SNP Array CGH testing

Chromosome abnormalities can be associated with developmental delay, autism spectrum disorder, learning difficulties, dysmorphic features and other congenital abnormalities. 

Array CGH can detect smaller genetic changes than is possible by conventional karyotyping and can provide accurate information on the size and possible consequences of the gains (duplications) or losses (deletions) identified. Multiple studies have shown that Array CGH, when applied to appropriate patients, will detect up to three times more pathogenic chromosome imbalances than karyotyping due to its greater precision and sensitivity. SNP (Single Nucleotide Polymorphism) arrays enable low-level mosaicism visualisation, loss of heterozygosity (LOH) and UPD detection, copy number change confirmation, triploidy detection and parent-of-origin analysis.

Array CGH testing is now considered to be the front line test for patients presenting with developmental delay (motor or growth), autism spectrum disorder, moderate to severe learning difficulties, dysmorphic features, with or without congenital abnormalities. Consortiums in the USA and many EU countries have adopted Array CGH as the front line test in this patient cohort.

Array CGH is now more frequently used for prenatal studies as an adjunct or replacement for conventional cytogenetic studies, particularly where structural fetal abnormalities are seen at ultrasound scan but also at a patient’s or doctor’s request. The technique may also be utilised as a follow up test to characterise anomalies detected by a previous study (e.g. an apparently balanced de novo rearrangement or marker chromosome). 

When to use SNP Array 

In postnatal cases, patients should present with one or more of the following:

• Mental retardation
• Developmental delay 
• Autism/autism spectrum disorder
• Dysmorphic features
• Congenital malformations

In prenatal cases, patients may present with:

• Abnormalities or increased nuchal translucency on ultrasound scan which may be associated with a chromosome imbalance.

Approximately 10-20% of results identify extra or missing DNA which may or may not be relevant to the clinical phenotype, and will require further family studies to assist with interpretation. 

What can SNP Array detect?

Deletions and duplications with greater sensitivity than conventional karyotyping and loss of heterozygosity (LOH). 

What does SNP Array not detect?

• Balanced chromosome rearrangements such as translocations or inversions. The chromosome location of duplications (this would require additional FISH testing).
• Fragile X syndrome, genetic diseases caused by point mutations or multifactorial inheritance.

Further information is provided by the UNIQUE website.

* Blood from both parents may also be provided in case of follow up studies. 

** EDTA and heparin blood from both parents should be provided at the time of prenatal sampling, if possible, in case of follow up studies.