The Cytoscan HD Array in the Diagnosis of Neurodevelopmental Disorders

Abstract

Submicroscopic chromosomal copy number variations (CNVs), such as deletions and duplications, account for about 15⁻20% of patients affected with developmental delay, intellectual disability, multiple congenital anomalies, and autism spectrum disorder. Most of CNVs are de novo or inherited rearrangements with clinical relevance, but there are also rare inherited imbalances with unknown significance that make difficult the clinical management and genetic counselling. Chromosomal microarrays analysis (CMA) are recognized as the first-line test for CNV detection and are now routinely used in the clinical diagnostic laboratory. The recent use of CMA platforms that combine classic copy number analysis with single-nucleotide polymorphism (SNP) genotyping has increased the diagnostic yields. Here we discuss the application of the Cytoscan high-density (HD) SNP-array for the detection of CNVs. We provide an overview of molecular analyses involved in identifying pathogenic CNVs and highlight important guidelines to establish pathogenicity of CNV.

Keywords: SNP-array; copy number variations; neurodevelopmental disorders.

Figure 1

Workflow of Cytoscan High-density (HD) analysis.

Figure 2

Genotype values in Allele difference plot (a) and B-allele frequency plot (b).

Figure 3

Copy number variations analysis using ChAS 3.3 software displaying a hemizygous deletion in (a) and a hemizygous duplication in (b). Each dot represents a single SNP in the array. Deletion is associated with loss of signal intensity consistent with a decrease in Log2 ratio, Weighted Log2 ratio, CN state and smooth signal. In contrast, duplication region shows increased values. Allele difference plot and B-allele frequency (BAF) plot of copy number variations (CNVs) regions are designated within the highlighted boxes. In the deletion both plots show two tracts (A and B) instead of three indicating a presence of a single allele (c). These two tracts are at 0.5 and −0.5 in allele difference plot while in BAF plot are at 0 and 1. In duplication, the allele difference and the BAF plots show four tracts (AAA, AAB, BBA, and BBB) instead of three (d). These four tracts are at 1.5, 0.5, −0.5, −1.5 in allele difference plot, while in BAF plot are at 0, 0.33, 0.67, 1.

Figure 4

Flowchart of CNV interpretation process. MCA: multiple congenital abnormalities, ASD: autism spectrum disorder, MLPA: multiple ligation-dependent probe amplification, FISH: fluorescence in situ hybridization, qPCR: quantitative PCR.