Nanopore long-read sequencing for the critically ill facilitates ultrarapid diagnostics and urgent clinical decision making

Daphne J. Smits; Federico Ferraro; Mark Drost; Herma C. van der Linde; Bianca M. de Graaf; Yolande van Bever; Alice S. Brooks; Livija Bardina; Hennie T. Brüggenwirth; Christophe Debuy; Laura Donker Kaat; Bastiaan T. van Dijk; Nienke van Engelen; Geert Geeven; Raoul van de Graaf; Désirée Y. van Haaften-Visser; Peter M. van Hasselt; Daphne Heijsman; Yvonne M.C. Hendriks; Rebekkah J. Hitti-Malin; Lies H. Hoefsloot; Glenn Huijbregts; Hanna IJspeert; Sander Lamballais; Jona Mijalkovic; Merel O. Mol; Diënna Nawawi; Nadine Nederpelt; Esther A.R. Nibbeling; Wouter te Rijdt; Rachel Schot; Marjon van Slegtenhorst; Frank Sleutels; Eva L.M. Ulenkate; Monique Van Veghel – Plandsoen; Judith M.A. Verhagen; David Vos; Erwin Wauters; Martina Wilke; Marc Sylva; Tahsin Stefan Barakat; Tjakko J. van Ham; Tjitske Kleefstra; Dmitrijs Rots; Virginie J.M. Verhoeven

doi:10.1038/s41431-025-01959-x

Nanopore long-read sequencing for the critically ill facilitates ultrarapid diagnostics and urgent clinical decision making

Daphne J. Smits
, Federico Ferraro
, Mark Drost
, Herma C. van der Linde
, Bianca M. de Graaf
, Yolande van Bever
, Alice S. Brooks
, Livija Bardina
, Hennie T. Brüggenwirth
, Christophe Debuy
, Laura Donker Kaat
, Bastiaan T. van Dijk
, Nienke van Engelen
, Geert Geeven
, Raoul van de Graaf
, Désirée Y. van Haaften-Visser
, Peter M. van Hasselt
, Daphne Heijsman
, Yvonne M.C. Hendriks
, Rebekkah J. Hitti-Malin

Lies H. Hoefsloot, Glenn Huijbregts, Hanna IJspeert, Sander Lamballais, Jona Mijalkovic, Merel O. Mol, Diënna Nawawi, Nadine Nederpelt, Esther A.R. Nibbeling, Wouter te Rijdt, Rachel Schot, Marjon van Slegtenhorst, Frank Sleutels, Eva L.M. Ulenkate, Monique Van Veghel – Plandsoen, Judith M.A. Verhagen, David Vos, Erwin Wauters, Martina Wilke, Marc Sylva, Tahsin Stefan Barakat, Tjakko J. van Ham, Tjitske Kleefstra, Dmitrijs Rots^*, Virginie J.M. Verhoeven^*

^*Corresponding author for this work

Research output: Contribution to journal › Article › Academic › peer-review

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Abstract

Critically ill pediatric patients often have genetic disorders requiring a rapid diagnosis to guide urgent care decisions. Standard genetic testing typically takes weeks and requires multiple tests. Nanopore long-read genome sequencing (LR-GS) delivers genome-wide results within days as a one-test-fits-all solution. As one of the first centers in Europe, we implement ultrarapid LR-GS for critically ill patients. We enrolled 26 critically ill patients (median age 2 months) suspected of having a genetic disorder at the intensive care unit to perform (ultra)rapid nanopore LR-GS alongside standard genomic care. We compared diagnostic yield, turnaround time (TAT), and evaluated the impact on clinical decision making. In 11/26 cases a genetic diagnosis was made with (ultra)rapid LR-GS. From sample receipt to result, the average TAT was 5.3 days (range 2.0–10.8) for LR-GS and 18.4 days (range 6.1–29.1) for standard genomic care. DNA methylation analysis from LR-GS expedited the diagnosis in 3/26 cases. In 7/11 solved cases ultrarapid LR-GS led to immediate adjustments in patient care, e.g., medication switch or termination of treatment. Our findings underscore the clinical impact of ultrarapid LR-GS, including added value of methylation analysis, for critically ill patients and highlight existing challenges, paving the way to ultrarapid LR-GS integration into standard diagnostics.

Original language	English
Pages (from-to)	108-118
Number of pages	11
Journal	European Journal of Human Genetics
Volume	34
Issue number	1
Early online date	20 Oct 2025
DOIs	https://doi.org/10.1038/s41431-025-01959-x
Publication status	Published - Jan 2026

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Smits, D. J., Ferraro, F., Drost, M., van der Linde, H. C., de Graaf, B. M., van Bever, Y., Brooks, A. S., Bardina, L., Brüggenwirth, H. T., Debuy, C., Donker Kaat, L., van Dijk, B. T., van Engelen, N., Geeven, G., van de Graaf, R., van Haaften-Visser, D. Y., van Hasselt, P. M., Heijsman, D., Hendriks, Y. M. C., ... Verhoeven, V. J. M. (2026). Nanopore long-read sequencing for the critically ill facilitates ultrarapid diagnostics and urgent clinical decision making. European Journal of Human Genetics, 34(1), 108-118. https://doi.org/10.1038/s41431-025-01959-x

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title = "Nanopore long-read sequencing for the critically ill facilitates ultrarapid diagnostics and urgent clinical decision making",

abstract = "Critically ill pediatric patients often have genetic disorders requiring a rapid diagnosis to guide urgent care decisions. Standard genetic testing typically takes weeks and requires multiple tests. Nanopore long-read genome sequencing (LR-GS) delivers genome-wide results within days as a one-test-fits-all solution. As one of the first centers in Europe, we implement ultrarapid LR-GS for critically ill patients. We enrolled 26 critically ill patients (median age 2 months) suspected of having a genetic disorder at the intensive care unit to perform (ultra)rapid nanopore LR-GS alongside standard genomic care. We compared diagnostic yield, turnaround time (TAT), and evaluated the impact on clinical decision making. In 11/26 cases a genetic diagnosis was made with (ultra)rapid LR-GS. From sample receipt to result, the average TAT was 5.3 days (range 2.0–10.8) for LR-GS and 18.4 days (range 6.1–29.1) for standard genomic care. DNA methylation analysis from LR-GS expedited the diagnosis in 3/26 cases. In 7/11 solved cases ultrarapid LR-GS led to immediate adjustments in patient care, e.g., medication switch or termination of treatment. Our findings underscore the clinical impact of ultrarapid LR-GS, including added value of methylation analysis, for critically ill patients and highlight existing challenges, paving the way to ultrarapid LR-GS integration into standard diagnostics.",

author = "Smits, \{Daphne J.\} and Federico Ferraro and Mark Drost and \{van der Linde\}, \{Herma C.\} and \{de Graaf\}, \{Bianca M.\} and \{van Bever\}, Yolande and Brooks, \{Alice S.\} and Livija Bardina and Br{\"u}ggenwirth, \{Hennie T.\} and Christophe Debuy and \{Donker Kaat\}, Laura and \{van Dijk\}, \{Bastiaan T.\} and \{van Engelen\}, Nienke and Geert Geeven and \{van de Graaf\}, Raoul and \{van Haaften-Visser\}, \{D{\'e}sir{\'e}e Y.\} and \{van Hasselt\}, \{Peter M.\} and Daphne Heijsman and Hendriks, \{Yvonne M.C.\} and Hitti-Malin, \{Rebekkah J.\} and Hoefsloot, \{Lies H.\} and Glenn Huijbregts and Hanna IJspeert and Sander Lamballais and Jona Mijalkovic and Mol, \{Merel O.\} and Di{\"e}nna Nawawi and Nadine Nederpelt and Nibbeling, \{Esther A.R.\} and \{te Rijdt\}, Wouter and Rachel Schot and \{van Slegtenhorst\}, Marjon and Frank Sleutels and Ulenkate, \{Eva L.M.\} and \{Van Veghel – Plandsoen\}, Monique and Verhagen, \{Judith M.A.\} and David Vos and Erwin Wauters and Martina Wilke and Marc Sylva and Barakat, \{Tahsin Stefan\} and \{van Ham\}, \{Tjakko J.\} and Tjitske Kleefstra and Dmitrijs Rots and Verhoeven, \{Virginie J.M.\}",

note = "Publisher Copyright: {\textcopyright} The Author(s) 2025.",

year = "2026",

month = jan,

doi = "10.1038/s41431-025-01959-x",

language = "English",

volume = "34",

pages = "108--118",

journal = "European Journal of Human Genetics",

issn = "1018-4813",

publisher = "Springer Nature",

number = "1",

}

Smits, DJ, Ferraro, F, Drost, M, van der Linde, HC, de Graaf, BM, van Bever, Y, Brooks, AS, Bardina, L, Brüggenwirth, HT, Debuy, C, Donker Kaat, L, van Dijk, BT, van Engelen, N, Geeven, G, van de Graaf, R, van Haaften-Visser, DY, van Hasselt, PM, Heijsman, D, Hendriks, YMC, Hitti-Malin, RJ, Hoefsloot, LH, Huijbregts, G, IJspeert, H, Lamballais, S, Mijalkovic, J, Mol, MO, Nawawi, D, Nederpelt, N, Nibbeling, EAR, te Rijdt, W, Schot, R, van Slegtenhorst, M, Sleutels, F, Ulenkate, ELM, Van Veghel – Plandsoen, M, Verhagen, JMA, Vos, D, Wauters, E, Wilke, M, Sylva, M, Barakat, TS, van Ham, TJ, Kleefstra, T, Rots, D & Verhoeven, VJM 2026, 'Nanopore long-read sequencing for the critically ill facilitates ultrarapid diagnostics and urgent clinical decision making', European Journal of Human Genetics, vol. 34, no. 1, pp. 108-118. https://doi.org/10.1038/s41431-025-01959-x

TY - JOUR

T1 - Nanopore long-read sequencing for the critically ill facilitates ultrarapid diagnostics and urgent clinical decision making

AU - Smits, Daphne J.

AU - Ferraro, Federico

AU - Drost, Mark

AU - van der Linde, Herma C.

AU - de Graaf, Bianca M.

AU - van Bever, Yolande

AU - Brooks, Alice S.

AU - Bardina, Livija

AU - Brüggenwirth, Hennie T.

AU - Debuy, Christophe

AU - Donker Kaat, Laura

AU - van Dijk, Bastiaan T.

AU - van Engelen, Nienke

AU - Geeven, Geert

AU - van de Graaf, Raoul

AU - van Haaften-Visser, Désirée Y.

AU - van Hasselt, Peter M.

AU - Heijsman, Daphne

AU - Hendriks, Yvonne M.C.

AU - Hitti-Malin, Rebekkah J.

AU - Hoefsloot, Lies H.

AU - Huijbregts, Glenn

AU - IJspeert, Hanna

AU - Lamballais, Sander

AU - Mijalkovic, Jona

AU - Mol, Merel O.

AU - Nawawi, Diënna

AU - Nederpelt, Nadine

AU - Nibbeling, Esther A.R.

AU - te Rijdt, Wouter

AU - Schot, Rachel

AU - van Slegtenhorst, Marjon

AU - Sleutels, Frank

AU - Ulenkate, Eva L.M.

AU - Van Veghel – Plandsoen, Monique

AU - Verhagen, Judith M.A.

AU - Vos, David

AU - Wauters, Erwin

AU - Wilke, Martina

AU - Sylva, Marc

AU - Barakat, Tahsin Stefan

AU - van Ham, Tjakko J.

AU - Kleefstra, Tjitske

AU - Rots, Dmitrijs

AU - Verhoeven, Virginie J.M.

PY - 2026/1

Y1 - 2026/1

N2 - Critically ill pediatric patients often have genetic disorders requiring a rapid diagnosis to guide urgent care decisions. Standard genetic testing typically takes weeks and requires multiple tests. Nanopore long-read genome sequencing (LR-GS) delivers genome-wide results within days as a one-test-fits-all solution. As one of the first centers in Europe, we implement ultrarapid LR-GS for critically ill patients. We enrolled 26 critically ill patients (median age 2 months) suspected of having a genetic disorder at the intensive care unit to perform (ultra)rapid nanopore LR-GS alongside standard genomic care. We compared diagnostic yield, turnaround time (TAT), and evaluated the impact on clinical decision making. In 11/26 cases a genetic diagnosis was made with (ultra)rapid LR-GS. From sample receipt to result, the average TAT was 5.3 days (range 2.0–10.8) for LR-GS and 18.4 days (range 6.1–29.1) for standard genomic care. DNA methylation analysis from LR-GS expedited the diagnosis in 3/26 cases. In 7/11 solved cases ultrarapid LR-GS led to immediate adjustments in patient care, e.g., medication switch or termination of treatment. Our findings underscore the clinical impact of ultrarapid LR-GS, including added value of methylation analysis, for critically ill patients and highlight existing challenges, paving the way to ultrarapid LR-GS integration into standard diagnostics.

AB - Critically ill pediatric patients often have genetic disorders requiring a rapid diagnosis to guide urgent care decisions. Standard genetic testing typically takes weeks and requires multiple tests. Nanopore long-read genome sequencing (LR-GS) delivers genome-wide results within days as a one-test-fits-all solution. As one of the first centers in Europe, we implement ultrarapid LR-GS for critically ill patients. We enrolled 26 critically ill patients (median age 2 months) suspected of having a genetic disorder at the intensive care unit to perform (ultra)rapid nanopore LR-GS alongside standard genomic care. We compared diagnostic yield, turnaround time (TAT), and evaluated the impact on clinical decision making. In 11/26 cases a genetic diagnosis was made with (ultra)rapid LR-GS. From sample receipt to result, the average TAT was 5.3 days (range 2.0–10.8) for LR-GS and 18.4 days (range 6.1–29.1) for standard genomic care. DNA methylation analysis from LR-GS expedited the diagnosis in 3/26 cases. In 7/11 solved cases ultrarapid LR-GS led to immediate adjustments in patient care, e.g., medication switch or termination of treatment. Our findings underscore the clinical impact of ultrarapid LR-GS, including added value of methylation analysis, for critically ill patients and highlight existing challenges, paving the way to ultrarapid LR-GS integration into standard diagnostics.

UR - https://www.scopus.com/pages/publications/105019232542

U2 - 10.1038/s41431-025-01959-x

DO - 10.1038/s41431-025-01959-x

M3 - Article

C2 - 41116046

AN - SCOPUS:105019232542

SN - 1018-4813

VL - 34

SP - 108

EP - 118

JO - European Journal of Human Genetics

JF - European Journal of Human Genetics

IS - 1

ER -

Nanopore long-read sequencing for the critically ill facilitates ultrarapid diagnostics and urgent clinical decision making

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