Genomic diagnostics of neurodevelopmental disorders: current opportunities and future potential
DOI:
https://doi.org/10.13112/pc.1050Keywords:
NEURODEVELOPMENTAL DISORDERS; GENOME; DIAGNOSTIC TECHNIQUES AND PROCEDURESAbstract
Neurodevelopmental disorders comprise a heterogeneous group of developmental disorders associated with cognitive, motor, social, and behavioral abnormalities. In addition to the above, affected patients usually have additional developmental abnormalities: dysmorphic features, congenital anomalies, epilepsy as well as various functional abnormalities. The etiological basis of neurodevelopmental disorders is complex and includes genomic alterations, epigenetic mechanisms, environmental factors, and gene-environment interactions. Knowledge of genomic diagnosis and disease mechanisms is crucial for adequate therapeutic procedures, prevention of potential associated healthcare issues, and identification of family relatives at risk. Until about 15 years ago, classic genetic and molecular genetic diagnostic methods could provide genomic basis in 10-15 % of these patients. In the last years, the introduction of next-generation sequencing technology has provided simultaneous analysis of a large set of genes and the whole genome. It significantly improved the diagnosis of neurodevelopmental disorders. Next-generation sequencing technology connects the methods of molecular biology, information technology, and clinical genetics. Despite the impressive progress in this field, the genomic basis of neurodevelopmental disorders is still not elucidated in many patients. At the same time, other technological platforms dedicated to genome analysis are evolving, such as methylation pattern analysis (episignature), more advanced sequencing technologies (long read), RNA sequencing, and analysis of structural variants using optical genome mapping technology. The development of these methods will certainly improve genome diagnostics of neurodevelopmental disorders and create the basis for the creation of therapeutic procedures in the future.
References
1. Parenti I, Rabaneda LG, Schoen H, Novarino G. Neurodevelopmental Disorders: From Genetics to Functional Pathways. Trends Neurosci. 2020;43(8):608-21. doi:10.1016/j.tins.2020.05.005
2. Cainelli E, Bisiacchi P. Neurodevelopmental Disorders: Past, Present, and Future. Children. 2023;10(1):31. doi:10.3390/children10010031
3. Pietropaolo S, Crusio WE, Feldon J. Gene-Environment Interactions in Neurodevelopmental Disorders. Neural Plast. 2017;2017:9272804. doi:10.1155/2017/9272804
4. Gholamalizadeh H, Amiri-Shahri M, Rasouli F, Ansari A, Baradaran Rahimi V, Reza Askari V. DNA Methylation in Autism Spectrum Disorders: Biomarker or Pharmacological Target? Brain Sci. 2024;14(8):737. doi:10.3390/brainsci14080737
5. Khoodoruth MAS, Khoodoruth WNC, Uroos M, Al-Abdulla M, Khan YS, Mohammad F. Diagnostic and mechanistic roles of MicroRNAs in neurodevelopmental & neurodegenerative disorders. Neurobiol Dis. 2024;202:106717. doi:10.1016/j.nbd.2023.106717
6. Schaefer GB, Mendelsohn NJ; Professional Practice and Guidelines Committee. Clinical genetics evaluation in identifying the etiology of autism spectrum disorders. Genet Med. 2008;10(4):301-5. doi:10.1097/GIM.0b013e31816b5b7e
7. Taylor SE, Taylor RD, Price J, Andreae LC. Single-molecule fluorescence in-situ hybridization reveals that human SHANK3 mRNA expression varies during development and in autism-associated SHANK3 heterozygosity. Stem Cell Res Ther. 2018;9(1):206. doi:10.1186/s13287-018-0965-x
8. Medina A, Piñeros L, Arteaga C, Velasco H, Izquierdo A, Giraldo A, Espinosa E. Multiplex ligation-dependent probe amplification to subtelomeric rearrangements in idiopathic intellectual disability in Colombia. Pediatr Neurol. 2014;50(3):250-4. doi:10.1016/j.pediatrneurol.2013.10.020
9. Miller DT, Adam MP, Aradhya S, et al. Consensus statement: chromosomal microarray is a first-tier clinical diagnostic test for individuals with developmental disabilities or congenital anomalies. Am J Hum Genet. 2010;86(5):749-64. doi:10.1016/j.ajhg.2010.04.006
10. Bowling KM, Thompson ML, Amaral MD, et al. Genomic diagnosis for children with intellectual disability and/or developmental delay. Genome Med. 2017;9(1):43. doi:10.1186/s13073-017-0469-5
11. Martin CL, Ledbetter DH. Chromosomal Microarray Testing for Children With Unexplained Neurodevelopmental Disorders. JAMA. 2017;317(24):2545-6. doi:10.1001/jama.2017.6462
12. Battaglia A, Doccini V, Bernardini L, et al. Confirmation of chromosomal microarray as a first-tier clinical diagnostic test for individuals with developmental delay, intellectual disability, autism spectrum disorders and dysmorphic features. Eur J Paediatr Neurol. 2013;17(6):589-99. doi:10.1016/j.ejpn.2013.06.004
13. Maia N, Nabais Sá MJ, Melo-Pires M, de Brouwer APM, Jorge P. Intellectual disability genomics: current state, pitfalls and future challenges. BMC Genomics. 2021: 20;22(1):909. doi:10.1186/s12864-021-08227-4.
14. Buxbaum JD, Daly MJ, Devlin B, Lehner T, Roeder K, State MW; Autism Sequencing Consortium. The autism sequencing consortium: large-scale, high-throughput sequencing in autism spectrum disorders. Neuron. 2012;76(6):1052-6. doi:10.1016/j.neuron.2012.12.018
15. Ní Ghrálaigh F, Gallagher L, Lopez LM. Autism spectrum disorder genomics: The progress and potential of genomic technologies. Genomics. 2020;112(6):5136-42. doi:10.1016/j.ygeno.2020.07.017
16. Richards S, Aziz N, Bale S, et al. ACMG Laboratory Quality Assurance Committee. Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology. Genet Med. 2015;17(5):405-24. doi:10.1038/gim.2015.30
17. Mellone S, Puricelli C, Vurchio D, et al. The Usefulness of a Targeted Next Generation Sequencing Gene Panel in Providing Molecular Diagnosis to Patients With a Broad Spectrum of Neurodevelopmental Disorders. Front Genet. 2022;13:875182. doi:10.3389/fgene.2022.875182
18. Castellotti B, Ragona F, Freri E, et al. Next-generation sequencing in pediatric-onset epilepsies: Analysis with target panels and personalized therapeutic approach. Epilepsia Open. 2024;9(5):1922-30. doi:10.1002/epi4.12645
19. Kim SH, Kim B, Lee JS, et al. Proband-Only Clinical Exome Sequencing for Neurodevelopmental Disabilities. Pediatr Neurol. 2019;99:47-54. doi:10.1016/j.pediatrneurol.2019.03.003
20. Baldridge D, Heeley J, Vineyard M, et al. The Exome Clinic and the role of medical genetics expertise in the interpretation of exome sequencing results. Genet Med. 2017;19(9):1040-8. doi:10.1038/gim.2017.50
21. Harris HK, Sideridis GD, Barbaresi WJ, Harstad E. Pathogenic Yield of Genetic Testing in Autism Spectrum Disorder. Pediatrics. 2020;146(4):e20193211. doi:10.1542/peds.2019-3211
22. Ballesta-Martínez MJ, Pérez-Fernández V, López-González V, et al. Validation of clinical exome sequencing in the diagnostic procedure of patients with intellectual disability in clinical practice. Orphanet J Rare Dis. 2023;18(1):201. doi:10.1186/s13023-023-02391-0
23. Jo YH, Choi SH, Yoo HW, et al. Clinical use of whole exome sequencing in children with developmental delay/intellectual disability. Pediatr Neonatol. 2024;65(5):445-50. doi:10.1016/j.pedneo.2023.09.003
24. Charouf D, Miller D, Haddad L, White FA, Boustany RM, Obeid M. High Diagnostic Yield and Clinical Utility of Next-Generation Sequencing in Children with Epilepsy and Neurodevelopmental Delays: A Retrospective Study. Int J Mol Sci. 2024;25(17):9645. doi:10.3390/ijms25179645
25. Wang W, Corominas R, Lin GN. De novo Mutations From Whole Exome Sequencing in Neurodevelopmental and Psychiatric Disorders: From Discovery to Application. Front Genet. 2019;10:258. doi:10.3389/fgene.2019.00258
26. van Slobbe M, van Haeringen A, Vissers LELM, et al. Reanalysis of whole-exome sequencing (WES) data of children with neurodevelopmental disorders in a standard patient care context. Eur J Pediatr. 2024;183(1):345-55. doi:10.1007/s00431-023-05044-5
27. Sánchez Suárez A, Martínez Menéndez B, Escolar Escamilla E, et al. Whole Exome Sequencing and Panel-Based Analysis in 176 Spanish Children with Neurodevelopmental Disorders: Focus on Autism Spectrum Disorder and/or Intellectual Disability/Global Developmental Delay. Genes (Basel). 2024;15(10):1310. doi:10.3390/genes15101310
28. Malinowski J, Miller DT, Demmer L, et al. ACMG Professional Practice and Guidelines Committee. Systematic evidence-based review: outcomes from exome and genome sequencing for pediatric patients with congenital anomalies or intellectual disability. Genet Med. 2020;22(6):986-1004. doi:10.1038/s41436-019-0751-4
29. Manickam K, McClain MR, Demmer LA, et al. ACMG Board of Directors. Exome and genome sequencing for pediatric patients with congenital anomalies or intellectual disability: an evidence-based clinical guideline of the American College of Medical Genetics and Genomics (ACMG). Genet Med. 2021;23(11):2029-37. doi:10.1038/s41436-021-01156-6
30. van der Sanden BPGH, Schobers G, Corominas Galbany J, et al. The performance of genome sequencing as a first-tier test for neurodevelopmental disorders. Eur J Hum Genet. 2023;31(1):81-8. doi:10.1038/s41431-022-01085-7
31. Miller DT, Lee K, Abul-Husn NS, et al. ACMG Secondary Findings Working Group. ACMG SF v3.2 list for reporting of secondary findings in clinical exome and genome sequencing: A policy statement of the American College of Medical Genetics and Genomics (ACMG). Genet Med. 2023;25(8):100866. doi:10.1016/j.gim.2023.100866
32. Srivastava S, Love-Nichols JA, Dies KA, et al. Meta-analysis and multidisciplinary consensus statement: exome sequencing is a first-tier clinical diagnostic test for individuals with neurodevelopmental disorders. Genet Med. 2019;21(11):2413-21. doi:10.1038/s41436-019-0488-3
33. Kerkhof J, Rastin C, Levy MA, et al. Diagnostic utility and reporting recommendations for clinical DNA methylation episignature testing in genetically undiagnosed rare diseases. Genet Med. 2024;26(5):101075. doi:10.1038/s41436-023-02072-5
34. Dekker J, Schot R, Bongaerts M, et al. Web-accessible application for identifying pathogenic transcripts with RNA-seq: Increased sensitivity in diagnosis of neurodevelopmental disorders. Am J Hum Genet. 2023 2;110(2):251-72. doi:10.1016/j.ajhg.2022.12.016
35. Schrauwen I, Rajendran Y, Acharya A, et al. Optical genome mapping unveils hidden structural variants in neurodevelopmental disorders. Sci Rep. 2024;14(1):11239. doi:10.1038/s41598-024-39090-z
Downloads
Published
Issue
Section
License
Copyright (c) 2025 Ljubica Odak, Katarina Vulin, Leona Morožin Pohovski, Ivona Sansović, Ana-Maria Meašić, Adriana Bobinec, Morana Mikloš

This work is licensed under a Creative Commons Attribution 4.0 International License.
By publishing in Paediatria Croatica, authors retain the copyright to their work and grant others the right to use, reproduce, and share their research articles in accordance with the Creative Commons Attribution License (CC BY 4.0), which allows others to distribute and build upon the work as long as they credit the author for the original creation.

