SNP Array

Chromosomal microarray analysis provides the ability to identify genomic copy number losses and copy number gains at a resolution that is much higher than the traditional chromosomal karyotype analysis. SNP microarray is recommended as a first-tier genetic test for the postnatal evaluation of individuals with multiple congenital anomalies, developmental delay, intellectual disability, and autism spectrum disorders. In addition, SNP microarray studies can also identify copy number neutral regions of homozygosity (ROHs) which can be suggestive of an increased risk for autosomal recessive disorders due to genes located within the ROH, uniparental disomy, or consanguinity.

Please note: SNP Array cannot be performed on prenatal specimens.

Quick Reference
Test Code 5490
Turnaround Time (TAT) 14-21 days
Number of Genes Whole Genome

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We offer family variant testing at no additional cost

for all blood relatives of patients who undergo full single gene sequencing, multigene panel testing or exome sequencing at Ambry Genetics and are found to have a pathogenic or likely pathogenic variant. No-cost testing of blood relatives must be completed within 90 days of the original report date. Whenever possible, more closely related relatives should be tested before more distant relatives.

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Why Is This Important?

The American Academy of Neurology, American Academy of Pediatrics, and the American College of Medical Genetics and Genomics all recommend chromosomal microarray, as well as fragile X testing, as a first-tier genetic test in the evaluation of individuals with developmental delay, intellectual disability, and/or an autism spectrum disorder.

When To Consider Testing

SNP array testing should be considered for all individuals with syndromic or non-syndromic conditions that may be due to a genomic copy number imbalance. This could include individuals with neurodevelopmental conditions, dysmorphic features, congenital birth defects, multiple congenital anomalies, seizure disorders, as well as other health and developmental concerns. SNP array can be very helpful in determining breakpoints and further characterizing some of the unbalanced chromosomal abnormalities detected via conventional karyotype analysis. In addition, SNP array can also be a test of choice if there is an additional concern for autosomal recessive disorders due to identity by decent.

Test Description

The SNP array uses >1.9 million copy number probes and ~750.000 SNP probes for genotyping and copy number analysis. These probes cover the genome at a mean probe spacing of 1.1kb and also include probes in the pericentromeric and subtelomeric regions. Copy losses greater than 100kb in size and copy gains greater than 300kb in size are reported, unless the copy number variant is classified as benign, does not include coding genes, or is located within the intron of a gene. Additionally, a copy loss less than 100kb and a copy gain less than 300kb is reported when it encompasses genes with potential clinical relevance to the indication for testing. Copy number neutral ROHs greater than 10Mb in size are reported, though this threshold may vary depending upon the location of the ROH and the overall percentage of ROH that is detected. ROHs comprising 2.5% or greater of the covered genome will be reported.   

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