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Singleton rapid long-read genome sequencing as first tier genetic test for critically Ill children with suspected genetic diseases

European Journal of Human Genetics volume 33, pages 768–774 (2025)Cite this article

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Abstract

Timely genetic testing is crucial for diagnosing pediatric patients in the intensive care units (ICUs) without known etiology. We aim to explore the benefits of singleton rapid long-read genome sequencing (rLR-GS) in critically ill children admitted to ICU with a suspected genetic etiology. Children younger than 18 years of age admitted to the ICU with a suspected genetic etiology at two tertiary hospitals in Thailand from August 2023 to May 2024 were included. rLR-GS was performed. The value of a molecular diagnosis for changing patient management outcomes was assessed. Eighteen patients were recruited. Singleton rLR-GS identified seventeen likely pathogenic (LP) or pathogenic (P) variants, resulting in the diagnosis of eleven distinct genetic disorders with autosomal recessive, autosomal dominant, and mitochondrial inheritance patterns. This yielded a diagnostic rate of 61% (11/18) with a median turnaround time of nine days. Specifically, rLR-GS identified three pathogenic structural variants (SVs), including large deletions of 19 kb, 2.4 kb, and 10.1 kb. Additionally, it provided phasing information for the two variants in each of the six patients with autosomal recessive disorders. Furthermore, the identification of two SVs and the phasing information led to the reclassification of three single nucleotide variants (SNV), one in each patient, from variants of unknown significance (VUS) to LP. The application of rLR-GS resulted in significant changes in the management of all eleven patients. This proof-of-concept study demonstrated the utility of singleton rLR-GS as a first-tier diagnostic approach for critically ill patients with unknown causes.

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Fig. 1: The differences between rES and rLR-GS through the analysis of BAM files for Cases 1 and 2.

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Any data not published within the article will be shared by the corresponding author upon reasonable request.

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Acknowledgements

We would like to express our gratitude to the Health Systems Research Institute (HSRI), under grant number HSRI 67-095, for their generous support and funding of this research. We are also grateful to the patients and their families who participated in this study.

Funding

Health Systems Research Institute (HSRI 67-095).

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Authors and Affiliations

  1. Center of Excellence for Medical Genomics, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand

    Wuttichart Kamolvisit, Chanatjit Cheawsamoot, Wanna Chetruengchai, Phawin Kor-anantakul, Rungroj Thangpong, Chalurmpon Srichomthong, Adjima Assawapitaksakul, Aayalida Buasong, Phichittra Od-Ek, Kanya Suphapeetiporn & Vorasuk Shotelersuk

  2. Excellence Center for Genomics and Precision Medicine, King Chulalongkorn Memorial Hospital, The Thai Red Cross Society, Bangkok, Thailand

    Wuttichart Kamolvisit, Chanatjit Cheawsamoot, Wanna Chetruengchai, Phawin Kor-anantakul, Rungroj Thangpong, Chalurmpon Srichomthong, Adjima Assawapitaksakul, Aayalida Buasong, Phichittra Od-Ek, Kanya Suphapeetiporn & Vorasuk Shotelersuk

  3. Respiratory Unit, Pediatric Department, Buddhachinaraj Phitsanulok Hospital, Phitsanulok, Thailand

    Kusuma Syananondh

  4. Neurology Unit, Pediatric Department, Buddhachinaraj Phitsanulok Hospital, Phitsanulok, Thailand

    Sineenat Kontun

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  1. Wuttichart Kamolvisit
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  2. Chanatjit Cheawsamoot
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Contributions

WK - conceptualization, patient recruitment, sample collection, data analysis, clinical input, writing—original draft, and writing— review & editing, CC - data analysis, writing—review & editing, WC - bioinformatics processing, PK - data analysis, patient recruitment, sample collection, clinical input, RT - data analysis, patient recruitment, sample collection, clinical input, CS - technical sequencing, AA - technical sequencing, KSa - patient recruitment, sample collection, clinical input, SK - patient recruitment, sample collection, clinical input, AB - sample processing, PO - technical sequencing, data analysis, KSu - clinical input, writing—review & editing, VS - conceptualisation, funding acquisition, clinical input, supervision, writing—review & editing.

Corresponding author

Correspondence to Vorasuk Shotelersuk.

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Competing interests

The authors declare no competing interests.

Ethical approval

The study has been approved by the Institutional Review Board of the Faculty of Medicine, Chulalongkorn University. The authority granting approval for this study is the Faculty of Medicine, Chulalongkorn University, under Research Project No. 264/62. The approval was granted on July 18, 2023. The consent was obtained from the guardians of the patients. All participants involved in this study provided informed consent prior to their participation to ensure participants were fully aware of the study’s objectives, procedures, potential risks, and benefits.

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Kamolvisit, W., Cheawsamoot, C., Chetruengchai, W. et al. Singleton rapid long-read genome sequencing as first tier genetic test for critically Ill children with suspected genetic diseases. Eur J Hum Genet 33, 768–774 (2025). https://doi.org/10.1038/s41431-025-01818-9

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