Comparative Evaluation of CNVs Detection:  A Case Study of
Optical Genome Mapping and Long-Read Whole-Genome  Sequencing
versus Chromosomal Microarray

a 2025

Comparative Evaluation of CNVs Detection: A Case Study of Optical Genome Mapping and Long-Read Whole-Genome Sequencing versus Chromosomal Microarray

ŠTOLFA, Miroslav; Eva HLADÍLKOVÁ; Hana FILKOVÁ; Dominik REŽNÝ; Kamila RÉBLOVÁ et al.

Základní údaje

Originální název

Comparative Evaluation of CNVs Detection: A Case Study of Optical Genome Mapping and Long-Read Whole-Genome Sequencing versus Chromosomal Microarray

Autoři

ŠTOLFA, Miroslav; Eva HLADÍLKOVÁ; Hana FILKOVÁ; Dominik REŽNÝ; Kamila RÉBLOVÁ ; Rastislav BEHARKA; Jana ŠOUKALOVÁ; Petr KUGLÍK a Vladimíra VALLOVÁ

Vydání

15th EUROPEAN CYTOGENOMICS CONFERENCE, Leuven, Belgium, 2025

Další údaje

Jazyk

angličtina

Typ výsledku

Konferenční abstrakt

Obor

10600 1.6 Biological sciences

Utajení

není předmětem státního či obchodního tajemství

Označené pro přenos do RIV

Organizační jednotka

Přírodovědecká fakulta

Klíčová slova anglicky

Copy number variations; Chromosomal microarray; Optical genome mapping; Long-read whole-genome sequencing

Příznaky

Mezinárodní význam

Změněno: 5. 3. 2026 10:20, Mgr. Marie Novosadová Šípková, DiS.

Anotace

V originále

The contribution of copy number variations (CNVs) to the pathogenesis of various diseases has been increasingly recognized. Chromosomal microarray (CMA) remains the gold standard for genome-wide CNVs analysis. However, emerging cytogenomic techniques, such as optical genome mapping (OGM) and long-read whole-genome sequencing (LR-WGS), offer the potential to not only detect structural variations but also to provide more detailed insights into CNVs. In this study, we compared and evaluated the CNV profiles obtained using CMA (Agilent), OGM (Bionano), and LR-WGS (Oxford Nanopore Technologies) in a patient with neurodevelopmental symptoms and negative classical cytogenetic results. Our primary aim was to assess the success and accuracy of CNVs detection by OGM and LR-WGS, relative to the CMA method, which is firmly established in clinical diagnostics. The CMA analysis identified a duplication and a deletion of chromosome 12, both of which were also detected by OGM and LR-WGS. Notably, LR-WGS provided a more detailed and comprehensive view of the affected regions, offering refined coordinates of the CNVs and a deeper examination of the associated genes. This case report suggests that OGM and LR-WGS hold significant potential for CNV detection in clinical practice. However, it is crucial to understand the limitations of these methods and integrate them carefully into diagnostic algorithms for optimal clinical utility.

Návaznosti

EH23_020/0008555, projekt VaV

Název: Využití komplexního genomického testování - na cestě k lepší diagnostice

Citovat

ŠTOLFA, Miroslav; Eva HLADÍLKOVÁ; Hana FILKOVÁ; Dominik REŽNÝ; Kamila RÉBLOVÁ; Rastislav BEHARKA; Jana ŠOUKALOVÁ; Petr KUGLÍK a Vladimíra VALLOVÁ. Comparative Evaluation of CNVs Detection: A Case Study of Optical Genome Mapping and Long-Read Whole-Genome Sequencing versus Chromosomal Microarray. In 15th EUROPEAN CYTOGENOMICS CONFERENCE, Leuven, Belgium. 2025.

@proceedings{2507678,
   author = {Štolfa, Miroslav and Hladílková, Eva and Filková, Hana and Režný, Dominik and Réblová, Kamila and Beharka, Rastislav and Šoukalová, Jana and Kuglík, Petr and Vallová, Vladimíra},
   booktitle = {15th EUROPEAN CYTOGENOMICS CONFERENCE, Leuven, Belgium},
   keywords = {Copy number variations; Chromosomal microarray; Optical genome mapping; Long-read whole-genome sequencing},
   language = {eng},
   title = {Comparative Evaluation of CNVs Detection: A Case Study of Optical Genome Mapping and Long-Read Whole-Genome Sequencing versus Chromosomal Microarray},
   year = {2025}
}

TY  - CONF
ID  - 2507678
AU  - Štolfa, Miroslav - Hladílková, Eva - Filková, Hana - Režný, Dominik - Réblová, Kamila - Beharka, Rastislav - Šoukalová, Jana - Kuglík, Petr - Vallová, Vladimíra
PY  - 2025
TI  - Comparative Evaluation of CNVs Detection: A Case Study of Optical Genome Mapping and Long-Read Whole-Genome Sequencing versus Chromosomal Microarray
KW  - Copy number variations
KW  - Chromosomal microarray
KW  - Optical genome mapping
KW  - Long-read whole-genome sequencing
N2  - The contribution of copy number variations (CNVs) to the pathogenesis of various diseases has been increasingly recognized. Chromosomal microarray (CMA) remains the gold standard for genome-wide CNVs analysis. However, emerging cytogenomic techniques, such as optical genome mapping (OGM) and long-read whole-genome sequencing (LR-WGS), offer the potential to not only detect structural variations but also to provide more detailed insights into CNVs. In this study, we compared and evaluated the CNV profiles obtained using CMA (Agilent), OGM (Bionano), and LR-WGS (Oxford Nanopore Technologies) in a patient with neurodevelopmental symptoms and negative classical cytogenetic results. Our primary aim was to assess the success and accuracy of CNVs detection by OGM and LR-WGS, relative to the CMA method, which is firmly established in clinical diagnostics. The CMA analysis identified a duplication and a deletion of chromosome 12, both of which were also detected by OGM and LR-WGS. Notably, LR-WGS provided a more detailed and comprehensive view of the affected regions, offering refined coordinates of the CNVs and a deeper examination of the associated genes. This case report suggests that OGM and LR-WGS hold significant potential for CNV detection in clinical practice. However, it is crucial to understand the limitations of these methods and integrate them carefully into diagnostic algorithms for optimal clinical utility.
ER  -

ŠTOLFA, Miroslav; Eva HLADÍLKOVÁ; Hana FILKOVÁ; Dominik REŽNÝ; Kamila RÉBLOVÁ; Rastislav BEHARKA; Jana ŠOUKALOVÁ; Petr KUGLÍK a Vladimíra VALLOVÁ. Comparative Evaluation of CNVs Detection: A Case Study of Optical Genome Mapping and Long-Read Whole-Genome Sequencing versus Chromosomal Microarray. In \textit{15th EUROPEAN CYTOGENOMICS CONFERENCE, Leuven, Belgium}. 2025.

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