) enhance their predictive ability, allowing patient stratification and personal selection of treatment. These techniques are expected to gain significant importance in clinical practice as well as population-based programs of public health because of current developments in sequencing technologies, greater access, and better quality.1-5.
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The shift from single-gene tests to sequencing-based biomarkers

Molecular diagnostics has been completely altered by next-generation sequencing (NGS). Traditional single-gene tests, which were once thought to be the gold standard, are performed using sequential testing, requiring additional tissue, time, and resources for each test. This strategy was particularly ineffective in genetically heterogeneous diseases, in which pathogenic variants in more than one gene may cause overlapping clinical phenotypes. Consequently, the stepwise testing process may take months- or even years- leaving patients without a definite diagnosis and delaying the initiation of specific therapies.

The introduction of NGS-based gene panel has transformed the diagnostic paradigm because it has the potential to provide an analysis of dozens to hundreds of genes in a single sample. For example, Illumina’s TruSight One panel examines > 4,813 clinically significant genes across 12 Mb of genomic content; disease-specific panels that target inherited cardiac conditions, such as Illumina’s TruSight Cardio, or gene panels specifically designed for epilepsy, enable targeted examination of condition-relevant variants with high depth of coverage. Together with complementary methods (e.g., Sanger sequencing or array comparative genomic hybridization (aCGH)), such assays can reveal the entire repertoire of genetic modifications, between single-nucleotide variants and small insertions/deletions up to large-scale structural changes, in one experiment. Thus, this shift bears substantial clinical implications.  NGS panels have the potential to significantly shorten the diagnostic odyssey (years to weeks), enhance diagnostic yield, and enable distinction between conditions of overlapping phenotype. However, SGT is still applicable in established diseases where pathogenic mutations are mainly linked to a single gene, including achondroplasia or cystic fibrosis, in instances necessitating specific tests for trinucleotide repeat expansions or epigenetics. NGS-based panels enhance the efficiency of diagnosis by combining several tests into a single diagnostic assay, simplifying rapid therapeutic decision-making and enhancing patient care, hence underscoring their vital role in the era of precision medicine. 1,2,6-8
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Ultrarapid whole-genome sequencing in precision medicine

Ultra-rapid whole-genome sequencing (urWGS) is a fast diagnostic modality that sequences and analyzes the whole genome of an individual in a few hours. Platforms such as the Oxford Nanopore PromethION have proved this potential in critically ill newborns, yielding genome-wide data within hours of sample collection. Integrating NGS technology with streamlined laboratory procedures and real-time bioinformatic analysis, urWGS can identify single-nucleotide variations as well as small insertions, deletions, and structural variants within a single assay. When conducted as a trio sequencing, the analysis of the affected infant with both biological parents’ urWGS enables the identification of de novo variants and the pattern of inheritance, thus enhancing the accuracy of diagnosis.

The application of urWGS in pediatric and neonatal intensive care units (ICUs) has substantially transformed the diagnostic approach for critically ill infants. It is estimated that about 15 percent of infants in the ICU carry a genetic disorder that is a key root cause of morbidity and mortality among this population. These patients have complex, multi-system phenotypes that cannot be addressed using conventional genetic testing approaches, which may take weeks to months, and in most cases, cannot be applied to make urgent clinical decisions.
Why sequencing-based biomarkers are reshaping precision medicine
Van der Vreken, P., et al. (2023). Rapid Whole Genome Sequencing Diagnoses and Guides Treatment in Critically Ill Children in Belgium in Less than 40 Hours. Genes.
UrWGS not only facilitates rapid molecular diagnosis but also has a major impact on the management of the patient. It informs decisions on targeted medicines, treatment termination, surgical procedures, dietary adjustments, and prognosis planning. Effective implementation needs timely genetic counseling, interdisciplinary case assessment, and structured routes to transform genomic results into meaningful therapeutic interventions. Challenges still persist, such as incomplete genomic coverage, interpretation of new variants, ethical considerations, and inaccessibility because of financial limitations. interpretation of novel variants, the ethical issues, and the lack of access due to financial constraints. Nonetheless, advancements in technology and cost-reduction are likely to positively affect the diagnostic rate, and, therefore, urWGS is set to become a first-line diagnostic tool in the ICU and a cornerstone of precision medicine in susceptible populations. 3,9-12
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Comprehensive genomic profiling for cancer and rare diseases

Comprehensive genomic profiling (CGP) is an approach that uses NGS to identify genetic defects in multiple genes and molecular biomarkers using a single test. It is essential in personalized medicine for cancer diagnosis, treatment selection, and prognostic assessment. CGP identifies genomic alterations, including single-nucleotide variants (SNVs), insertions and deletions (indels), copy number variants (CNVs), and fusions. It can also assess complicated biomarkers, e.g., homologous recombination deficiency (HRD), tumor mutational burden (TMB), and microsatellite instability (MSI). Besides the identification of personalized genomic changes, CGP is a multifaceted decision-support system within the area of precision oncology. CGP facilitates the early discovery of actionable driver and resistance mechanisms to inform treatment decisions across tumour types through the simultaneous interrogation of hundreds of cancer genes. This is of particular significance in the case of dealing with more complex and rare tumors, where molecular diversity and limited tissue availability restrict the utilization of sequential single-gene assays.  The capability of CGP in measuring genomic signatures such as tumour mutational burden and microsatellite instability further extends the use of CGP beyond the discovery of mutations. These biomarkers aid in predicting immune checkpoint inhibitor response, and these are the basis of most tumour-agnostic approvals, providing patients with tumour-agnostic immunotherapy regardless of the tumour type.

From a health-system and clinical perspective, CGP enhances the diagnostic outcome of a single specimen and addresses tissue insufficiency issues in the oncology setting, specifically in metastatic cancer. It reduces the need for repeated testing and biopsies, accelerating treatment decisions and reducing the risks and expenses associated with procedures. The addition of RNA sequencing and liquid biopsy technology improves the detection of key alterations when tissue is scarce. In rare cancers, CGP aids in decision-making concerning treatment selection and enrolment in clinical trials.  Precision oncology studies have demonstrated that patients who receive targeted treatments have better outcomes. In general, CGP promotes a data-driven approach in oncology, which has a significant impact on the development of therapies and value-based precision medicine. 13 – 15
Why sequencing-based biomarkers are reshaping precision medicine
Kim, J., et al. (2024). Target-Enhanced Whole-Genome Sequencing Shows Clinical Validity Equivalent to Commercially Available Targeted Oncology Panel. Cancer Res Treat.
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Population-scale genomic initiatives and AI-driven biomarkers

Population-scale genomic initiatives have transformed biomarker discovery by enabling the systematic analysis of genetic variation across very large cohorts. Whole-genome sequencing initiatives like the UK Biobank offer an in-depth coverage of both the coding and non-coding regions, both common and rare variants, structural variation, and mosaic events on a population scale. With the availability of whole-genome data in combination with well-documented longitudinal health records, genetic variation can be directly linked to disease risk, progression, and clinical outcomes of various conditions. Population-scale whole-genome sequencing provides a global picture of the genomic architecture in comparison to earlier array-based research. It enables the identification of new disease-related genes, enhances the mapping of causal variations, and determines ancestry-specific genetic effects important for precision medicine. This approach has contributed to the discovery of clinically meaningful phenomena such as clonal hematopoiesis and rare pathogenic variants associated with undiagnosed disease. Their complexity has increased the application of artificial intelligence and ML to discover biomarkers, with recent data highlighting applications in oncology, rare diseases, and chronic diseases to predict disease risk and stratify patients. Notably, population-scale genomics combined with AI analytics allow a shift from single-marker associations to making predictive models of genetic, molecular, and clinical characteristics. This convergence helps in detecting diseases earlier, better risk stratification, and identification of individuals who may benefit from targeted screening or intervention. Thus, population-scale genetic resources and AI-driven biomarker discoveries constitute a fundamental basis for scalable precision medicine and data-informed public health measures. 5,16,17

Future of sequencing-based biomarkers: multiomics and real-time analytics

Ultra-rapid whole-genome sequencing is increasingly recognized as a basic component of modern precision medicine, particularly when implemented in integrated multi-omics approaches. urWGS enables the rapid generation of comprehensive genomic information in a matter of hours, enabling the timely identification of disease-causing mutations in alignment with urgent clinical decision-making. However, genetic variation by itself does not provide a clear explanation of disease mechanisms. The integration of urWGS with transcriptomics and proteomics offers functional insights, explaining the biological significance of genetic variants, resolving variants of uncertain significance, and improving diagnostic confidence. Large-scale clinical research has demonstrated that this hierarchical, multi-omics approach significantly improves diagnostic rates over genome sequencing alone and often leads to changes in the management of patients, including the use of personalized therapies and the avoidance of unnecessary or ineffective therapies.

The rapid sequencing provides the option of providing an immediate and practical diagnosis, which can make a considerable impression on the treatment of patients, as demonstrated in the medical literature that has repeatedly supported it in critically ill patients. These findings underscore the importance of the discussed approach as a diagnostic resource and a driving force towards more accurate, timely, and cost-effective patient care in ICUs. With the advancement of these technologies and the integration with other layers of omics becoming more plausible, the role of urWGS-based multi-omics in the delivery of precision medicine becomes central, particularly in settings where speed and accuracy are the most important factors. 4,9,18,19
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Frequently asked questions about sequencing-based biomarkers

Sequencing-based biomarkers are molecular markers identified through next-generation sequencing (NGS) that capture genetic variants, genomic signatures, and complex molecular patterns associated with disease. Unlike traditional biomarkers, they provide a comprehensive, genome-wide view of disease biology and support diagnosis, prognosis, patient stratification, and treatment selection in precision medicine.
Sequencing-based biomarkers assess multiple genes and genomic features simultaneously, whereas single-gene tests require sequential analysis and are limited in genetically heterogeneous diseases. NGS-based approaches shorten diagnostic timelines, increase diagnostic yield, and enable the detection of diverse variant types, including SNVs, indels, CNVs, and structural variants, within a single assay.
Ultra-rapid whole-genome sequencing (urWGS) delivers a comprehensive genetic diagnosis within hours, making it particularly valuable in critical care settings such as neonatal and pediatric ICUs. By rapidly identifying disease-causing variants, urWGS enables timely therapeutic decisions, including targeted treatment, surgical planning, or changes in clinical management that would not be possible with conventional genetic testing.
Comprehensive genomic profiling (CGP) uses NGS to detect actionable genomic alterations and complex biomarkers such as tumor mutational burden (TMB), microsatellite instability (MSI), and homologous recombination deficiency (HRD). CGP supports personalized oncology by guiding targeted therapy selection, immunotherapy eligibility, and clinical trial enrolment, especially in rare or molecularly complex cancers.
Population-scale whole-genome sequencing combined with artificial intelligence and machine learning enables the discovery of predictive biomarkers across large cohorts. By integrating genomic, molecular, and longitudinal clinical data, AI-driven models move beyond single-variant associations toward risk prediction, early disease detection, and patient stratification, forming the basis of scalable precision medicine and data-driven public health.

References

  1. Ng, K. W., Chin, H. L., Chin, A. X., & Goh, D. L. M. (2022). Using gene panels in the diagnosis of neuromuscular disorders: A mini-review. Frontiers in Neurology, 13, 997551.

  2. Vinkšel, M., Writzl, K., Maver, A., & Peterlin, B. (2021). Improving diagnostics of rare genetic diseases with NGS approaches. Journal of community genetics, 12(2), 247-256.

  3. Dimmock, D., Caylor, S., Waldman, B., Benson, W., Ashburner, C., Carmichael, J. L., … & Farnaes, L. (2021). Project Baby Bear: Rapid precision care incorporating rWGS in 5 California children’s hospitals demonstrates improved clinical outcomes and reduced costs of care. The American Journal of Human Genetics, 108(7), 1231-1238.

  4. Lunke, S., Bouffler, S. E., Patel, C. V., Sandaradura, S. A., Wilson, M., Pinner, J., … & Stark, Z. (2023). Integrated multi-omics for rapid rare disease diagnosis on a national scale. Nature medicine, 29(7), 1681-1691.

  5. Abbasi, A. F., Naveed, S., Asim, M. N., Sajjad, M., Vollmer, S., & Dengel, A. (2025). Artificial intelligence powered biomarker discovery: a large-scale analysis of 236 studies across 19 therapeutic areas and 147 diseases. BioRxiv, 2025-08.

  6. TruSight™ One Sequencing Panels. High-performing comprehensive panels targeting disease-associated regions of the exome. Assessed from https://www.illumina.com/content/dam/illumina/gcs/assembled-assets/marketing-literature/trusight-one-sequencing-panels-data-sheet-m-gl-02149/trusight-one-sequencing-panels-data-sheet-m-gl-02149.pdf.

  7. TruSight One Expanded Sequencing Panel. Assessed from https://emea.illumina.com/library-prep-array-kit-selector/kits-and-arrays/trusight-one-expanded-panel.html.

  8. Pua, C. J., Bhalshankar, J., Miao, K., Walsh, R., John, S., Lim, S. Q., … & Cook, S. A. (2016). Development of a comprehensive sequencing assay for inherited cardiac condition genes. Journal of cardiovascular translational research, 9(1), 3-11.

  9. Kingsmore, S. F., & Cole, F. S. (2022). The role of genome sequencing in neonatal intensive care units. Annual review of genomics and human genetics, 23(1), 427-448.

  10. Petrikin, J. E., Cakici, J. A., Clark, M. M., Willig, L. K., Sweeney, N. M., Farrow, E. G., … & Kingsmore, S. F. (2018). The NSIGHT1-randomized controlled trial: rapid whole-genome sequencing for accelerated etiologic diagnosis in critically ill infants. NPJ Genomic Medicine, 3(1), 6.

  11. Dimmock, D. P., Clark, M. M., Gaughran, M., Cakici, J. A., Caylor, S. A., Clarke, C., … & Yamada, C. (2020). An RCT of rapid genomic sequencing among seriously ill infants results in high clinical utility, changes in management, and low perceived harm. The American Journal of Human Genetics, 107(5), 942-952.

  12. Gorzynski, J. E., Goenka, S. D., Shafin, K., Jensen, T. D., Fisk, D. G., Grove, M. E., … & Ashley, E. A. (2022). Ultrarapid nanopore genome sequencing in a critical care setting. New England Journal of Medicine, 386(7), 700-702.

  13. Subbiah, V., & Kurzrock, R. (2025). Imperative of Comprehensive Molecular Profiling as Standard of Care for Patients With Rare Cancers. JCO Oncology Practice, OP-25.

  14. Tjota, M. Y., Segal, J. P., & Wang, P. (2024). Clinical utility and benefits of comprehensive genomic profiling in cancer. The Journal of Applied Laboratory Medicine, 9(1), 76-91.

  15. What is Comprehensive Genomic Profiling and is it the Right Solution for You? Assessed from https://www.thermofisher.com/fr/fr/home/clinical/preclinical-companion-diagnostic-development/oncomine-oncology/education/what-is-comprehensive-genomic-profiling.html.

  16. Zhao, J., & Shen, S. (2025). Discover novel biomarkers using population-scale whole-genome sequencing. Innovation Medicine, 3(4), 100168.

  17. Sivadas, A., & Scaria, V. (2019). Population-scale genomics—Enabling precision public health. Advances in genetics, 103, 119-161.

  18. Xiao, F., Yan, K., Tang, M., Ji, X., Hu, L., Yang, L., & Zhou, W. (2022). Diagnostic utility of rapid sequencing in critically ill infants: a systematic review and meta-analysis. Expert Review of Molecular Diagnostics, 22(8), 833-840.

  19. Lunke, S., Eggers, S., Wilson, M., Patel, C., Barnett, C. P., Pinner, J., … & Stark, Z. (2020). Feasibility of ultra-rapid exome sequencing in critically ill infants and children with suspected monogenic conditions in the Australian public health care system. Jama, 323(24), 2503-2511.

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