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Microarrays are high-throughput and relatively inexpensive assays that can be automated to analyze large quantities of data at a time. They are used in genome-wide studies to compare gene or protein expression under two varied conditions, such as healthy and diseased states. Microarrays consist of glass or silica slides on which probe molecules are covalently attached through surface functionalization. Most commonly, the slides are prepared through the chemisorption of silanes to silica...

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High resolution chromosomal microarray in undiagnosed neurological disorders.

Katherine B Howell1, Andrew J Kornberg, A Simon Harvey

  • 1Department of Neurology, Royal Children's Hospital, Melbourne, Victoria, Australia.

Journal of Paediatrics and Child Health
|June 5, 2013
PubMed
Summary

Chromosomal microarray (CMA) testing identified significant genetic abnormalities in 14% of children with unexplained neurological conditions. This diagnostic tool is valuable for a wide range of pediatric neurological disorders, especially severe epilepsies.

Keywords:
chromosomal microarraycopy number variantlong continuous stretch homozygositysingle nucleotide polymorphism microarray.

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Area of Science:

  • Genetics and genomics
  • Pediatric neurology
  • Medical diagnostics

Background:

  • Many children with neurological conditions lack a diagnosis, despite suspected genetic causes.
  • Chromosomal microarray (CMA) detects copy number variants (CNVs) and long continuous stretches of homozygosity (LCSH), potentially improving diagnostic yield.
  • Previous studies focused on specific conditions like intellectual disability, autism, and epilepsy, leaving the utility of CMA in broader pediatric neurological cohorts unclear.

Purpose of the Study:

  • To evaluate the diagnostic utility of CMA in a broad cohort of pediatric patients with neurological disorders of unknown etiology.
  • To determine the detection rate of pathogenic copy number variants (CNVs) and significant homozygosity by CMA in this patient group.
  • To assess the clinical relevance of CMA findings across diverse neurological phenotypes.

Main Methods:

  • Prospective testing of 215 pediatric patients with neurological conditions of unknown etiology over a 6-month period.
  • Utilized high-resolution single nucleotide polymorphism (SNP) microarrays (Illumina HumanCytoSNP-12 v2.1 or Affymetrix 2.7M) for CMA analysis.
  • Analysis included screening for copy number variants (CNVs) and long continuous stretches of homozygosity (LCSH).

Main Results:

  • Chromosomal microarray (CMA) identified abnormalities in 30 out of 215 patients (14%).
  • Copy number variants (CNVs) were found in 13% of patients, and a clinically significant stretch of homozygosity in 0.5%.
  • Pathogenic or susceptibility-related findings were identified in 9.3% of patients, with 4.7% having findings of unknown significance. Phenotypes included epilepsies, neuromuscular conditions, ataxia, movement disorders, microcephaly, and cortical malformations. Notably, over a third of patients did not meet national funding criteria for CMA.

Conclusions:

  • Chromosomal microarray (CMA) effectively detected clinically significant genetic abnormalities in a diverse range of pediatric neurological conditions with unknown etiology.
  • CMA should be considered a primary diagnostic investigation for children with neurological disorders when initial clinical assessment does not reveal a clear cause.
  • The test is particularly recommended for children with severe epilepsies and neurologically compromised neonates.